chip-seq peak detection: Topics by WorldWideScience.org

Sample records for chip-seq peak detection

Combining multiple ChIP-seq peak detection systems using combinatorial fusion.

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Schweikert, Christina; Brown, Stuart; Tang, Zuojian; Smith, Phillip R; Hsu, D Frank

2012-01-01

Due to the recent rapid development in ChIP-seq technologies, which uses high-throughput next-generation DNA sequencing to identify the targets of Chromatin Immunoprecipitation, there is an increasing amount of sequencing data being generated that provides us with greater opportunity to analyze genome-wide protein-DNA interactions. In particular, we are interested in evaluating and enhancing computational and statistical techniques for locating protein binding sites. Many peak detection systems have been developed; in this study, we utilize the following six: CisGenome, MACS, PeakSeq, QuEST, SISSRs, and TRLocator. We define two methods to merge and rescore the regions of two peak detection systems and analyze the performance based on average precision and coverage of transcription start sites. The results indicate that ChIP-seq peak detection can be improved by fusion using score or rank combination. Our method of combination and fusion analysis would provide a means for generic assessment of available technologies and systems and assist researchers in choosing an appropriate system (or fusion method) for analyzing ChIP-seq data. This analysis offers an alternate approach for increasing true positive rates, while decreasing false positive rates and hence improving the ChIP-seq peak identification process.
PolyaPeak: Detecting Transcription Factor Binding Sites from ChIP-seq Using Peak Shape Information

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Wu, Hao; Ji, Hongkai

2014-01-01

ChIP-seq is a powerful technology for detecting genomic regions where a protein of interest interacts with DNA. ChIP-seq data for mapping transcription factor binding sites (TFBSs) have a characteristic pattern: around each binding site, sequence reads aligned to the forward and reverse strands of the reference genome form two separate peaks shifted away from each other, and the true binding site is located in between these two peaks. While it has been shown previously that the accuracy and resolution of binding site detection can be improved by modeling the pattern, efficient methods are unavailable to fully utilize that information in TFBS detection procedure. We present PolyaPeak, a new method to improve TFBS detection by incorporating the peak shape information. PolyaPeak describes peak shapes using a flexible Pólya model. The shapes are automatically learnt from the data using Minorization-Maximization (MM) algorithm, then integrated with the read count information via a hierarchical model to distinguish true binding sites from background noises. Extensive real data analyses show that PolyaPeak is capable of robustly improving TFBS detection compared with existing methods. An R package is freely available. PMID:24608116
Optimizing ChIP-seq peak detectors using visual labels and supervised machine learning.

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Hocking, Toby Dylan; Goerner-Potvin, Patricia; Morin, Andreanne; Shao, Xiaojian; Pastinen, Tomi; Bourque, Guillaume

2017-02-15

Many peak detection algorithms have been proposed for ChIP-seq data analysis, but it is not obvious which algorithm and what parameters are optimal for any given dataset. In contrast, regions with and without obvious peaks can be easily labeled by visual inspection of aligned read counts in a genome browser. We propose a supervised machine learning approach for ChIP-seq data analysis, using labels that encode qualitative judgments about which genomic regions contain or do not contain peaks. The main idea is to manually label a small subset of the genome, and then learn a model that makes consistent peak predictions on the rest of the genome. We created 7 new histone mark datasets with 12 826 visually determined labels, and analyzed 3 existing transcription factor datasets. We observed that default peak detection parameters yield high false positive rates, which can be reduced by learning parameters using a relatively small training set of labeled data from the same experiment type. We also observed that labels from different people are highly consistent. Overall, these data indicate that our supervised labeling method is useful for quantitatively training and testing peak detection algorithms. Labeled histone mark data http://cbio.ensmp.fr/~thocking/chip-seq-chunk-db/ , R package to compute the label error of predicted peaks https://github.com/tdhock/PeakError. toby.hocking@mail.mcgill.ca or guil.bourque@mcgill.ca. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.
ASPeak: an abundance sensitive peak detection algorithm for RIP-Seq.

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Kucukural, Alper; Özadam, Hakan; Singh, Guramrit; Moore, Melissa J; Cenik, Can

2013-10-01

Unlike DNA, RNA abundances can vary over several orders of magnitude. Thus, identification of RNA-protein binding sites from high-throughput sequencing data presents unique challenges. Although peak identification in ChIP-Seq data has been extensively explored, there are few bioinformatics tools tailored for peak calling on analogous datasets for RNA-binding proteins. Here we describe ASPeak (abundance sensitive peak detection algorithm), an implementation of an algorithm that we previously applied to detect peaks in exon junction complex RNA immunoprecipitation in tandem experiments. Our peak detection algorithm yields stringent and robust target sets enabling sensitive motif finding and downstream functional analyses. ASPeak is implemented in Perl as a complete pipeline that takes bedGraph files as input. ASPeak implementation is freely available at https://sourceforge.net/projects/as-peak under the GNU General Public License. ASPeak can be run on a personal computer, yet is designed to be easily parallelizable. ASPeak can also run on high performance computing clusters providing efficient speedup. The documentation and user manual can be obtained from http://master.dl.sourceforge.net/project/as-peak/manual.pdf.
An improved ChIP-seq peak detection system for simultaneously identifying post-translational modified transcription factors by combinatorial fusion, using SUMOylation as an example.

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Cheng, Chia-Yang; Chu, Chia-Han; Hsu, Hung-Wei; Hsu, Fang-Rong; Tang, Chung Yi; Wang, Wen-Ching; Kung, Hsing-Jien; Chang, Pei-Ching

2014-01-01

Post-translational modification (PTM) of transcriptional factors and chromatin remodelling proteins is recognized as a major mechanism by which transcriptional regulation occurs. Chromatin immunoprecipitation (ChIP) in combination with high-throughput sequencing (ChIP-seq) is being applied as a gold standard when studying the genome-wide binding sites of transcription factor (TFs). This has greatly improved our understanding of protein-DNA interactions on a genomic-wide scale. However, current ChIP-seq peak calling tools are not sufficiently sensitive and are unable to simultaneously identify post-translational modified TFs based on ChIP-seq analysis; this is largely due to the wide-spread presence of multiple modified TFs. Using SUMO-1 modification as an example; we describe here an improved approach that allows the simultaneous identification of the particular genomic binding regions of all TFs with SUMO-1 modification. Traditional peak calling methods are inadequate when identifying multiple TF binding sites that involve long genomic regions and therefore we designed a ChIP-seq processing pipeline for the detection of peaks via a combinatorial fusion method. Then, we annotate the peaks with known transcription factor binding sites (TFBS) using the Transfac Matrix Database (v7.0), which predicts potential SUMOylated TFs. Next, the peak calling result was further analyzed based on the promoter proximity, TFBS annotation, a literature review, and was validated by ChIP-real-time quantitative PCR (qPCR) and ChIP-reChIP real-time qPCR. The results show clearly that SUMOylated TFs are able to be pinpointed using our pipeline. A methodology is presented that analyzes SUMO-1 ChIP-seq patterns and predicts related TFs. Our analysis uses three peak calling tools. The fusion of these different tools increases the precision of the peak calling results. TFBS annotation method is able to predict potential SUMOylated TFs. Here, we offer a new approach that enhances ChIP-seq
CMT: a constrained multi-level thresholding approach for ChIP-Seq data analysis.

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Iman Rezaeian

Full Text Available Genome-wide profiling of DNA-binding proteins using ChIP-Seq has emerged as an alternative to ChIP-chip methods. ChIP-Seq technology offers many advantages over ChIP-chip arrays, including but not limited to less noise, higher resolution, and more coverage. Several algorithms have been developed to take advantage of these abilities and find enriched regions by analyzing ChIP-Seq data. However, the complexity of analyzing various patterns of ChIP-Seq signals still needs the development of new algorithms. Most current algorithms use various heuristics to detect regions accurately. However, despite how many formulations are available, it is still difficult to accurately determine individual peaks corresponding to each binding event. We developed Constrained Multi-level Thresholding (CMT, an algorithm used to detect enriched regions on ChIP-Seq data. CMT employs a constraint-based module that can target regions within a specific range. We show that CMT has higher accuracy in detecting enriched regions (peaks by objectively assessing its performance relative to other previously proposed peak finders. This is shown by testing three algorithms on the well-known FoxA1 Data set, four transcription factors (with a total of six antibodies for Drosophila melanogaster and the H3K4ac antibody dataset.
Systematic evaluation of the impact of ChIP-seq read designs on genome coverage, peak identification, and allele-specific binding detection.

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Zhang, Qi; Zeng, Xin; Younkin, Sam; Kawli, Trupti; Snyder, Michael P; Keleş, Sündüz

2016-02-24

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) experiments revolutionized genome-wide profiling of transcription factors and histone modifications. Although maturing sequencing technologies allow these experiments to be carried out with short (36-50 bps), long (75-100 bps), single-end, or paired-end reads, the impact of these read parameters on the downstream data analysis are not well understood. In this paper, we evaluate the effects of different read parameters on genome sequence alignment, coverage of different classes of genomic features, peak identification, and allele-specific binding detection. We generated 101 bps paired-end ChIP-seq data for many transcription factors from human GM12878 and MCF7 cell lines. Systematic evaluations using in silico variations of these data as well as fully simulated data, revealed complex interplay between the sequencing parameters and analysis tools, and indicated clear advantages of paired-end designs in several aspects such as alignment accuracy, peak resolution, and most notably, allele-specific binding detection. Our work elucidates the effect of design on the downstream analysis and provides insights to investigators in deciding sequencing parameters in ChIP-seq experiments. We present the first systematic evaluation of the impact of ChIP-seq designs on allele-specific binding detection and highlights the power of pair-end designs in such studies.
A non-parametric peak calling algorithm for DamID-Seq.

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Renhua Li

Full Text Available Protein-DNA interactions play a significant role in gene regulation and expression. In order to identify transcription factor binding sites (TFBS of double sex (DSX-an important transcription factor in sex determination, we applied the DNA adenine methylation identification (DamID technology to the fat body tissue of Drosophila, followed by deep sequencing (DamID-Seq. One feature of DamID-Seq data is that induced adenine methylation signals are not assured to be symmetrically distributed at TFBS, which renders the existing peak calling algorithms for ChIP-Seq, including SPP and MACS, inappropriate for DamID-Seq data. This challenged us to develop a new algorithm for peak calling. A challenge in peaking calling based on sequence data is estimating the averaged behavior of background signals. We applied a bootstrap resampling method to short sequence reads in the control (Dam only. After data quality check and mapping reads to a reference genome, the peaking calling procedure compromises the following steps: 1 reads resampling; 2 reads scaling (normalization and computing signal-to-noise fold changes; 3 filtering; 4 Calling peaks based on a statistically significant threshold. This is a non-parametric method for peak calling (NPPC. We also used irreproducible discovery rate (IDR analysis, as well as ChIP-Seq data to compare the peaks called by the NPPC. We identified approximately 6,000 peaks for DSX, which point to 1,225 genes related to the fat body tissue difference between female and male Drosophila. Statistical evidence from IDR analysis indicated that these peaks are reproducible across biological replicates. In addition, these peaks are comparable to those identified by use of ChIP-Seq on S2 cells, in terms of peak number, location, and peaks width.
A non-parametric peak calling algorithm for DamID-Seq.

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Li, Renhua; Hempel, Leonie U; Jiang, Tingbo

2015-01-01

Protein-DNA interactions play a significant role in gene regulation and expression. In order to identify transcription factor binding sites (TFBS) of double sex (DSX)-an important transcription factor in sex determination, we applied the DNA adenine methylation identification (DamID) technology to the fat body tissue of Drosophila, followed by deep sequencing (DamID-Seq). One feature of DamID-Seq data is that induced adenine methylation signals are not assured to be symmetrically distributed at TFBS, which renders the existing peak calling algorithms for ChIP-Seq, including SPP and MACS, inappropriate for DamID-Seq data. This challenged us to develop a new algorithm for peak calling. A challenge in peaking calling based on sequence data is estimating the averaged behavior of background signals. We applied a bootstrap resampling method to short sequence reads in the control (Dam only). After data quality check and mapping reads to a reference genome, the peaking calling procedure compromises the following steps: 1) reads resampling; 2) reads scaling (normalization) and computing signal-to-noise fold changes; 3) filtering; 4) Calling peaks based on a statistically significant threshold. This is a non-parametric method for peak calling (NPPC). We also used irreproducible discovery rate (IDR) analysis, as well as ChIP-Seq data to compare the peaks called by the NPPC. We identified approximately 6,000 peaks for DSX, which point to 1,225 genes related to the fat body tissue difference between female and male Drosophila. Statistical evidence from IDR analysis indicated that these peaks are reproducible across biological replicates. In addition, these peaks are comparable to those identified by use of ChIP-Seq on S2 cells, in terms of peak number, location, and peaks width.
iTAR: a web server for identifying target genes of transcription factors using ChIP-seq or ChIP-chip data.

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Yang, Chia-Chun; Andrews, Erik H; Chen, Min-Hsuan; Wang, Wan-Yu; Chen, Jeremy J W; Gerstein, Mark; Liu, Chun-Chi; Cheng, Chao

2016-08-12

Chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) or microarray hybridization (ChIP-chip) has been widely used to determine the genomic occupation of transcription factors (TFs). We have previously developed a probabilistic method, called TIP (Target Identification from Profiles), to identify TF target genes using ChIP-seq/ChIP-chip data. To achieve high specificity, TIP applies a conservative method to estimate significance of target genes, with the trade-off being a relatively low sensitivity of target gene identification compared to other methods. Additionally, TIP's output does not render binding-peak locations or intensity, information highly useful for visualization and general experimental biological use, while the variability of ChIP-seq/ChIP-chip file formats has made input into TIP more difficult than desired. To improve upon these facets, here we present are fined TIP with key extensions. First, it implements a Gaussian mixture model for p-value estimation, increasing target gene identification sensitivity and more accurately capturing the shape of TF binding profile distributions. Second, it enables the incorporation of TF binding-peak data by identifying their locations in significant target gene promoter regions and quantifies their strengths. Finally, for full ease of implementation we have incorporated it into a web server ( http://syslab3.nchu.edu.tw/iTAR/ ) that enables flexibility of input file format, can be used across multiple species and genome assembly versions, and is freely available for public use. The web server additionally performs GO enrichment analysis for the identified target genes to reveal the potential function of the corresponding TF. The iTAR web server provides a user-friendly interface and supports target gene identification in seven species, ranging from yeast to human. To facilitate investigating the quality of ChIP-seq/ChIP-chip data, the web server generates the chart of the
Multiplexing of ChIP-Seq Samples in an Optimized Experimental Condition Has Minimal Impact on Peak Detection.

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Thadeous J Kacmarczyk

Full Text Available Multiplexing samples in sequencing experiments is a common approach to maximize information yield while minimizing cost. In most cases the number of samples that are multiplexed is determined by financial consideration or experimental convenience, with limited understanding on the effects on the experimental results. Here we set to examine the impact of multiplexing ChIP-seq experiments on the ability to identify a specific epigenetic modification. We performed peak detection analyses to determine the effects of multiplexing. These include false discovery rates, size, position and statistical significance of peak detection, and changes in gene annotation. We found that, for histone marker H3K4me3, one can multiplex up to 8 samples (7 IP + 1 input at ~21 million single-end reads each and still detect over 90% of all peaks found when using a full lane for sample (~181 million reads. Furthermore, there are no variations introduced by indexing or lane batch effects and importantly there is no significant reduction in the number of genes with neighboring H3K4me3 peaks. We conclude that, for a well characterized antibody and, therefore, model IP condition, multiplexing 8 samples per lane is sufficient to capture most of the biological signal.
Multiplexing of ChIP-Seq Samples in an Optimized Experimental Condition Has Minimal Impact on Peak Detection

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Kacmarczyk, Thadeous J.; Bourque, Caitlin; Zhang, Xihui; Jiang, Yanwen; Houvras, Yariv; Alonso, Alicia; Betel, Doron

2015-01-01

Multiplexing samples in sequencing experiments is a common approach to maximize information yield while minimizing cost. In most cases the number of samples that are multiplexed is determined by financial consideration or experimental convenience, with limited understanding on the effects on the experimental results. Here we set to examine the impact of multiplexing ChIP-seq experiments on the ability to identify a specific epigenetic modification. We performed peak detection analyses to determine the effects of multiplexing. These include false discovery rates, size, position and statistical significance of peak detection, and changes in gene annotation. We found that, for histone marker H3K4me3, one can multiplex up to 8 samples (7 IP + 1 input) at ~21 million single-end reads each and still detect over 90% of all peaks found when using a full lane for sample (~181 million reads). Furthermore, there are no variations introduced by indexing or lane batch effects and importantly there is no significant reduction in the number of genes with neighboring H3K4me3 peaks. We conclude that, for a well characterized antibody and, therefore, model IP condition, multiplexing 8 samples per lane is sufficient to capture most of the biological signal. PMID:26066343
Multiplexing of ChIP-Seq Samples in an Optimized Experimental Condition Has Minimal Impact on Peak Detection.

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Kacmarczyk, Thadeous J; Bourque, Caitlin; Zhang, Xihui; Jiang, Yanwen; Houvras, Yariv; Alonso, Alicia; Betel, Doron

2015-01-01

Multiplexing samples in sequencing experiments is a common approach to maximize information yield while minimizing cost. In most cases the number of samples that are multiplexed is determined by financial consideration or experimental convenience, with limited understanding on the effects on the experimental results. Here we set to examine the impact of multiplexing ChIP-seq experiments on the ability to identify a specific epigenetic modification. We performed peak detection analyses to determine the effects of multiplexing. These include false discovery rates, size, position and statistical significance of peak detection, and changes in gene annotation. We found that, for histone marker H3K4me3, one can multiplex up to 8 samples (7 IP + 1 input) at ~21 million single-end reads each and still detect over 90% of all peaks found when using a full lane for sample (~181 million reads). Furthermore, there are no variations introduced by indexing or lane batch effects and importantly there is no significant reduction in the number of genes with neighboring H3K4me3 peaks. We conclude that, for a well characterized antibody and, therefore, model IP condition, multiplexing 8 samples per lane is sufficient to capture most of the biological signal.
Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks

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Courdy Samir J

2008-12-01

Full Text Available Abstract Background High throughput signature sequencing holds many promises, one of which is the ready identification of in vivo transcription factor binding sites, histone modifications, changes in chromatin structure and patterns of DNA methylation across entire genomes. In these experiments, chromatin immunoprecipitation is used to enrich for particular DNA sequences of interest and signature sequencing is used to map the regions to the genome (ChIP-Seq. Elucidation of these sites of DNA-protein binding/modification are proving instrumental in reconstructing networks of gene regulation and chromatin remodelling that direct development, response to cellular perturbation, and neoplastic transformation. Results Here we present a package of algorithms and software that makes use of control input data to reduce false positives and estimate confidence in ChIP-Seq peaks. Several different methods were compared using two simulated spike-in datasets. Use of control input data and a normalized difference score were found to more than double the recovery of ChIP-Seq peaks at a 5% false discovery rate (FDR. Moreover, both a binomial p-value/q-value and an empirical FDR were found to predict the true FDR within 2–3 fold and are more reliable estimators of confidence than a global Poisson p-value. These methods were then used to reanalyze Johnson et al.'s neuron-restrictive silencer factor (NRSF ChIP-Seq data without relying on extensive qPCR validated NRSF sites and the presence of NRSF binding motifs for setting thresholds. Conclusion The methods developed and tested here show considerable promise for reducing false positives and estimating confidence in ChIP-Seq data without any prior knowledge of the chIP target. They are part of a larger open source package freely available from http://useq.sourceforge.net/.
"Peak tracking chip" for label-free optical detection of bio-molecular interaction and bulk sensing.

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Bougot-Robin, Kristelle; Li, Shunbo; Zhang, Yinghua; Hsing, I-Ming; Benisty, Henri; Wen, Weijia

2012-10-21

A novel imaging method for bulk refractive index sensing or label-free bio-molecular interaction sensing is presented. This method is based on specially designed "Peak tracking chip" (PTC) involving "tracks" of adjacent resonant waveguide gratings (RWG) "micropads" with slowly evolving resonance position. Using a simple camera the spatial information robustly retrieves the diffraction efficiency, which in turn transduces either the refractive index of the liquids on the tracks or the effective thickness of an immobilized biological layer. Our intrinsically multiplex chip combines tunability and versatility advantages of dielectric guided wave biochips without the need of costly hyperspectral instrumentation. The current success of surface plasmon imaging techniques suggests that our chip proposal could leverage an untapped potential to routinely extend such techniques in a convenient and sturdy optical configuration toward, for instance for large analytes detection. PTC design and fabrication are discussed with challenging process to control micropads properties by varying their period (step of 2 nm) or their duty cycle through the groove width (steps of 4 nm). Through monochromatic imaging of our PTC, we present experimental demonstration of bulk index sensing on the range [1.33-1.47] and of surface biomolecule detection of molecular weight 30 kDa in aqueous solution using different surface densities. A sensitivity of the order of 10(-5) RIU for bulk detection and a sensitivity of the order of ∼10 pg mm(-2) for label-free surface detection are expected, therefore opening a large range of application of our chip based imaging technique. Exploiting and chip design, we expect as well our chip to open new direction for multispectral studies through imaging.
Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data.

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Chung, Dongjun; Kuan, Pei Fen; Li, Bo; Sanalkumar, Rajendran; Liang, Kun; Bresnick, Emery H; Dewey, Colin; Keleş, Sündüz

2011-07-01

Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is rapidly replacing chromatin immunoprecipitation combined with genome-wide tiling array analysis (ChIP-chip) as the preferred approach for mapping transcription-factor binding sites and chromatin modifications. The state of the art for analyzing ChIP-seq data relies on using only reads that map uniquely to a relevant reference genome (uni-reads). This can lead to the omission of up to 30% of alignable reads. We describe a general approach for utilizing reads that map to multiple locations on the reference genome (multi-reads). Our approach is based on allocating multi-reads as fractional counts using a weighted alignment scheme. Using human STAT1 and mouse GATA1 ChIP-seq datasets, we illustrate that incorporation of multi-reads significantly increases sequencing depths, leads to detection of novel peaks that are not otherwise identifiable with uni-reads, and improves detection of peaks in mappable regions. We investigate various genome-wide characteristics of peaks detected only by utilization of multi-reads via computational experiments. Overall, peaks from multi-read analysis have similar characteristics to peaks that are identified by uni-reads except that the majority of them reside in segmental duplications. We further validate a number of GATA1 multi-read only peaks by independent quantitative real-time ChIP analysis and identify novel target genes of GATA1. These computational and experimental results establish that multi-reads can be of critical importance for studying transcription factor binding in highly repetitive regions of genomes with ChIP-seq experiments.
Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data.

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Dongjun Chung

2011-07-01

Full Text Available Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq is rapidly replacing chromatin immunoprecipitation combined with genome-wide tiling array analysis (ChIP-chip as the preferred approach for mapping transcription-factor binding sites and chromatin modifications. The state of the art for analyzing ChIP-seq data relies on using only reads that map uniquely to a relevant reference genome (uni-reads. This can lead to the omission of up to 30% of alignable reads. We describe a general approach for utilizing reads that map to multiple locations on the reference genome (multi-reads. Our approach is based on allocating multi-reads as fractional counts using a weighted alignment scheme. Using human STAT1 and mouse GATA1 ChIP-seq datasets, we illustrate that incorporation of multi-reads significantly increases sequencing depths, leads to detection of novel peaks that are not otherwise identifiable with uni-reads, and improves detection of peaks in mappable regions. We investigate various genome-wide characteristics of peaks detected only by utilization of multi-reads via computational experiments. Overall, peaks from multi-read analysis have similar characteristics to peaks that are identified by uni-reads except that the majority of them reside in segmental duplications. We further validate a number of GATA1 multi-read only peaks by independent quantitative real-time ChIP analysis and identify novel target genes of GATA1. These computational and experimental results establish that multi-reads can be of critical importance for studying transcription factor binding in highly repetitive regions of genomes with ChIP-seq experiments.
Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq

NARCIS (Netherlands)

Johannes, Frank; Wardenaar, Rene; Colomé Tatché, Maria; Mousson, Florence; de Graaf, Petra; Mokry, Michal; Guryev, Victor; Timmers, H. Th. Marc; Cuppen, Edwin; Jansen, Ritsert C.; Bateman, Alex

2010-01-01

Motivation: ChIP-chip and ChIP-seq technologies provide genomewide measurements of various types of chromatin marks at an unprecedented resolution. With ChIP samples collected from different tissue types and/ or individuals, we can now begin to characterize stochastic or systematic changes in
Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq

NARCIS (Netherlands)

Johannes, F.; Wardenaar, R.; Colome-Tatche, M.; Mousson, F.; de Graaf, P.; Mokry, M.; Guryev, V.; Timmers, H.T.; Cuppen, E.; Jansen, R.

2010-01-01

MOTIVATION: ChIP-chip and ChIP-seq technologies provide genome-wide measurements of various types of chromatin marks at an unprecedented resolution. With ChIP samples collected from different tissue types and/or individuals, we can now begin to characterize stochastic or systematic changes in
OccuPeak: ChIP-Seq peak calling based on internal background modelling

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de Boer, Bouke A.; van Duijvenboden, Karel; van den Boogaard, Malou; Christoffels, Vincent M.; Barnett, Phil; Ruijter, Jan M.

2014-01-01

ChIP-seq has become a major tool for the genome-wide identification of transcription factor binding or histone modification sites. Most peak-calling algorithms require input control datasets to model the occurrence of background reads to account for local sequencing and GC bias. However, the

Parallel factor ChIP provides essential internal control for quantitative differential ChIP-seq.

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Guertin, Michael J; Cullen, Amy E; Markowetz, Florian; Holding, Andrew N

2018-04-17

A key challenge in quantitative ChIP combined with high-throughput sequencing (ChIP-seq) is the normalization of data in the presence of genome-wide changes in occupancy. Analysis-based normalization methods were developed for transcriptomic data and these are dependent on the underlying assumption that total transcription does not change between conditions. For genome-wide changes in transcription factor (TF) binding, these assumptions do not hold true. The challenges in normalization are confounded by experimental variability during sample preparation, processing and recovery. We present a novel normalization strategy utilizing an internal standard of unchanged peaks for reference. Our method can be readily applied to monitor genome-wide changes by ChIP-seq that are otherwise lost or misrepresented through analytical normalization. We compare our approach to normalization by total read depth and two alternative methods that utilize external experimental controls to study TF binding. We successfully resolve the key challenges in quantitative ChIP-seq analysis and demonstrate its application by monitoring the loss of Estrogen Receptor-alpha (ER) binding upon fulvestrant treatment, ER binding in response to estrodiol, ER mediated change in H4K12 acetylation and profiling ER binding in patient-derived xenographs. This is supported by an adaptable pipeline to normalize and quantify differential TF binding genome-wide and generate metrics for differential binding at individual sites.
BinQuasi: a peak detection method for ChIP-sequencing data with biological replicates.

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Goren, Emily; Liu, Peng; Wang, Chao; Wang, Chong

2018-04-19

ChIP-seq experiments that are aimed at detecting DNA-protein interactions require biological replication to draw inferential conclusions, however there is no current consensus on how to analyze ChIP-seq data with biological replicates. Very few methodologies exist for the joint analysis of replicated ChIP-seq data, with approaches ranging from combining the results of analyzing replicates individually to joint modeling of all replicates. Combining the results of individual replicates analyzed separately can lead to reduced peak classification performance compared to joint modeling. Currently available methods for joint analysis may fail to control the false discovery rate at the nominal level. We propose BinQuasi, a peak caller for replicated ChIP-seq data, that jointly models biological replicates using a generalized linear model framework and employs a one-sided quasi-likelihood ratio test to detect peaks. When applied to simulated data and real datasets, BinQuasi performs favorably compared to existing methods, including better control of false discovery rate than existing joint modeling approaches. BinQuasi offers a flexible approach to joint modeling of replicated ChIP-seq data which is preferable to combining the results of replicates analyzed individually. Source code is freely available for download at https://cran.r-project.org/package=BinQuasi, implemented in R. pliu@iastate.edu or egoren@iastate.edu. Supplementary material is available at Bioinformatics online.
"Peak-tracking chip" (PTC) for bulk refractive index sensing and bioarray sensing

KAUST Repository

Bougot-Robin, Kristelle; Austin, H. Robert; Benisty, Henri; Hsing, I-Ming; Kodzius, Rimantas; Li, Shunbo; Wen, Weijia; Zhang, Yinghua

2013-01-01

Resonant techniques are of wide interest to detect variation of effective refractive index at a chip surface. Both Surface Plasmon Resonance (SPR) and dielectric resonant waveguide (RWGs) can be exploited. Through their design, RWGs allow more flexibility (size of the biomolecule to detect, detection angle…). Using specially designed RWG “Peak-tracking chip”, we propose to use spatial information from a simple monochromatic picture as a new label-free bioarray technique. We discuss robustness, sensitivity, multiplex detection, fluidic integration of the technique and illustrate it through bulk refractive index sensing as well as specific recognition of DNA fragment from gyrase A.
"Peak-tracking chip" (PTC) for bulk refractive index sensing and bioarray sensing

KAUST Repository

Bougot-Robin, Kristelle

2013-10-20

Resonant techniques are of wide interest to detect variation of effective refractive index at a chip surface. Both Surface Plasmon Resonance (SPR) and dielectric resonant waveguide (RWGs) can be exploited. Through their design, RWGs allow more flexibility (size of the biomolecule to detect, detection angle…). Using specially designed RWG “Peak-tracking chip”, we propose to use spatial information from a simple monochromatic picture as a new label-free bioarray technique. We discuss robustness, sensitivity, multiplex detection, fluidic integration of the technique and illustrate it through bulk refractive index sensing as well as specific recognition of DNA fragment from gyrase A.
In Silico Pooling of ChIP-seq Control Experiments

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Sun, Guannan; Srinivasan, Rajini; Lopez-Anido, Camila; Hung, Holly A.; Svaren, John; Keleş, Sündüz

2014-01-01

As next generation sequencing technologies are becoming more economical, large-scale ChIP-seq studies are enabling the investigation of the roles of transcription factor binding and epigenome on phenotypic variation. Studying such variation requires individual level ChIP-seq experiments. Standard designs for ChIP-seq experiments employ a paired control per ChIP-seq sample. Genomic coverage for control experiments is often sacrificed to increase the resources for ChIP samples. However, the quality of ChIP-enriched regions identifiable from a ChIP-seq experiment depends on the quality and the coverage of the control experiments. Insufficient coverage leads to loss of power in detecting enrichment. We investigate the effect of in silico pooling of control samples within multiple biological replicates, multiple treatment conditions, and multiple cell lines and tissues across multiple datasets with varying levels of genomic coverage. Our computational studies suggest guidelines for performing in silico pooling of control experiments. Using vast amounts of ENCODE data, we show that pairwise correlations between control samples originating from multiple biological replicates, treatments, and cell lines/tissues can be grouped into two classes representing whether or not in silico pooling leads to power gain in detecting enrichment between the ChIP and the control samples. Our findings have important implications for multiplexing samples. PMID:25380244
WaveSeq: a novel data-driven method of detecting histone modification enrichments using wavelets.

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Apratim Mitra

Full Text Available BACKGROUND: Chromatin immunoprecipitation followed by next-generation sequencing is a genome-wide analysis technique that can be used to detect various epigenetic phenomena such as, transcription factor binding sites and histone modifications. Histone modification profiles can be either punctate or diffuse which makes it difficult to distinguish regions of enrichment from background noise. With the discovery of histone marks having a wide variety of enrichment patterns, there is an urgent need for analysis methods that are robust to various data characteristics and capable of detecting a broad range of enrichment patterns. RESULTS: To address these challenges we propose WaveSeq, a novel data-driven method of detecting regions of significant enrichment in ChIP-Seq data. Our approach utilizes the wavelet transform, is free of distributional assumptions and is robust to diverse data characteristics such as low signal-to-noise ratios and broad enrichment patterns. Using publicly available datasets we showed that WaveSeq compares favorably with other published methods, exhibiting high sensitivity and precision for both punctate and diffuse enrichment regions even in the absence of a control data set. The application of our algorithm to a complex histone modification data set helped make novel functional discoveries which further underlined its utility in such an experimental setup. CONCLUSIONS: WaveSeq is a highly sensitive method capable of accurate identification of enriched regions in a broad range of data sets. WaveSeq can detect both narrow and broad peaks with a high degree of accuracy even in low signal-to-noise ratio data sets. WaveSeq is also suited for application in complex experimental scenarios, helping make biologically relevant functional discoveries.
A comparison of the whole genome approach of MeDIP-seq to the targeted approach of the Infinium HumanMethylation450 BeadChip(® for methylome profiling.

Directory of Open Access Journals (Sweden)

Christine Clark

Full Text Available DNA methylation is one of the most studied epigenetic marks in the human genome, with the result that the desire to map the human methylome has driven the development of several methods to map DNA methylation on a genomic scale. Our study presents the first comparison of two of these techniques - the targeted approach of the Infinium HumanMethylation450 BeadChip® with the immunoprecipitation and sequencing-based method, MeDIP-seq. Both methods were initially validated with respect to bisulfite sequencing as the gold standard and then assessed in terms of coverage, resolution and accuracy. The regions of the methylome that can be assayed by both methods and those that can only be assayed by one method were determined and the discovery of differentially methylated regions (DMRs by both techniques was examined. Our results show that the Infinium HumanMethylation450 BeadChip® and MeDIP-seq show a good positive correlation (Spearman correlation of 0.68 on a genome-wide scale and can both be used successfully to determine differentially methylated loci in RefSeq genes, CpG islands, shores and shelves. MeDIP-seq however, allows a wider interrogation of methylated regions of the human genome, including thousands of non-RefSeq genes and repetitive elements, all of which may be of importance in disease. In our study MeDIP-seq allowed the detection of 15,709 differentially methylated regions, nearly twice as many as the array-based method (8070, which may result in a more comprehensive study of the methylome.
HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data

Directory of Open Access Journals (Sweden)

Maher Christopher A

2010-07-01

Full Text Available Abstract Background Protein-DNA interaction constitutes a basic mechanism for the genetic regulation of target gene expression. Deciphering this mechanism has been a daunting task due to the difficulty in characterizing protein-bound DNA on a large scale. A powerful technique has recently emerged that couples chromatin immunoprecipitation (ChIP with next-generation sequencing, (ChIP-Seq. This technique provides a direct survey of the cistrom of transcription factors and other chromatin-associated proteins. In order to realize the full potential of this technique, increasingly sophisticated statistical algorithms have been developed to analyze the massive amount of data generated by this method. Results Here we introduce HPeak, a Hidden Markov model (HMM-based Peak-finding algorithm for analyzing ChIP-Seq data to identify protein-interacting genomic regions. In contrast to the majority of available ChIP-Seq analysis software packages, HPeak is a model-based approach allowing for rigorous statistical inference. This approach enables HPeak to accurately infer genomic regions enriched with sequence reads by assuming realistic probability distributions, in conjunction with a novel weighting scheme on the sequencing read coverage. Conclusions Using biologically relevant data collections, we found that HPeak showed a higher prevalence of the expected transcription factor binding motifs in ChIP-enriched sequences relative to the control sequences when compared to other currently available ChIP-Seq analysis approaches. Additionally, in comparison to the ChIP-chip assay, ChIP-Seq provides higher resolution along with improved sensitivity and specificity of binding site detection. Additional file and the HPeak program are freely available at http://www.sph.umich.edu/csg/qin/HPeak.
Is this the right normalization? A diagnostic tool for ChIP-seq normalization.

Science.gov (United States)

Angelini, Claudia; Heller, Ruth; Volkinshtein, Rita; Yekutieli, Daniel

2015-05-09

Chip-seq experiments are becoming a standard approach for genome-wide profiling protein-DNA interactions, such as detecting transcription factor binding sites, histone modification marks and RNA Polymerase II occupancy. However, when comparing a ChIP sample versus a control sample, such as Input DNA, normalization procedures have to be applied in order to remove experimental source of biases. Despite the substantial impact that the choice of the normalization method can have on the results of a ChIP-seq data analysis, their assessment is not fully explored in the literature. In particular, there are no diagnostic tools that show whether the applied normalization is indeed appropriate for the data being analyzed. In this work we propose a novel diagnostic tool to examine the appropriateness of the estimated normalization procedure. By plotting the empirical densities of log relative risks in bins of equal read count, along with the estimated normalization constant, after logarithmic transformation, the researcher is able to assess the appropriateness of the estimated normalization constant. We use the diagnostic plot to evaluate the appropriateness of the estimates obtained by CisGenome, NCIS and CCAT on several real data examples. Moreover, we show the impact that the choice of the normalization constant can have on standard tools for peak calling such as MACS or SICER. Finally, we propose a novel procedure for controlling the FDR using sample swapping. This procedure makes use of the estimated normalization constant in order to gain power over the naive choice of constant (used in MACS and SICER), which is the ratio of the total number of reads in the ChIP and Input samples. Linear normalization approaches aim to estimate a scale factor, r, to adjust for different sequencing depths when comparing ChIP versus Input samples. The estimated scaling factor can easily be incorporated in many peak caller algorithms to improve the accuracy of the peak identification. The
Experiment list: SRX186172 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 1=YY1 || chip antibody manufacturer 1=Abcam || chip antibody 2=YY1 || chip antibody manufacturer 2=Santa Cru...ip-Seq; Mus musculus; ChIP-Seq source_name=Rag1 -/- pro-B cells || chip antibody
rSeqNP: a non-parametric approach for detecting differential expression and splicing from RNA-Seq data.

Science.gov (United States)

Shi, Yang; Chinnaiyan, Arul M; Jiang, Hui

2015-07-01

High-throughput sequencing of transcriptomes (RNA-Seq) has become a powerful tool to study gene expression. Here we present an R package, rSeqNP, which implements a non-parametric approach to test for differential expression and splicing from RNA-Seq data. rSeqNP uses permutation tests to access statistical significance and can be applied to a variety of experimental designs. By combining information across isoforms, rSeqNP is able to detect more differentially expressed or spliced genes from RNA-Seq data. The R package with its source code and documentation are freely available at http://www-personal.umich.edu/∼jianghui/rseqnp/. jianghui@umich.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
Experiment list: SRX150684 [Chip-atlas[Archive

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Full Text Available sue Diagnosis=Fibrocystic Disease 174026370,97.9,12.7,1654 GSM935605: Harvard ChipSeq MCF10A-Er-Src Input Harvard... Control source_name=MCF10A-Er-Src || biomaterial_provider=Struhl laboratory || lab=Harvard || lab description=Struhl - Harvard...before peaks are called. || control=Harvard_Control || control description=input library was prepared at Harvard. || control=Harvard..._Control || control description=input library was prepared at Harvard. || controlid=
DETECTION OF BACTERIAL SMALL TRANSCRIPTS FROM RNA-SEQ DATA: A COMPARATIVE ASSESSMENT.

Science.gov (United States)

Peña-Castillo, Lourdes; Grüell, Marc; Mulligan, Martin E; Lang, Andrew S

2016-01-01

Small non-coding RNAs (sRNAs) are regulatory RNA molecules that have been identified in a multitude of bacterial species and shown to control numerous cellular processes through various regulatory mechanisms. In the last decade, next generation RNA sequencing (RNA-seq) has been used for the genome-wide detection of bacterial sRNAs. Here we describe sRNA-Detect, a novel approach to identify expressed small transcripts from prokaryotic RNA-seq data. Using RNA-seq data from three bacterial species and two sequencing platforms, we performed a comparative assessment of five computational approaches for the detection of small transcripts. We demonstrate that sRNA-Detect improves upon current standalone computational approaches for identifying novel small transcripts in bacteria.
Experiment list: SRX150661 [Chip-atlas[Archive

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Full Text Available is=Adenocarcinoma 59396606,71.7,11.1,1200 GSM935582: Harvard ChipSeq HeLa-S3 BRF1 std source_name=HeLa-S3 ||... biomaterial_provider=ATCC || lab=Harvard || lab description=Struhl - Harvard University || datatype=ChipSeq
Experiment list: SRX150495 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available is=Adenocarcinoma 62508352,67.6,8.4,1556 GSM935416: Harvard ChipSeq HeLa-S3 ZZZ3 std source_name=HeLa-S3 || ...biomaterial_provider=ATCC || lab=Harvard || lab description=Struhl - Harvard University || datatype=ChipSeq
Experiment list: SRX150565 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available =Adenocarcinoma 54953593,74.3,12.2,1703 GSM935486: Harvard ChipSeq HeLa-S3 BDP1 std source_name=HeLa-S3 || b...iomaterial_provider=ATCC || lab=Harvard || lab description=Struhl - Harvard University || datatype=ChipSeq |
Experiment list: SRX150586 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available -Barr Virus 33195472,90.4,25.9,15633 GSM935507: Harvard ChipSeq GM12878 NF-YB IgG-mus source_name=GM12878 ||...?PgId=165&q=GM12878 || lab=Harvard || lab description=Struhl - Harvard University || datatype=ChipSeq || dat
Experiment list: SRX150496 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available ein-Barr Virus 63040797,85.0,19.7,1435 GSM935417: Harvard ChipSeq GM12878 SPT20 std source_name=GM12878 || b...gId=165&q=GM12878 || lab=Harvard || lab description=Struhl - Harvard University || datatype=ChipSeq || datat
Experiment list: SRX150585 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available -Barr Virus 32926476,94.0,12.0,2668 GSM935506: Harvard ChipSeq GM12878 NF-YA IgG-mus source_name=GM12878 || ...PgId=165&q=GM12878 || lab=Harvard || lab description=Struhl - Harvard University || datatype=ChipSeq || data
Fish the ChIPs: a pipeline for automated genomic annotation of ChIP-Seq data

Directory of Open Access Journals (Sweden)

Minucci Saverio

2011-10-01

Full Text Available Abstract Background High-throughput sequencing is generating massive amounts of data at a pace that largely exceeds the throughput of data analysis routines. Here we introduce Fish the ChIPs (FC, a computational pipeline aimed at a broad public of users and designed to perform complete ChIP-Seq data analysis of an unlimited number of samples, thus increasing throughput, reproducibility and saving time. Results Starting from short read sequences, FC performs the following steps: 1 quality controls, 2 alignment to a reference genome, 3 peak calling, 4 genomic annotation, 5 generation of raw signal tracks for visualization on the UCSC and IGV genome browsers. FC exploits some of the fastest and most effective tools today available. Installation on a Mac platform requires very basic computational skills while configuration and usage are supported by a user-friendly graphic user interface. Alternatively, FC can be compiled from the source code on any Unix machine and then run with the possibility of customizing each single parameter through a simple configuration text file that can be generated using a dedicated user-friendly web-form. Considering the execution time, FC can be run on a desktop machine, even though the use of a computer cluster is recommended for analyses of large batches of data. FC is perfectly suited to work with data coming from Illumina Solexa Genome Analyzers or ABI SOLiD and its usage can potentially be extended to any sequencing platform. Conclusions Compared to existing tools, FC has two main advantages that make it suitable for a broad range of users. First of all, it can be installed and run by wet biologists on a Mac machine. Besides it can handle an unlimited number of samples, being convenient for large analyses. In this context, computational biologists can increase reproducibility of their ChIP-Seq data analyses while saving time for downstream analyses. Reviewers This article was reviewed by Gavin Huttley, George

PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci

Directory of Open Access Journals (Sweden)

Tammoja Kairi

2010-08-01

Full Text Available Abstract Background Functional genomic studies involving high-throughput sequencing and tiling array applications, such as ChIP-seq and ChIP-chip, generate large numbers of experimentally-derived signal peaks across the genome under study. In analyzing these loci to determine their potential regulatory functions, areas of signal enrichment must be considered relative to proximal genes and regulatory elements annotated throughout the target genome Regions of chromatin association by transcriptional regulators should be distinguished as individual binding sites in order to enhance downstream analyses, such as the identification of known and novel consensus motifs. Results PeakAnalyzer is a set of high-performance utilities for the automated processing of experimentally-derived peak regions and annotation of genomic loci. The programs can accurately subdivide multimodal regions of signal enrichment into distinct subpeaks corresponding to binding sites or chromatin modifications, retrieve genomic sequences encompassing the computed subpeak summits, and identify positional features of interest such as intersection with exon/intron gene components, proximity to up- or downstream transcriptional start sites and cis-regulatory elements. The software can be configured to run either as a pipeline component for high-throughput analyses, or as a cross-platform desktop application with an intuitive user interface. Conclusions PeakAnalyzer comprises a number of utilities essential for ChIP-seq and ChIP-chip data analysis. High-performance implementations are provided for Unix pipeline integration along with a GUI version for interactive use. Source code in C++ and Java is provided, as are native binaries for Linux, Mac OS X and Windows systems.
Analysis of ChIP-seq Data in R/Bioconductor.

Science.gov (United States)

de Santiago, Ines; Carroll, Thomas

2018-01-01

The development of novel high-throughput sequencing methods for ChIP (chromatin immunoprecipitation) has provided a very powerful tool to study gene regulation in multiple conditions at unprecedented resolution and scale. Proactive quality-control and appropriate data analysis techniques are of critical importance to extract the most meaningful results from the data. Over the last years, an array of R/Bioconductor tools has been developed allowing researchers to process and analyze ChIP-seq data. This chapter provides an overview of the methods available to analyze ChIP-seq data based primarily on software packages from the open-source Bioconductor project. Protocols described in this chapter cover basic steps including data alignment, peak calling, quality control and data visualization, as well as more complex methods such as the identification of differentially bound regions and functional analyses to annotate regulatory regions. The steps in the data analysis process were demonstrated on publicly available data sets and will serve as a demonstration of the computational procedures routinely used for the analysis of ChIP-seq data in R/Bioconductor, from which readers can construct their own analysis pipelines.
Experiment list: SRX107410 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Adenocarcinoma 37378122,96.3,56.7,376 GSM838388: h3k36me3 si23 ChIP-Seq; Homo sapiens; ChIP-Seq source_name=Hela cells knock...down Med23 || chip antibody=H3K36me3 || treatment=knockdown Med23 || cell line=HeLa || chip
An effective approach for identification of in vivo protein-DNA binding sites from paired-end ChIP-Seq data

Directory of Open Access Journals (Sweden)

Wilson Zoe A

2010-02-01

Full Text Available Abstract Background ChIP-Seq, which combines chromatin immunoprecipitation (ChIP with high-throughput massively parallel sequencing, is increasingly being used for identification of protein-DNA interactions in vivo in the genome. However, to maximize the effectiveness of data analysis of such sequences requires the development of new algorithms that are able to accurately predict DNA-protein binding sites. Results Here, we present SIPeS (Site Identification from Paired-end Sequencing, a novel algorithm for precise identification of binding sites from short reads generated by paired-end solexa ChIP-Seq technology. In this paper we used ChIP-Seq data from the Arabidopsis basic helix-loop-helix transcription factor ABORTED MICROSPORES (AMS, which is expressed within the anther during pollen development, the results show that SIPeS has better resolution for binding site identification compared to two existing ChIP-Seq peak detection algorithms, Cisgenome and MACS. Conclusions When compared to Cisgenome and MACS, SIPeS shows better resolution for binding site discovery. Moreover, SIPeS is designed to calculate the mappable genome length accurately with the fragment length based on the paired-end reads. Dynamic baselines are also employed to effectively discriminate closely adjacent binding sites, for effective binding sites discovery, which is of particular value when working with high-density genomes.
Experiment list: SRX085443 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available SRX085443 mm9 Input control Input control Neural Cerebellum MeSH Description=The pa...ntain balance, and learn motor skills. 38330550,73.2,10.7,866 GSM769020: lab ChipSeq Cerebellum Input source_name=Cerebellum... Cancer Research || datatype=ChipSeq || datatype description=ChIP-Seq || cell=Cerebellum... || cell organism=mouse || cell description=Cerebellum || cell sex=M || antibody=Input || antibody de...on=Standard input signal for most experiments. || controlid=Cerebellum/Input/std || labversion=05/27/09 Lane
Experiment list: SRX150629 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available sue Diagnosis=Fibrocystic Disease 27949151,89.1,5.9,589 GSM935550: Harvard ChipSeq MCF10A-Er-Src EtOH 0.01pc...t 12hr Input std source_name=MCF10A-Er-Src || biomaterial_provider=Struhl laboratory || lab=Harvard || lab description=Struhl - Harva...rd University || datatype=ChipSeq || datatype descriptio
Experiment list: SRX150494 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available n-Barr Virus 44912180,85.6,7.7,1806 GSM935415: Harvard ChipSeq GM12878 GCN5 std source_name=GM12878 || bioma...ard || lab description=Struhl - Harvard University || datatype=ChipSeq || datatype ...terial_provider=Coriell; http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM12878 || lab=Harv
Experiment list: SRX150667 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available t|Tissue Diagnosis=Fibrocystic Disease 69172664,86.5,35.3,28780 GSM935588: Harvard ChipSeq MCF10A-Er-Src EtO...H 0.01pct Pol2 std source_name=MCF10A-Er-Src || biomaterial_provider=Struhl laboratory || lab=Harvard || lab description=Struhl - Har...vard University || datatype=ChipSeq || datatype descript
Experiment list: SRX150535 [Chip-atlas[Archive

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Full Text Available t|Tissue Diagnosis=Fibrocystic Disease 69171580,86.8,43.7,20874 GSM935456: Harvard ChipSeq MCF10A-Er-Src 4OH...TAM 1uM 36hr Pol2 std source_name=MCF10A-Er-Src || biomaterial_provider=Struhl laboratory || lab=Harvard || ...lab description=Struhl - Harvard University || datatype=ChipSeq || datatype descr
Experiment list: SRX150562 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available -Barr Virus 57294082,73.4,6.6,1909 GSM935483: Harvard ChipSeq GM12878 ZZZ3 std source_name=GM12878 || biomat...rd || lab description=Struhl - Harvard University || datatype=ChipSeq || datatype d...erial_provider=Coriell; http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM12878 || lab=Harva
Fabrication Localized Surface Plasmon Resonance sensor chip of gold nanoparticles and detection lipase–osmolytes interaction

Energy Technology Data Exchange (ETDEWEB)

Ghodselahi, T., E-mail: t_ghodselahi@yahoo.com [Nano Mabna Iranian Inc., PO Box 1676664116, Tehran (Iran, Islamic Republic of); School of Physics, Institute for Research in Fundamental Sciences, PO Box 19395-5531, Tehran (Iran, Islamic Republic of); Hoornam, S. [Nano Mabna Iranian Inc., PO Box 1676664116, Tehran (Iran, Islamic Republic of); School of Physics, Institute for Research in Fundamental Sciences, PO Box 19395-5531, Tehran (Iran, Islamic Republic of); Department of Science, Central Tehran Branch, Islamic Azad University, Tehran (Iran, Islamic Republic of); Vesaghi, M.A. [Department of Physics, Sharif University of Technology, PO Box 11365-9161, Tehran (Iran, Islamic Republic of); Ranjbar, B.; Azizi, A. [Department of Biophysics, Tarbiat Modares University, Tehran (Iran, Islamic Republic of); Mobasheri, H. [Laboratory of Membrane Biophysics, Institute of Biochemistry and Biophysics, University of Tehran, PO Box 13145-1384, Tehran (Iran, Islamic Republic of); Biomaterials Research Institute (BRC), University of Tehran, Tehran (Iran, Islamic Republic of)

2014-09-30

Highlights: • We synthesized localized surface plasmon resonance sensor of gold nanoparticles by RF-sputtering and RF-PECVD. • LSPR sensor was characterized by TEM, XPS, AFM. • LSPR sensor was utilized to detect interaction between sorbitol and trehalose, with Pesudomonace Cepacia Lipase (PCL). • Unlike to trehalose, sorbitol interacts with the PCL. • Refractive index of PCL was obtained by Mie theory modeling. - Abstract: Co-deposition of RF-sputtering and RF-PECVD from acetylene gas and Au target were used to prepare sensor chip of gold nanoparticles (Au NPs). Deposition conditions were optimized to reach a Localized Surface Plasmon Resonance (LSPR) sensor chip of Au NPs with particle size less than 10 nm. The RF power was set at 180 W and the initial gas pressure was set at 0.035 mbar. Transmission Electron Microscopy (TEM) images and Atomic Force Microscopy (AFM) data were used to investigate particles size and surface morphology of LSPR sensor chip. The Au and C content of the LSPR sensor chip of Au NPs was obtained from X-ray photoelectron spectroscopy (XPS). The hydrogenated amorphous carbon (a-C:H) thin film was used as intermediate material to immobilize Au NPs on the SiO{sub 2} substrate. The interaction between two types of osmolytes, i.e. sorbitol and trehalose, with Pseudomonas cepacia lipase (PCL) were detected by the prepared LSPR biosensor chip. The detection mechanism is based on LSPR spectroscopy in which the wavelength of absorption peak is sensitive to the refractive index of the environment of the Au NPs. This mechanism eliminates the use of a probe or immobilization of PCL on the Au NPs of LSPR sensor chip. The interaction between PCL and osmolytes can change refractive index of the mixture or solution. We found that unlike to trehalose, sorbitol interacts with the PCL. This interaction increases refractive index of the PCL and sorbitol mixture. Refractive index of PCL in the presence of different concentration of sorbitol was
Experiment list: SRX085450 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available SRX085450 mm9 Histone H3K4me3 Neural Cerebellum MeSH Description=The part of brain ...e, and learn motor skills. 40109154,65.1,24.9,36907 GSM769027: lab ChipSeq Cerebellum H3K4me3 source_name=Cerebellum...Research || datatype=ChipSeq || datatype description=ChIP-Seq || cell=Cerebellum ...|| cell organism=mouse || cell description=Cerebellum || cell sex=M || antibody=H3K4me3 || antibody antibody...Standard input signal for most experiments. || controlid=Cerebellum/Input/std || labversion=5/26/09 Lane 6 |
Experiment list: SRX085441 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available SRX085441 mm9 Histone H3K4me1 Neural Cerebellum MeSH Description=The part of brain ...e, and learn motor skills. 34909537,81.0,5.9,29316 GSM769018: lab ChipSeq Cerebellum H3K4me1 source_name=Cerebellum...esearch || datatype=ChipSeq || datatype description=ChIP-Seq || cell=Cerebellum |...| cell organism=mouse || cell description=Cerebellum || cell sex=M || antibody=H3K4me1 || antibody antibodyd...iption=Standard input signal for most experiments. || controlid=Cerebellum/Input/std || labversion=12/09/09
Experiment list: SRX758028 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available agnosis=Carcinoma 82846335,87.8,5.7,22076 GSM1543791: LNCaP TOP1 ChIP-seq 30min vehicle; Homo sapiens; ChIP-...Seq source_name=ChIP-seq with BLRP-tagged TOP1, 30min treatment with vehicle || cell line=LNCaP || chip anti
Experiment list: SRX148878 [Chip-atlas[Archive

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Full Text Available nosis=Carcinoma 71832151,98.1,33.1,1626 GSM934593: H2B ChIP-Seq USP49 knockdown; Homo sapiens; ChIP-Seq sour...ce_name=H2B ChIP-Seq USP49 knockdown || cell line=HCT116 || cell type=colorectal carcinoma || chip antibody=
An empirical strategy to detect bacterial transcript structure from directional RNA-seq transcriptome data.

Science.gov (United States)

Wang, Yejun; MacKenzie, Keith D; White, Aaron P

2015-05-07

As sequencing costs are being lowered continuously, RNA-seq has gradually been adopted as the first choice for comparative transcriptome studies with bacteria. Unlike microarrays, RNA-seq can directly detect cDNA derived from mRNA transcripts at a single nucleotide resolution. Not only does this allow researchers to determine the absolute expression level of genes, but it also conveys information about transcript structure. Few automatic software tools have yet been established to investigate large-scale RNA-seq data for bacterial transcript structure analysis. In this study, 54 directional RNA-seq libraries from Salmonella serovar Typhimurium (S. Typhimurium) 14028s were examined for potential relationships between read mapping patterns and transcript structure. We developed an empirical method, combined with statistical tests, to automatically detect key transcript features, including transcriptional start sites (TSSs), transcriptional termination sites (TTSs) and operon organization. Using our method, we obtained 2,764 TSSs and 1,467 TTSs for 1331 and 844 different genes, respectively. Identification of TSSs facilitated further discrimination of 215 putative sigma 38 regulons and 863 potential sigma 70 regulons. Combining the TSSs and TTSs with intergenic distance and co-expression information, we comprehensively annotated the operon organization in S. Typhimurium 14028s. Our results show that directional RNA-seq can be used to detect transcriptional borders at an acceptable resolution of ±10-20 nucleotides. Technical limitations of the RNA-seq procedure may prevent single nucleotide resolution. The automatic transcript border detection methods, statistical models and operon organization pipeline that we have described could be widely applied to RNA-seq studies in other bacteria. Furthermore, the TSSs, TTSs, operons, promoters and unstranslated regions that we have defined for S. Typhimurium 14028s may constitute valuable resources that can be used for
Experiment list: SRX148876 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available agnosis=Carcinoma 62096923,98.1,90.9,255 GSM934591: uH2b ChIP-Seq USP49 knockdown; Homo sapiens; ChIP-Seq so...urce_name=uH2b ChIP-Seq USP49 knockdown || cell line=HCT116 || cell type=colorectal carcinoma || chip antibo
An Annotation Agnostic Algorithm for Detecting Nascent RNA Transcripts in GRO-Seq.

Science.gov (United States)

Azofeifa, Joseph G; Allen, Mary A; Lladser, Manuel E; Dowell, Robin D

2017-01-01

We present a fast and simple algorithm to detect nascent RNA transcription in global nuclear run-on sequencing (GRO-seq). GRO-seq is a relatively new protocol that captures nascent transcripts from actively engaged polymerase, providing a direct read-out on bona fide transcription. Most traditional assays, such as RNA-seq, measure steady state RNA levels which are affected by transcription, post-transcriptional processing, and RNA stability. GRO-seq data, however, presents unique analysis challenges that are only beginning to be addressed. Here, we describe a new algorithm, Fast Read Stitcher (FStitch), that takes advantage of two popular machine-learning techniques, hidden Markov models and logistic regression, to classify which regions of the genome are transcribed. Given a small user-defined training set, our algorithm is accurate, robust to varying read depth, annotation agnostic, and fast. Analysis of GRO-seq data without a priori need for annotation uncovers surprising new insights into several aspects of the transcription process.
Experiment list: SRX485203 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 346544: Rhino ChIP from control germline knock-down ovaries, replicate 2; Drosophila melanogaster; ChIP-Seq ...source_name=Rhino ChIP from control germline knock-down ovaries || developmental stage=4-6 days old adult ||... Sex=female || tissue=ovary || germline knock-down=control || chip antibody=custo
Experiment list: SRX485202 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 346543: Rhino ChIP from control germline knock-down ovaries, replicate 1; Drosophila melanogaster; ChIP-Seq ...source_name=Rhino ChIP from control germline knock-down ovaries || developmental stage=4-6 days old adult ||... Sex=female || tissue=ovary || germline knock-down=control || chip antibody=custo

Experiment list: SRX485210 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 6551: Deadlock ChIP from deadlock germline knock-down ovaries; Drosophila melanogaster; ChIP-Seq source_name...=Deadlock ChIP from deadlock germline knock-down ovaries || developmental stage=4-6 days old adult || Sex=fe...male || tissue=ovary || germline knock-down=deadlock || chip antibody=custom-made
Experiment list: SRX485211 [Chip-atlas[Archive

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Full Text Available 346552: Cutoff ChIP from control germline knock-down ovaries; Drosophila melanogaster; ChIP-Seq source_name=...Cutoff ChIP from control germline knock-down ovaries || developmental stage=4-6 days old adult || Sex=female... || tissue=ovary || germline knock-down=control || chip antibody=custom-made rabb
Experiment list: SRX185907 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Homo sapiens; ChIP-Seq source_name=MCF-7 breast adenocarcinoma cells, control, FOXM1 ChIP || cell_line=MCF-...7 || cell_type=ER-positive breast adenocarcinoma cells || treatment=DMSO || chip_
Experiment list: SRX150520 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available osis=Fibrocystic Disease 49296691,89.4,24.9,46885 GSM935441: Harvard ChipSeq MCF10A-Er-Src EtOH 0.01pct c-Myc Harvard... Control source_name=MCF10A-Er-Src || biomaterial_provider=Struhl laboratory || lab=Harvard || lab description=Struhl - Harv...|| antibody vendorid=sc-764 || control=Harvard_Control || control description=input library was prepared at Harvard. || control=Harva...rd_Control || control description=input library was prepared at Harvard...ard University || datatype=ChipSeq || datatype descripti
Experiment list: SRX150478 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available osis=Fibrocystic Disease 66690540,98.1,24.9,110111 GSM935398: Harvard ChipSeq MCF10A-Er-Src 4OHTAM 1uM 12hr c-Fos Harvard... Control source_name=MCF10A-Er-Src || biomaterial_provider=Struhl laboratory || lab=Harvard || ...lab description=Struhl - Harvard University || datatype=ChipSeq || datatype descr... is a leucine-zipper. || antibody vendorname=Santa Cruz Biotech || antibody vendorid=sc-7202 || control=Harvard..._Control || control description=input library was prepared at Harvard. || control=Harvard
Experiment list: SRX150696 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available -1 || cell organism=human || cell description=pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a panc...SRX150696 hg19 Input control Input control Pancreas PANC-1 Tissue=Pancreas/Duct|Dis...ease=Epithelioid Carcinoma 41671673,95.8,10.4,1584 GSM935617: USC ChipSeq PANC-1 Input UCDavis source_name=PANC... || datatype=ChipSeq || datatype description=Chromatin IP Sequencing || cell=PANC...reatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Cau
Experiment list: SRX199860 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available | cell organism=human || cell description=pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a panc...SRX199860 hg19 Input control Input control Pancreas PANC-1 Tissue=Pancreas/Duct|Dis...ease=Epithelioid Carcinoma 27365308,98.2,3.6,969 GSM1022632: UW ChipSeq PANC-1 InputRep1 source_name=PANC-1 ...datatype=ChipSeq || datatype description=Chromatin IP Sequencing || cell=PANC-1 |...reatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasi
Experiment list: SRX977433 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available ates NA 65512838,98.3,15.4,34790 GSM1648684: RNAPII ChipSeq day15; Mus musculus; ChIP-Seq source_name=reprogramming... intermediate after 15days of induction || cell type=reprogramming intermediate || genotype=RNAPII-GF
Experiment list: SRX977429 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available ates NA 57685706,97.8,16.7,27894 GSM1648680: RNAPII ChipSeq day3; Mus musculus; ChIP-Seq source_name=reprogramming... intermediate after 3days of induction || cell type=reprogramming intermediate || genotype=RNAPII-GFP/
Experiment list: SRX977432 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available ates NA 56429535,98.1,16.9,32459 GSM1648683: RNAPII ChipSeq day11; Mus musculus; ChIP-Seq source_name=reprogramming... intermediate after 11days of induction || cell type=reprogramming intermediate || genotype=RNAPII-GF
Experiment list: SRX185915 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available mo sapiens; ChIP-Seq source_name=MCF-7 breast adenocarcinoma cells, control, FOXM1 ChIP || cell_line=MCF-7 |...| cell_type=ER-positive breast adenocarcinoma cells || treatment=DMSO || chip_tar
Experiment list: SRX185909 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available omo sapiens; ChIP-Seq source_name=MCF-7 breast adenocarcinoma cells, control, FOXM1 ChIP || cell_line=MCF-7 ...|| cell_type=ER-positive breast adenocarcinoma cells || treatment=DMSO || chip_ta
Experiment list: SRX185917 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available omo sapiens; ChIP-Seq source_name=MCF-7 breast adenocarcinoma cells, control, FOXM1 ChIP || cell_line=MCF-7 ...|| cell_type=ER-positive breast adenocarcinoma cells || treatment=DMSO || chip_ta
Experiment list: SRX485205 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 46546: Rhino ChIP from deadlock germline knock-down ovaries; Drosophila melanogaster; ChIP-Seq source_name=R...hino ChIP from deadlock germline knock-down ovaries || developmental stage=4-6 days old adult || Sex=female ...|| tissue=ovary || germline knock-down=deadlock || chip antibody=custom-made rabb
Experiment list: SRX485212 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 346553: Cutoff ChIP from cutoff germline knock-down ovaries; Drosophila melanogaster; ChIP-Seq source_name=C...utoff ChIP from cutoff germline knock-down ovaries || developmental stage=4-6 days old adult || Sex=female |...| tissue=ovary || germline knock-down=cutoff || chip antibody=custom-made rabbit
Experiment list: SRX485206 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 346547: Rhino ChIP from cutoff germline knock-down ovaries; Drosophila melanogaster; ChIP-Seq source_name=Rh...ino ChIP from cutoff germline knock-down ovaries || developmental stage=4-6 days old adult || Sex=female || ...tissue=ovary || germline knock-down=cutoff || chip antibody=custom-made rabbit po
Experiment list: SRX485209 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 346550: Deadlock ChIP from control germline knock-down ovaries; Drosophila melanogaster; ChIP-Seq source_nam...e=Deadlock ChIP from control germline knock-down ovaries || developmental stage=4-6 days old adult || Sex=fe...male || tissue=ovary || germline knock-down=control || chip antibody=custom-made
Automated asteroseismic peak detections

Science.gov (United States)

García Saravia Ortiz de Montellano, Andrés; Hekker, S.; Themeßl, N.

2018-05-01

Space observatories such as Kepler have provided data that can potentially revolutionize our understanding of stars. Through detailed asteroseismic analyses we are capable of determining fundamental stellar parameters and reveal the stellar internal structure with unprecedented accuracy. However, such detailed analyses, known as peak bagging, have so far been obtained for only a small percentage of the observed stars while most of the scientific potential of the available data remains unexplored. One of the major challenges in peak bagging is identifying how many solar-like oscillation modes are visible in a power density spectrum. Identification of oscillation modes is usually done by visual inspection that is time-consuming and has a degree of subjectivity. Here, we present a peak-detection algorithm especially suited for the detection of solar-like oscillations. It reliably characterizes the solar-like oscillations in a power density spectrum and estimates their parameters without human intervention. Furthermore, we provide a metric to characterize the false positive and false negative rates to provide further information about the reliability of a detected oscillation mode or the significance of a lack of detected oscillation modes. The algorithm presented here opens the possibility for detailed and automated peak bagging of the thousands of solar-like oscillators observed by Kepler.
Multiscale peak detection in wavelet space.

Science.gov (United States)

Zhang, Zhi-Min; Tong, Xia; Peng, Ying; Ma, Pan; Zhang, Ming-Jin; Lu, Hong-Mei; Chen, Xiao-Qing; Liang, Yi-Zeng

2015-12-07

Accurate peak detection is essential for analyzing high-throughput datasets generated by analytical instruments. Derivatives with noise reduction and matched filtration are frequently used, but they are sensitive to baseline variations, random noise and deviations in the peak shape. A continuous wavelet transform (CWT)-based method is more practical and popular in this situation, which can increase the accuracy and reliability by identifying peaks across scales in wavelet space and implicitly removing noise as well as the baseline. However, its computational load is relatively high and the estimated features of peaks may not be accurate in the case of peaks that are overlapping, dense or weak. In this study, we present multi-scale peak detection (MSPD) by taking full advantage of additional information in wavelet space including ridges, valleys, and zero-crossings. It can achieve a high accuracy by thresholding each detected peak with the maximum of its ridge. It has been comprehensively evaluated with MALDI-TOF spectra in proteomics, the CAMDA 2006 SELDI dataset as well as the Romanian database of Raman spectra, which is particularly suitable for detecting peaks in high-throughput analytical signals. Receiver operating characteristic (ROC) curves show that MSPD can detect more true peaks while keeping the false discovery rate lower than MassSpecWavelet and MALDIquant methods. Superior results in Raman spectra suggest that MSPD seems to be a more universal method for peak detection. MSPD has been designed and implemented efficiently in Python and Cython. It is available as an open source package at .
Experiment list: SRX485220 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 53 GSM1346561: RNA Polymerase II ChIP from rhino germline knock-down ovaries; Drosophila melanogaster; ChIP-...Seq source_name=RNA Polymerase II ChIP from rhino germline knock-down ovaries || developmental stage=4-6 day...s old adult || Sex=female || tissue=ovary || germline knock-down=rhino || chip an

Experiment list: SRX485204 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 346545: Rhino ChIP from rhino germline knock-down ovaries; Drosophila melanogaster; ChIP-Seq source_name=Rhi...no ChIP from rhino germline knock-down ovaries || developmental stage=4-6 days old adult || Sex=female || ti...ssue=ovary || germline knock-down=rhino || chip antibody=custom-made rabbit polyc
Experiment list: SRX485208 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 346549: Rhino ChIP from piwi germline knock-down ovaries, replicate 2; Drosophila melanogaster; ChIP-Seq sou...rce_name=Rhino ChIP from piwi germline knock-down ovaries || developmental stage=4-6 days old adult || Sex=f...emale || tissue=ovary || germline knock-down=piwi || chip antibody=custom-made ra
Experiment list: SRX190029 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available l organism=human || cell description=pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a panc...SRX190029 hg19 Input control Input control Pancreas PANC-1 Tissue=Pancreas/Duct|Dis...ease=Epithelioid Carcinoma 27365308,98.2,3.6,980 GSM945246: UW ChipSeq PANC-1 Input source_name=PANC-1 || bi...ype=ChipSeq || datatype description=Chromatin IP Sequencing || cell=PANC-1 || cel...reatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian in
Experiment list: SRX977378 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 23908,98.7,9.6,43208 GSM1648629: total Oct4 ChipSeq day11; Mus musculus; ChIP-Seq source_name=reprogramming ...intermediate after 11days of induction || cell type=reprogramming intermediate || genotype=Oct4-GFP/ Rosa26-
Experiment list: SRX977377 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 40719,98.1,13.8,57202 GSM1648628: total Oct4 ChipSeq day7; Mus musculus; ChIP-Seq source_name=reprogramming ...intermediate after 7days of induction || cell type=reprogramming intermediate || genotype=Oct4-GFP/ Rosa26-M
Experiment list: SRX977366 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available NA 60072229,98.6,9.6,78331 GSM1648617: flag Oct4 ChipSeq day1; Mus musculus; ChIP-Seq source_name=reprogramming... intermediate after 24hour of induction || cell type=reprogramming intermediate || genotype=Oct4-GFP/ Ros
Experiment list: SRX977375 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 20178,94.6,10.8,52926 GSM1648626: total Oct4 ChipSeq day3; Mus musculus; ChIP-Seq source_name=reprogramming ...intermediate after 3days of induction || cell type=reprogramming intermediate || genotype=Oct4-GFP/ Rosa26-M
Experiment list: SRX977379 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 93532,97.8,13.3,43901 GSM1648630: total Oct4 ChipSeq day15; Mus musculus; ChIP-Seq source_name=reprogramming... intermediate after 15days of induction || cell type=reprogramming intermediate || genotype=Oct4-GFP/ Rosa26
Experiment list: SRX977368 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available NA 58474287,97.8,9.8,84163 GSM1648619: flag Oct4 ChipSeq day5; Mus musculus; ChIP-Seq source_name=reprogramming... intermediate after 5days of induction || cell type=reprogramming intermediate || genotype=Oct4-GFP/ Rosa
Experiment list: SRX977369 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available NA 58631406,98.5,10.3,72036 GSM1648620: flag Oct4 ChipSeq day7; Mus musculus; ChIP-Seq source_name=reprogramming... intermediate after 7days of induction || cell type=reprogramming intermediate || genotype=Oct4-GFP/ Ros
Experiment list: SRX684775 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available ng || cell type=intermediate stage of somatic cell reprogramming || chip antibody=M...,29.2,290321 GSM1483904: pre-iPS.H3.MNase-ChIP-Seq; Mus musculus; ChIP-Seq source_name=intermediate stage of somatic cell reprogrammi
Experiment list: SRX977371 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available NA 63273752,96.7,14.1,37891 GSM1648622: flag Oct4 ChipSeq day15; Mus musculus; ChIP-Seq source_name=reprogramming... intermediate after 15days of induction || cell type=reprogramming intermediate || genotype=Oct4-GFP/ R
Experiment list: SRX1090864 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available ming || cell type=intermediate stage of somatic cell reprogramming || chip antibody...5,12.8,491 GSM1816301: pre-iPS rep.H3.MNase-ChIP-Seq; Mus musculus; ChIP-Seq source_name=intermediate stage of somatic cell reprogram
Experiment list: SRX107407 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available osis=Adenocarcinoma 37670219,66.5,15.7,675 GSM838385: hnrnpl sictrl ChIP-Seq; Homo sapiens; ChIP-Seq source_name=Hela cells knock...down control || chip antibody=hnRNP L || treatment=knockdown control || cell line=HeLa
A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data.

Science.gov (United States)

Tran, Ngoc Tam L; Huang, Chun-Hsi

2014-02-20

ChIP-Seq (chromatin immunoprecipitation sequencing) has provided the advantage for finding motifs as ChIP-Seq experiments narrow down the motif finding to binding site locations. Recent motif finding tools facilitate the motif detection by providing user-friendly Web interface. In this work, we reviewed nine motif finding Web tools that are capable for detecting binding site motifs in ChIP-Seq data. We showed each motif finding Web tool has its own advantages for detecting motifs that other tools may not discover. We recommended the users to use multiple motif finding Web tools that implement different algorithms for obtaining significant motifs, overlapping resemble motifs, and non-overlapping motifs. Finally, we provided our suggestions for future development of motif finding Web tool that better assists researchers for finding motifs in ChIP-Seq data.
Reagent-loaded plastic microfluidic chips for detecting homocysteine

International Nuclear Information System (INIS)

Suk, Ji Won; Jang, Jae-Young; Cho, Jun-Hyeong

2008-01-01

This report describes the preliminary study on plastic microfluidic chips with pre-loaded reagents for detecting homocysteine (Hcy). All reagents needed in an Hcy immunoassay were included in a microfluidic chip to remove tedious assay steps. A simple and cost-effective bonding method was developed to realize reagent-loaded microfluidic chips. This technique uses an intermediate layer between two plastic substrates by selectively patterning polydimethylsiloxane (PDMS) on the embossed surface of microchannels and fixing the substrates under pressure. Using this bonding method, the competitive immunoassay for SAH, a converted form of Hcy, was performed without any damage to reagents in chips, and the results showed that the fluorescent signal from antibody antigen binding decreased as the SAH concentration increased. Based on the SAH immunoassay, whole immunoassay steps for Hcy detection were carried out in plastic microfluidic chips with all necessary reagents. These experiments demonstrated the feasibility of the Hcy immunoassay in microfluidic devices
rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data.

Science.gov (United States)

Shen, Shihao; Park, Juw Won; Lu, Zhi-xiang; Lin, Lan; Henry, Michael D; Wu, Ying Nian; Zhou, Qing; Xing, Yi

2014-12-23

Ultra-deep RNA sequencing (RNA-Seq) has become a powerful approach for genome-wide analysis of pre-mRNA alternative splicing. We previously developed multivariate analysis of transcript splicing (MATS), a statistical method for detecting differential alternative splicing between two RNA-Seq samples. Here we describe a new statistical model and computer program, replicate MATS (rMATS), designed for detection of differential alternative splicing from replicate RNA-Seq data. rMATS uses a hierarchical model to simultaneously account for sampling uncertainty in individual replicates and variability among replicates. In addition to the analysis of unpaired replicates, rMATS also includes a model specifically designed for paired replicates between sample groups. The hypothesis-testing framework of rMATS is flexible and can assess the statistical significance over any user-defined magnitude of splicing change. The performance of rMATS is evaluated by the analysis of simulated and real RNA-Seq data. rMATS outperformed two existing methods for replicate RNA-Seq data in all simulation settings, and RT-PCR yielded a high validation rate (94%) in an RNA-Seq dataset of prostate cancer cell lines. Our data also provide guiding principles for designing RNA-Seq studies of alternative splicing. We demonstrate that it is essential to incorporate biological replicates in the study design. Of note, pooling RNAs or merging RNA-Seq data from multiple replicates is not an effective approach to account for variability, and the result is particularly sensitive to outliers. The rMATS source code is freely available at rnaseq-mats.sourceforge.net/. As the popularity of RNA-Seq continues to grow, we expect rMATS will be useful for studies of alternative splicing in diverse RNA-Seq projects.
Experiment list: SRX1122118 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available M1833874: ChIP-seq H3K27Ac DMSO; Homo sapiens; ChIP-Seq source_name=Cultured Leukemic Blasts || chip antibod...y=H3K27ac (ActiveMotif, ab4729) || tissue=Cultured Leukemic Blasts || treatment compound=DMSO http://dbarchi
Experiment list: SRX977374 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 16864,98.6,9.4,51198 GSM1648625: total Oct4 ChipSeq day1; Mus musculus; ChIP-Seq source_name=reprogramming i...ntermediate after 24hour of induction || cell type=reprogramming intermediate || genotype=Oct4-GFP/ Rosa26-M
Experiment list: SRX152077 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available ll organism=human || cell description=pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a panc...SRX152077 hg19 Histone H3K4me3 Pancreas PANC-1 Tissue=Pancreas/Duct|Disease=Epithel...ioid Carcinoma 53620150,97.5,34.9,29597 GSM945856: USC ChipSeq PANC-1 H3K4me3B UCDavis source_name=PANC-1 ||...type=ChipSeq || datatype description=Chromatin IP Sequencing || cell=PANC-1 || ce...reatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian i

Experiment list: SRX352046 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available SM1232564: CSB M CHIP; Homo sapiens; ChIP-Seq source_name=fibroblast_menadione_CSB-ChIP || cell type=fibroblast || treated with=menad...ione || chip antibody=Mouse monoclonal anti-CSB N Terminus (1B1) http://dbarchive.b
Experiment list: SRX144526 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available stein-Barr Virus transformed 11803840,92.5,91.6,38 GSM922971: NRF2 ChIP vehicle treated rep2; Homo sapiens; ...ChIP-Seq source_name=NRF2 ChIP vehicle treated || biomaterial_provider=Coriell; h
Experiment list: SRX151245 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 0: CTCF ChIPSeq; Homo sapiens; ChIP-Seq source_name=BCBL1 pleural effusion lymphoma, CTCF ChIP || cell line=...BCBL1 || cell type=KSHV-infected pleural effusion lymphoma cells || chip antibody=rabbit anti-CTCF || antibo
Experiment list: SRX485222 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 4me2 ChIP from control germline knock-down ovaries, replicate 2; Drosophila melanogaster; ChIP-Seq source_na...me=H3K4me2 ChIP from control germline knock-down ovaries || developmental stage=4-6 days old adult || Sex=fe...male || tissue=ovary || germline knock-down=control || chip antibody=Anti-dimethy
Experiment list: SRX485221 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available K4me2 ChIP from control germline knock-down ovaries, replicate 1; Drosophila melanogaster; ChIP-Seq source_n...ame=H3K4me2 ChIP from control germline knock-down ovaries || developmental stage=4-6 days old adult || Sex=f...emale || tissue=ovary || germline knock-down=control || chip antibody=Anti-dimeth
HMCan: A method for detecting chromatin modifications in cancer samples using ChIP-seq data

KAUST Repository

Ashoor, Haitham; Hé rault, Auré lie; Kamoun, Auré lie; Radvanyi, Franç ois; Bajic, Vladimir B.; Barillot, Emmanuel; Boeva, Valentina

2013-01-01

genes. Though several tools have been created to enable detection of histone marks in ChIP-seq data from normal samples, it is unclear whether these tools can be efficiently applied to ChIP-seq data generated from cancer samples. Indeed, cancer genomes
Experiment list: SRX684777 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available ing || cell type=intermediate stage of somatic cell reprogramming || chip antibody=...,98.5,5.8,239 GSM1483906: pre-iPS.H3K27me3.ChIP-Seq; Mus musculus; ChIP-Seq source_name=intermediate stage of somatic cell reprogramm
Experiment list: SRX1122119 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 04 GSM1833875: ChIP-seq H3K27Ac GSI; Homo sapiens; ChIP-Seq source_name=Cultured Leukemic Blasts || chip ant...ibody=H3K27ac (ActiveMotif, ab4729) || tissue=Cultured Leukemic Blasts || treatment compound=GSI BMS-906024
Experiment list: SRX1090865 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available amming || cell type=intermediate stage of somatic cell reprogramming || chip antibo...,95.9,8.5,270 GSM1816302: pre-iPS rep.H3K4me3.ChIP-Seq; Mus musculus; ChIP-Seq source_name=intermediate stage of somatic cell reprogr
Experiment list: SRX684776 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available ng || cell type=intermediate stage of somatic cell reprogramming || chip antibody=a...98.0,10.6,335 GSM1483905: pre-iPS.H3K4me3.ChIP-Seq; Mus musculus; ChIP-Seq source_name=intermediate stage of somatic cell reprogrammi
Experiment list: SRX897943 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 153,97.9,13.9,15440 GSM1624628: ChIP seq Renilla Sox2 IP day3; Mus musculus; ChIP-Seq source_name=OKSM reprogramming... intermediates from Mouse Embryonic Fibroblasts || strain=Black6-129X1/SvJ || cell type=OKSM reprogramming
Experiment list: SRX684778 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 98.0,9.9,325 GSM1483907: pre-iPS.H3K9me3.ChIP-Seq; Mus musculus; ChIP-Seq source_name=intermediate stage of somatic cell reprogrammin...g || cell type=intermediate stage of somatic cell reprogramming || chip antibody=an
Experiment list: SRX150568 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available is=Adenocarcinoma 59265240,72.4,16.4,4779 GSM935489: Harvard ChipSeq HeLa-S3 RPC155 std source_name=HeLa-S3 ...|| biomaterial_provider=ATCC || lab=Harvard || lab description=Struhl - Harvard University || datatype=ChipS
Experiment list: SRX507380 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available + (wildtype) || age of animals=1-5 day old || tissue=Ovaries || chip antibody=anti-HP1 || chip antibody vend...1770: WT anti-HP1- replicate#2; Drosophila melanogaster; ChIP-Seq source_name=WT_WT_anti-HP1 || strain=piwi/
Experiment list: SRX176054 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available nosis=Carcinoma 13338805,91.2,4.9,792 GSM984386: LNCAP AR vehicle; Homo sapiens; ChIP-Seq source_name=prosta...te cancer cells || cell line=LNCaP || chip antibody=AR || chip antibody manufacturer=Abcam || treatment=EtOH vehicle
Experiment list: SRX144525 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available neage=mesoderm|Description=parental cell type to lymphoblastoid cell lines 14487710,85.8,82.8,188 GSM922970: NRF2 ChIP vehicle... treated rep1; Homo sapiens; ChIP-Seq source_name=NRF2 ChIP vehicle treated || biomaterial
Experiment list: SRX144524 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available neage=mesoderm|Description=parental cell type to lymphoblastoid cell lines 4766716,6.2,89.4,0 GSM922969: NRF2 ChIP vehicle... treated pilot; Homo sapiens; ChIP-Seq source_name=NRF2 ChIP vehicle treated || biomaterial_pr
Experiment list: SRX151246 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 11: SMC1 ChIPSeq; Homo sapiens; ChIP-Seq source_name=BCBL1 pleural effusion lymphoma, SMC1 ChIP || cell line...=BCBL1 || cell type=KSHV-infected pleural effusion lymphoma cells || chip antibody=rabbit anti-SMC1 || antib
Amplification of pico-scale DNA mediated by bacterial carrier DNA for small-cell-number transcription factor ChIP-seq

DEFF Research Database (Denmark)

Jakobsen, Janus S; Bagger, Frederik O; Hasemann, Marie S

2015-01-01

BACKGROUND: Chromatin-Immunoprecipitation coupled with deep sequencing (ChIP-seq) is used to map transcription factor occupancy and generate epigenetic profiles genome-wide. The requirement of nano-scale ChIP DNA for generation of sequencing libraries has impeded ChIP-seq on in vivo tissues of low...... transcription factor (CEBPA) and histone mark (H3K4me3) ChIP. We further demonstrate that genomic profiles are highly resilient to changes in carrier DNA to ChIP DNA ratios. CONCLUSIONS: This represents a significant advance compared to existing technologies, which involve either complex steps of pre...... cell numbers. RESULTS: We describe a robust, simple and scalable methodology for ChIP-seq of low-abundant cell populations, verified down to 10,000 cells. By employing non-mammalian genome mapping bacterial carrier DNA during amplification, we reliably amplify down to 50 pg of ChIP DNA from...
Experiment list: SRX897941 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 081,98.0,12.4,11292 GSM1624626: ChIP seq Chaf1a.166 Sox2 IP day3; Mus musculus; ChIP-Seq source_name=OKSM reprogramming... intermediates from Mouse Embryonic Fibroblasts || strain=Black6-129X1/SvJ || cell type=OKSM reprogramming

Experiment list: SRX1090866 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available gramming || cell type=intermediate stage of somatic cell reprogramming || chip anti...1,96.8,4.5,197 GSM1816303: pre-iPS rep.H3K27me3.ChIP-Seq; Mus musculus; ChIP-Seq source_name=intermediate stage of somatic cell repro
Experiment list: SRX107409 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Adenocarcinoma 38890980,97.0,45.8,396 GSM838387: h3k36me3 sictrl ChIP-Seq; Homo sapiens; ChIP-Seq source_name=Hela cells knock...down control || chip antibody=H3K36me3 || treatment=knockdown control || cell line=HeLa ||
Experiment list: SRX485218 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available K9me3 ChIP from piwi germline knock-down ovaries, replicate 2; Drosophila melanogaster; ChIP-Seq source_name...=H3K9me3 ChIP from piwi germline knock-down ovaries || developmental stage=4-6 days old adult || Sex=female ...|| tissue=ovary || germline knock-down=piwi || chip antibody=Histone H3K9me3 anti
Experiment list: SRX485213 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available K9me3 ChIP from control germline knock-down ovaries, replicate 1; Drosophila melanogaster; ChIP-Seq source_n...ame=H3K9me3 ChIP from control germline knock-down ovaries || developmental stage=4-6 days old adult || Sex=f...emale || tissue=ovary || germline knock-down=control || chip antibody=Histone H3K
Experiment list: SRX485214 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available K9me3 ChIP from control germline knock-down ovaries, replicate 2; Drosophila melanogaster; ChIP-Seq source_n...ame=H3K9me3 ChIP from control germline knock-down ovaries || developmental stage=4-6 days old adult || Sex=f...emale || tissue=ovary || germline knock-down=control || chip antibody=Histone H3K
Experiment list: SRX153146 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available -Seq source_name=Human breast adenocarcinoma cell-line MCF7 || cell-line=MCF7 || passage=5 || chip antibody=...n=Pleura|Tissue Diagnosis=Adenocarcinoma 60170246,98.4,5.7,16756 GSM946850: MCF7 H3K27ac; Homo sapiens; ChIP
Experiment list: SRX176063 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available =Carcinoma 11279321,95.5,3.6,13985 GSM984395: LNCAP ACH3 vehicle; Homo sapiens; ChIP-Seq source_name=prostat...e cancer cells || cell line=LNCaP || chip antibody=AcH3 || chip antibody manufacturer=Millipore || treatment=EtOH vehicle
Experiment list: SRX176057 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available nosis=Carcinoma 21582823,90.1,7.3,1074 GSM984389: 22RV1 AR vehicle; Homo sapiens; ChIP-Seq source_name=prost...ate cancer cells || cell line=22RV1 || chip antibody=AR || chip antibody manufacturer=Abcam || treatment=EtOH vehicle
Experiment list: SRX144527 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available neage=mesoderm|Description=parental cell type to lymphoblastoid cell lines 8704444,92.1,92.5,9 GSM922972: NRF2 ChIP vehicle... treated rep3; Homo sapiens; ChIP-Seq source_name=NRF2 ChIP vehicle treated || biomaterial_pr
Experiment list: SRX160914 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available M970829: IgG for KSHV LANA; Homo sapiens; ChIP-Seq source_name=BCBL1 pleural effusion lymphoma, IgG ChIP || ...cell line=BCBL1 || cell type=KSHV-infected pleural effusion lymphoma cells || chip antibody=Rabbit IgG [Sant
Experiment list: SRX160915 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available M970828: IgG for CTCF SMC1; Homo sapiens; ChIP-Seq source_name=BCBL1 pleural effusion lymphoma, IgG ChIP || ...cell line=BCBL1 || cell type=KSHV-infected pleural effusion lymphoma cells || chip antibody=Mouse IgG [Santa
Experiment list: SRX977401 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 98.9,13.8,95651 GSM1648652: H3K27ac ChipSeq day1; Mus musculus; ChIP-Seq source_name=reprogramming intermedi...ate after 24hour of induction || cell type=reprogramming intermediate || genotype=H3K27ac-GFP/ Rosa26-M2rtTA
Experiment list: SRX977402 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 98.8,11.6,43739 GSM1648653: H3K27ac ChipSeq day3; Mus musculus; ChIP-Seq source_name=reprogramming intermedi...ate after 3days of induction || cell type=reprogramming intermediate || genotype=H3K27ac-GFP/ Rosa26-M2rtTA
Experiment list: SRX977406 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 98.9,8.3,18501 GSM1648657: H3K27ac ChipSeq day15; Mus musculus; ChIP-Seq source_name=reprogramming intermedi...ate after 15days of induction || cell type=reprogramming intermediate || genotype=H3K27ac-GFP/ Rosa26-M2rtTA
Experiment list: SRX218536 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available strain=C57Bl/6 || age/gender=2-3 month old males || chip antibody=Santa Cruz Tech. rIgG (sc-2027) http://db....7,16.5,1194 GSM1067409: Rabbit IgG mouse liver ChIP-seq; Mus musculus; ChIP-Seq GEO Accession=GSM1067409 ||
Experiment list: SRX977405 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 98.9,7.4,10239 GSM1648656: H3K27ac ChipSeq day11; Mus musculus; ChIP-Seq source_name=reprogramming intermedi...ate after 11days of induction || cell type=reprogramming intermediate || genotype=H3K27ac-GFP/ Rosa26-M2rtTA
Peak tree: a new tool for multiscale hierarchical representation and peak detection of mass spectrometry data.

Science.gov (United States)

Zhang, Peng; Li, Houqiang; Wang, Honghui; Wong, Stephen T C; Zhou, Xiaobo

2011-01-01

Peak detection is one of the most important steps in mass spectrometry (MS) analysis. However, the detection result is greatly affected by severe spectrum variations. Unfortunately, most current peak detection methods are neither flexible enough to revise false detection results nor robust enough to resist spectrum variations. To improve flexibility, we introduce peak tree to represent the peak information in MS spectra. Each tree node is a peak judgment on a range of scales, and each tree decomposition, as a set of nodes, is a candidate peak detection result. To improve robustness, we combine peak detection and common peak alignment into a closed-loop framework, which finds the optimal decomposition via both peak intensity and common peak information. The common peak information is derived and loopily refined from the density clustering of the latest peak detection result. Finally, we present an improved ant colony optimization biomarker selection method to build a whole MS analysis system. Experiment shows that our peak detection method can better resist spectrum variations and provide higher sensitivity and lower false detection rates than conventional methods. The benefits from our peak-tree-based system for MS disease analysis are also proved on real SELDI data.
Experiment list: SRX153147 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available -Seq source_name=Human breast adenocarcinoma cell-line MCF7 || cell-line=MCF7 || passage=5 || chip antibody=...on=Pleura|Tissue Diagnosis=Adenocarcinoma 64054379,98.7,5.2,764 GSM946851: MCF7 H3K27me3; Homo sapiens; ChIP
Experiment list: SRX153148 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available -Seq source_name=Human breast adenocarcinoma cell-line MCF7 || cell-line=MCF7 || passage=5 || chip antibody=...n=Pleura|Tissue Diagnosis=Adenocarcinoma 57306360,95.7,15.1,2666 GSM946852: MCF7 H3K9me3; Homo sapiens; ChIP
Experiment list: SRX485216 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 3K9me3 ChIP from rhino germline knock-down ovaries, replicate 2; Drosophila melanogaster; ChIP-Seq source_na...me=H3K9me3 ChIP from rhino germline knock-down ovaries || developmental stage=4-6 days old adult || Sex=fema...le || tissue=ovary || germline knock-down=rhino || chip antibody=Histone H3K9me3

Experiment list: SRX485215 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available K9me3 ChIP from rhino germline knock-down ovaries, replicate 1; Drosophila melanogaster; ChIP-Seq source_nam...e=H3K9me3 ChIP from rhino germline knock-down ovaries || developmental stage=4-6 days old adult || Sex=femal...e || tissue=ovary || germline knock-down=rhino || chip antibody=Histone H3K9me3 a
Experiment list: SRX485217 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 3K9me3 ChIP from piwi germline knock-down ovaries, replicate 1; Drosophila melanogaster; ChIP-Seq source_nam...e=H3K9me3 ChIP from piwi germline knock-down ovaries || developmental stage=4-6 days old adult || Sex=female... || tissue=ovary || germline knock-down=piwi || chip antibody=Histone H3K9me3 ant
Experiment list: SRX977412 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 99.3,28.8,54450 GSM1648663: H3K4me3 ChipSeq day5; Mus musculus; ChIP-Seq source_name=reprogramming intermedi...ate after 5days of induction || cell type=reprogramming intermediate || genotype=H3K4me3-GFP/ Rosa26-M2rtTA
Experiment list: SRX977420 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available ,98.5,9.4,5405 GSM1648671: H3K27me3 ChipSeq day3; Mus musculus; ChIP-Seq source_name=reprogramming intermedi...ate after 3days of induction || cell type=reprogramming intermediate || genotype=H3K27me3-GFP/ Rosa26-M2rtTA
Experiment list: SRX977415 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 97.4,25.7,24253 GSM1648666: H3K4me3 ChipSeq day15; Mus musculus; ChIP-Seq source_name=reprogramming intermed...iate after 15days of induction || cell type=reprogramming intermediate || genotype=H3K4me3-GFP/ Rosa26-M2rtT
Experiment list: SRX977394 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 99.1,7.7,102329 GSM1648645: H3K4me1 ChipSeq day5; Mus musculus; ChIP-Seq source_name=reprogramming intermedi...ate after 5days of induction || cell type=reprogramming intermediate || genotype=H3K4me1-GFP/ Rosa26-M2rtTA
Experiment list: SRX977423 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available ,99.0,6.9,4818 GSM1648674: H3K27me3 ChipSeq day11; Mus musculus; ChIP-Seq source_name=reprogramming intermed...iate after 11days of induction || cell type=reprogramming intermediate || genotype=H3K27me3-GFP/ Rosa26-M2rt
Experiment list: SRX977392 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 98.9,6.9,91916 GSM1648643: H3K4me1 ChipSeq day1; Mus musculus; ChIP-Seq source_name=reprogramming intermedia...te after 24hour of induction || cell type=reprogramming intermediate || genotype=H3K4me1-GFP/ Rosa26-M2rtTA
Experiment list: SRX977411 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 99.2,25.6,52503 GSM1648662: H3K4me3 ChipSeq day3; Mus musculus; ChIP-Seq source_name=reprogramming intermedi...ate after 3days of induction || cell type=reprogramming intermediate || genotype=H3K4me3-GFP/ Rosa26-M2rtTA
Experiment list: SRX977410 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 99.3,25.0,46365 GSM1648661: H3K4me3 ChipSeq day1; Mus musculus; ChIP-Seq source_name=reprogramming intermedi...ate after 24hour of induction || cell type=reprogramming intermediate || genotype=H3K4me3-GFP/ Rosa26-M2rtTA
Experiment list: SRX977421 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available ,98.5,10.5,6589 GSM1648672: H3K27me3 ChipSeq day5; Mus musculus; ChIP-Seq source_name=reprogramming intermed...iate after 5days of induction || cell type=reprogramming intermediate || genotype=H3K27me3-GFP/ Rosa26-M2rtT
Experiment list: SRX977396 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 99.3,8.4,86055 GSM1648647: H3K4me1 ChipSeq day11; Mus musculus; ChIP-Seq source_name=reprogramming intermedi...ate after 11days of induction || cell type=reprogramming intermediate || genotype=H3K4me1-GFP/ Rosa26-M2rtTA
Experiment list: SRX977413 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 97.5,28.8,20673 GSM1648664: H3K4me3 ChipSeq day7; Mus musculus; ChIP-Seq source_name=reprogramming intermedi...ate after 7days of induction || cell type=reprogramming intermediate || genotype=H3K4me3-GFP/ Rosa26-M2rtTA
Experiment list: SRX977419 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available ,99.0,7.8,3913 GSM1648670: H3K27me3 ChipSeq day1; Mus musculus; ChIP-Seq source_name=reprogramming intermedi...ate after 24hour of induction || cell type=reprogramming intermediate || genotype=H3K27me3-GFP/ Rosa26-M2rtT
Experiment list: SRX977404 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 99.1,5.7,17625 GSM1648655: H3K27ac ChipSeq day7; Mus musculus; ChIP-Seq source_name=reprogramming intermedia...te after 7days of induction || cell type=reprogramming intermediate || genotype=H3K27ac-GFP/ Rosa26-M2rtTA t
Experiment list: SRX977414 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 98.5,25.1,26501 GSM1648665: H3K4me3 ChipSeq day11; Mus musculus; ChIP-Seq source_name=reprogramming intermed...iate after 11days of induction || cell type=reprogramming intermediate || genotype=H3K4me3-GFP/ Rosa26-M2rtT
Experiment list: SRX977397 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 98.9,8.9,45421 GSM1648648: H3K4me1 ChipSeq day15; Mus musculus; ChIP-Seq source_name=reprogramming intermedi...ate after 15days of induction || cell type=reprogramming intermediate || genotype=H3K4me1-GFP/ Rosa26-M2rtTA
Experiment list: SRX977403 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 98.9,9.4,35286 GSM1648654: H3K27ac ChipSeq day5; Mus musculus; ChIP-Seq source_name=reprogramming intermedia...te after 5days of induction || cell type=reprogramming intermediate || genotype=H3K27ac-GFP/ Rosa26-M2rtTA t
Experiment list: SRX119679 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 8,18360 GSM874985: ES.H3K27me3; Homo sapiens; ChIP-Seq source_name=H1 human Embryonic stem cells || cell line=H1 || treatment=diagnos...tic sample (pre-treatment) || chip antibody=H3K27me3 || chip antibody manufacturer=
Experiment list: SRX119684 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 2,13603 GSM874990: ES.H3K79me2; Homo sapiens; ChIP-Seq source_name=H1 human Embryonic stem cell || cell line=H1 || treatment=diagnost...ic sample (pre-treatment) || chip antibody=H3K79me2 || chip antibody manufacturer=A

A new technique to detect antibody-antigen reaction (biological interactions) on a localized surface plasmon resonance (LSPR) based nano ripple gold chip

Energy Technology Data Exchange (ETDEWEB)

Saleem, Iram, E-mail: iiram.qau@gmail.com [Department of Physics and Texas Center for Superconductivity, University of Houston, Houston, TX 77204 (United States); Widger, William, E-mail: widger@uh.edu [Department of Biology and Biochemistry and Texas Center for Superconductivity, University of Houston, Houston, TX 77204 (United States); Chu, Wei-Kan, E-mail: wkchu@uh.edu [Department of Physics and Texas Center for Superconductivity, University of Houston, Houston, TX 77204 (United States)

2017-07-31

Highlights: • The nano ripple LSPR chip has monolayer molecule-coating sensitivity and specific selectivity. • Gold nano-ripple sensing chip is a low cost, and a label-free method for detecting the antibody-antigen reaction. • The plasmonic resonance shift depends upon the concentration of the biomolecules attached on the surface of the nano ripple pattern. - Abstract: We demonstrate that the gold nano-ripple localized surface plasmon resonance (LSPR) chip is a low cost and a label-free method for detecting the presence of an antigen. A uniform stable layer of an antibody was coated on the surface of a nano-ripple gold pattern chip followed by the addition of different concentrations of the antigen. A red shift was observed in the LSPR spectral peak caused by the change in the local refractive index in the vicinity of the nanostructure. The LSPR chip was fabricated using oblique gas cluster ion beam (GCIB) irradiation. The plasmon-resonance intensity of the scattered light was measured by a simple optical spectroscope. The gold nano ripple chip shows monolayer scale sensitivity and high selectivity. The LSPR substrate was used to detect antibody-antigen reaction of rabbit X-DENTT antibody and DENTT blocking peptide (antigen).
Experiment list: SRX977393 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 98.8,8.9,31577 GSM1648644: H3K4me1 ChipSeq day3; Mus musculus; ChIP-Seq source_name=reprogramming intermedia...te after 3days of induction || cell type=reprogramming intermediate || genotype=H3K4me1-GFP/ Rosa26-M2rtTA t
Experiment list: SRX977395 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 98.7,7.3,62664 GSM1648646: H3K4me1 ChipSeq day7; Mus musculus; ChIP-Seq source_name=reprogramming intermedia...te after 7days of induction || cell type=reprogramming intermediate || genotype=H3K4me1-GFP/ Rosa26-M2rtTA t
Experiment list: SRX507384 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available + (wildtype) || age of animals=1-5 day old || tissue=Ovaries || chip antibody=Anti-H3K4me2 || chip antibody ... Anti-H3K4me2- replicate#2; Drosophila melanogaster; ChIP-Seq source_name=WT_WT_Anti-H3K4me2 || strain=piwi/
Experiment list: SRX507382 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available + (wildtype) || age of animals=1-5 day old || tissue=Ovaries || chip antibody=Anti-H3K9me3 || chip antibody ... Anti-H3K9me3- replicate#2; Drosophila melanogaster; ChIP-Seq source_name=WT_WT_Anti-H3K9me3 || strain=piwi/
Accurate detection of carcinoma cells by use of a cell microarray chip.

Directory of Open Access Journals (Sweden)

Shohei Yamamura

Full Text Available BACKGROUND: Accurate detection and analysis of circulating tumor cells plays an important role in the diagnosis and treatment of metastatic cancer treatment. METHODS AND FINDINGS: A cell microarray chip was used to detect spiked carcinoma cells among leukocytes. The chip, with 20,944 microchambers (105 µm width and 50 µm depth, was made from polystyrene; and the formation of monolayers of leukocytes in the microchambers was observed. Cultured human T lymphoblastoid leukemia (CCRF-CEM cells were used to examine the potential of the cell microarray chip for the detection of spiked carcinoma cells. A T lymphoblastoid leukemia suspension was dispersed on the chip surface, followed by 15 min standing to allow the leukocytes to settle down into the microchambers. Approximately 29 leukocytes were found in each microchamber when about 600,000 leukocytes in total were dispersed onto a cell microarray chip. Similarly, when leukocytes isolated from human whole blood were used, approximately 89 leukocytes entered each microchamber when about 1,800,000 leukocytes in total were placed onto the cell microarray chip. After washing the chip surface, PE-labeled anti-cytokeratin monoclonal antibody and APC-labeled anti-CD326 (EpCAM monoclonal antibody solution were dispersed onto the chip surface and allowed to react for 15 min; and then a microarray scanner was employed to detect any fluorescence-positive cells within 20 min. In the experiments using spiked carcinoma cells (NCI-H1650, 0.01 to 0.0001%, accurate detection of carcinoma cells was achieved with PE-labeled anti-cytokeratin monoclonal antibody. Furthermore, verification of carcinoma cells in the microchambers was performed by double staining with the above monoclonal antibodies. CONCLUSION: The potential application of the cell microarray chip for the detection of CTCs was shown, thus demonstrating accurate detection by double staining for cytokeratin and EpCAM at the single carcinoma cell level.
An integrated micro-chip for rapid detection of magnetic particles

KAUST Repository

Gooneratne, Chinthaka P.

2012-03-09

This paper proposes an integrated micro-chip for the manipulation and detection of magnetic particles (MPs). A conducting ring structure is used to manipulate MPs toward giant magnetoresistance(GMR) sensing elements for rapid detection. The GMRsensor is fabricated in a horseshoe shape in order to detect the majority of MPs that are trapped around the conducting structure. The GMR sensing elements are connected in a Wheatstone bridge circuit topology for optimum noise suppression. Full fabrication details of the micro-chip, characterization of the GMRsensors, and experimental results with MPs are presented in this paper. Experimental results showed that the micro-chip can detect MPs from low concentration samples after they were guided toward the GMRsensors by applying current to the conducting ring structure.
Experiment list: SRX176067 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available sis=Carcinoma 6619400,91.7,7.2,13648 GSM984399: LNCAP H3K4ME3 vehicle; Homo sapiens; ChIP-Seq source_name=pr...ostate cancer cells || cell line=LNCaP || chip antibody=H3K4Me3 || chip antibody manufacturer=Millipore || treatment=EtOH vehicle
Experiment list: SRX485219 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 56 GSM1346560: RNA Polymerase II ChIP from control germline knock-down ovaries; Drosophila melanogaster; ChI...P-Seq source_name=RNA Polymerase II ChIP from control germline knock-down ovaries || developmental stage=4-6... days old adult || Sex=female || tissue=ovary || germline knock-down=control || c
CASSys: an integrated software-system for the interactive analysis of ChIP-seq data

Directory of Open Access Journals (Sweden)

Alawi Malik

2011-06-01

Full Text Available The mapping of DNA-protein interactions is crucial for a full understanding of transcriptional regulation. Chromatin-immunoprecipitation followed bymassively parallel sequencing (ChIP-seq has become the standard technique for analyzing these interactions on a genome-wide scale. We have developed a software system called CASSys (ChIP-seq data Analysis Software System spanning all steps of ChIP-seq data analysis. It supersedes the laborious application of several single command line tools. CASSys provides functionality ranging from quality assessment and -control of short reads, over the mapping of reads against a reference genome (readmapping and the detection of enriched regions (peakdetection to various follow-up analyses. The latter are accessible via a state-of-the-art web interface and can be performed interactively by the user. The follow-up analyses allow for flexible user defined association of putative interaction sites with genes, visualization of their genomic context with an integrated genome browser, the detection of putative binding motifs, the identification of over-represented Gene Ontology-terms, pathway analysis and the visualization of interaction networks. The system is client-server based, accessible via a web browser and does not require any software installation on the client side. To demonstrate CASSys’s functionality we used the system for the complete data analysis of a publicly available Chip-seq study that investigated the role of the transcription factor estrogen receptor-α in breast cancer cells.
Development of a cell microarray chip for detection of circulating tumor cells

Science.gov (United States)

Yamamura, S.; Yatsushiro, S.; Abe, K.; Baba, Y.; Kataoka, M.

2012-03-01

Detection of circulating tumor cells (CTCs) in the peripheral blood of metastatic cancer patients has clinical significance in earlier diagnosis of metastases. In this study, a novel cell microarray chip for accurate and rapid detection of tumor cells from human leukocytes was developed. The chip with 20,944 microchambers (105 μm diameter and 50 μm depth) was made from polystyrene, and the surface was rendered to hydrophilic by means of reactive-ion etching, which led to the formation of mono-layers of leukocytes on the microchambers. As the model of CTCs detection, we spiked human bronchioalveolar carcinoma (H1650) cells into human T lymphoblastoid leukemia (CEM) cells suspension and detected H1650 cells using the chip. A CEM suspension contained with H1650 cells was dispersed on the chip surface, followed by 10 min standing to allow the cells to settle down into the microchambers. About 30 CEM cells were accommodated in each microchamber, over 600,000 CEM cells in total being on a chip. We could detect 1 H1650 cell per 106 CEM cells on the microarray by staining with fluorescence-conjugated antibody (Anti-Cytokeratin) and cell membrane marker (DiD). Thus, this cell microarray chip has highly potential to be a novel tool of accurate and rapid detection of CTCs.
High-specificity detection of rare alleles with Paired-End Low Error Sequencing (PELE-Seq).

Science.gov (United States)

Preston, Jessica L; Royall, Ariel E; Randel, Melissa A; Sikkink, Kristin L; Phillips, Patrick C; Johnson, Eric A

2016-06-14

Polymorphic loci exist throughout the genomes of a population and provide the raw genetic material needed for a species to adapt to changes in the environment. The minor allele frequencies of rare Single Nucleotide Polymorphisms (SNPs) within a population have been difficult to track with Next-Generation Sequencing (NGS), due to the high error rate of standard methods such as Illumina sequencing. We have developed a wet-lab protocol and variant-calling method that identifies both sequencing and PCR errors, called Paired-End Low Error Sequencing (PELE-Seq). To test the specificity and sensitivity of the PELE-Seq method, we sequenced control E. coli DNA libraries containing known rare alleles present at frequencies ranging from 0.2-0.4 % of the total reads. PELE-Seq had higher specificity and sensitivity than standard libraries. We then used PELE-Seq to characterize rare alleles in a Caenorhabditis remanei nematode worm population before and after laboratory adaptation, and found that minor and rare alleles can undergo large changes in frequency during lab-adaptation. We have developed a method of rare allele detection that mitigates both sequencing and PCR errors, called PELE-Seq. PELE-Seq was evaluated using control E. coli populations and was then used to compare a wild C. remanei population to a lab-adapted population. The PELE-Seq method is ideal for investigating the dynamics of rare alleles in a broad range of reduced-representation sequencing methods, including targeted amplicon sequencing, RAD-Seq, ddRAD, and GBS. PELE-Seq is also well-suited for whole genome sequencing of mitochondria and viruses, and for high-throughput rare mutation screens.
Microfluidic PCR Amplification and MiSeq Amplicon Sequencing Techniques for High-Throughput Detection and Genotyping of Human Pathogenic RNA Viruses in Human Feces, Sewage, and Oysters

Directory of Open Access Journals (Sweden)

Mamoru Oshiki

2018-04-01

Full Text Available Detection and genotyping of pathogenic RNA viruses in human and environmental samples are useful for monitoring the circulation and prevalence of these pathogens, whereas a conventional PCR assay followed by Sanger sequencing is time-consuming and laborious. The present study aimed to develop a high-throughput detection-and-genotyping tool for 11 human RNA viruses [Aichi virus; astrovirus; enterovirus; norovirus genogroup I (GI, GII, and GIV; hepatitis A virus; hepatitis E virus; rotavirus; sapovirus; and human parechovirus] using a microfluidic device and next-generation sequencer. Microfluidic nested PCR was carried out on a 48.48 Access Array chip, and the amplicons were recovered and used for MiSeq sequencing (Illumina, Tokyo, Japan; genotyping was conducted by homology searching and phylogenetic analysis of the obtained sequence reads. The detection limit of the 11 tested viruses ranged from 100 to 103 copies/μL in cDNA sample, corresponding to 101–104 copies/mL-sewage, 105–108 copies/g-human feces, and 102–105 copies/g-digestive tissues of oyster. The developed assay was successfully applied for simultaneous detection and genotyping of RNA viruses to samples of human feces, sewage, and artificially contaminated oysters. Microfluidic nested PCR followed by MiSeq sequencing enables efficient tracking of the fate of multiple RNA viruses in various environments, which is essential for a better understanding of the circulation of human pathogenic RNA viruses in the human population.
Performance of a Fast Binary Readout CMOS Active Pixel Sensor Chip Designed for Charged Particle Detection

Science.gov (United States)

Deerli, Yavuz; Besanon, Marc; Besson, Auguste; Claus, Gilles; Deptuch, Grzegorz; Dulinski, Wojciech; Fourches, Nicolas; Goffe, Mathieu; Himmi, Abdelkader; Li, Yan; Lutz, Pierre; Orsini, Fabienne; Szelezniak, Michal

2006-12-01

We report on the performance of the MIMOSA8 (HiMAPS1) chip. The chip is a 128times32 pixels array where 24 columns have discriminated binary outputs and eight columns analog test outputs. Offset correction techniques are used extensively in this chip to overcome process related mismatches. The array is divided in four blocks of pixels with different conversion factors and is controlled by a serially programmable sequencer. MIMOSA8 is a representative of the CMOS sensors development option considered as a promising candidate for the Vertex Detector of the future International Linear Collider (ILC). The readout technique, implemented on the chip, combines high spatial resolution capabilities with high processing readout speed. Data acquisition, providing control of the chip and signal buffering and linked to a VME system, was made on the eight analog outputs. Analog data, without and with a 55Fe X-ray source, were acquired and processed using off-line analysis software. From the reconstruction of pixel clusters, built around a central pixel, we deduce that the charge spread is limited to the closest 25 pixels and almost all the available charge is collected. The position of the total charge collection peak (and subsequently the charge-to-voltage conversion factor) stays unaffected when the clock frequency is increased even up to 150 MHz (13.6 mus readout time per frame). The discriminators, placed in the readout chain, have proved to be fully functional. Beam tests have been made with high energy electrons at DESY (Germany) to study detection efficiency. The results prove that MIMOSA8 is the first and fastest successful monolithic active pixel sensor with on-chip signal discrimination for detection of MIPs
Limitations and possibilities of low cell number ChIP-seq

Directory of Open Access Journals (Sweden)

Gilfillan Gregor D

2012-11-01

Full Text Available Abstract Background Chromatin immunoprecipitation coupled with high-throughput DNA sequencing (ChIP-seq offers high resolution, genome-wide analysis of DNA-protein interactions. However, current standard methods require abundant starting material in the range of 1–20 million cells per immunoprecipitation, and remain a bottleneck to the acquisition of biologically relevant epigenetic data. Using a ChIP-seq protocol optimised for low cell numbers (down to 100,000 cells / IP, we examined the performance of the ChIP-seq technique on a series of decreasing cell numbers. Results We present an enhanced native ChIP-seq method tailored to low cell numbers that represents a 200-fold reduction in input requirements over existing protocols. The protocol was tested over a range of starting cell numbers covering three orders of magnitude, enabling determination of the lower limit of the technique. At low input cell numbers, increased levels of unmapped and duplicate reads reduce the number of unique reads generated, and can drive up sequencing costs and affect sensitivity if ChIP is attempted from too few cells. Conclusions The optimised method presented here considerably reduces the input requirements for performing native ChIP-seq. It extends the applicability of the technique to isolated primary cells and rare cell populations (e.g. biobank samples, stem cells, and in many cases will alleviate the need for cell culture and any associated alteration of epigenetic marks. However, this study highlights a challenge inherent to ChIP-seq from low cell numbers: as cell input numbers fall, levels of unmapped sequence reads and PCR-generated duplicate reads rise. We discuss a number of solutions to overcome the effects of reducing cell number that may aid further improvements to ChIP performance.
Integrated sample-to-detection chip for nucleic acid test assays.

Science.gov (United States)

Prakash, R; Pabbaraju, K; Wong, S; Tellier, R; Kaler, K V I S

2016-06-01

Nucleic acid based diagnostic techniques are routinely used for the detection of infectious agents. Most of these assays rely on nucleic acid extraction platforms for the extraction and purification of nucleic acids and a separate real-time PCR platform for quantitative nucleic acid amplification tests (NATs). Several microfluidic lab on chip (LOC) technologies have been developed, where mechanical and chemical methods are used for the extraction and purification of nucleic acids. Microfluidic technologies have also been effectively utilized for chip based real-time PCR assays. However, there are few examples of microfluidic systems which have successfully integrated these two key processes. In this study, we have implemented an electro-actuation based LOC micro-device that leverages multi-frequency actuation of samples and reagents droplets for chip based nucleic acid extraction and real-time, reverse transcription (RT) PCR (qRT-PCR) amplification from clinical samples. Our prototype micro-device combines chemical lysis with electric field assisted isolation of nucleic acid in a four channel parallel processing scheme. Furthermore, a four channel parallel qRT-PCR amplification and detection assay is integrated to deliver the sample-to-detection NAT chip. The NAT chip combines dielectrophoresis and electrostatic/electrowetting actuation methods with resistive micro-heaters and temperature sensors to perform chip based integrated NATs. The two chip modules have been validated using different panels of clinical samples and their performance compared with standard platforms. This study has established that our integrated NAT chip system has a sensitivity and specificity comparable to that of the standard platforms while providing up to 10 fold reduction in sample/reagent volumes.
Experiment list: SRX688848 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available d prostate cancer cell line || treatment=vehicle || chip antibody=rabbit anti-ASH... prostate cancer cells, vehicle, ASH2 ChIP || cell line=VCaP || cell type=vertebral metastatic lesion-derive...agnosis=Carcinoma 25750434,89.3,6.2,7152 GSM1489926: vcap ash2l veh; Homo sapiens; ChIP-Seq source_name=VCaP
SOAPsplice: genome-wide ab initio detection of splice junctions from RNA-Seq data

Directory of Open Access Journals (Sweden)

Songbo eHuang

2011-07-01

Full Text Available RNA-Seq, a method using next generation sequencing technologies to sequence the transcriptome, facilitates genome-wide analysis of splice junction sites. In this paper, we introduce SOAPsplice, a robust tool to detect splice junctions using RNA-Seq data without using any information of known splice junctions. SOAPsplice uses a novel two-step approach consisting of first identifying as many reasonable splice junction candidates as possible, and then, filtering the false positives with two effective filtering strategies. In both simulated and real datasets, SOAPsplice is able to detect many reliable splice junctions with low false positive rate. The improvement gained by SOAPsplice, when compared to other existing tools, becomes more obvious when the depth of sequencing is low. SOAPsplice is freely available at http://soap.genomics.org.cn/soapsplice.html.
A Single-Chip CMOS Pulse Oximeter with On-Chip Lock-In Detection

Directory of Open Access Journals (Sweden)

Diwei He

2015-07-01

Full Text Available Pulse oximetry is a noninvasive and continuous method for monitoring the blood oxygen saturation level. This paper presents the design and testing of a single-chip pulse oximeter fabricated in a 0.35 µm CMOS process. The chip includes photodiode, transimpedance amplifier, analogue band-pass filters, analogue-to-digital converters, digital signal processor and LED timing control. The experimentally measured AC and DC characteristics of individual circuits including the DC output voltage of the transimpedance amplifier, transimpedance gain of the transimpedance amplifier, and the central frequency and bandwidth of the analogue band-pass filters, show a good match (within 1% with the circuit simulations. With modulated light source and integrated lock-in detection the sensor effectively suppresses the interference from ambient light and 1/f noise. In a breath hold and release experiment the single chip sensor demonstrates consistent and comparable performance to commercial pulse oximetry devices with a mean of 1.2% difference. The single-chip sensor enables a compact and robust design solution that offers a route towards wearable devices for health monitoring.
A Single-Chip CMOS Pulse Oximeter with On-Chip Lock-In Detection.

Science.gov (United States)

He, Diwei; Morgan, Stephen P; Trachanis, Dimitrios; van Hese, Jan; Drogoudis, Dimitris; Fummi, Franco; Stefanni, Francesco; Guarnieri, Valerio; Hayes-Gill, Barrie R

2015-07-14

Pulse oximetry is a noninvasive and continuous method for monitoring the blood oxygen saturation level. This paper presents the design and testing of a single-chip pulse oximeter fabricated in a 0.35 µm CMOS process. The chip includes photodiode, transimpedance amplifier, analogue band-pass filters, analogue-to-digital converters, digital signal processor and LED timing control. The experimentally measured AC and DC characteristics of individual circuits including the DC output voltage of the transimpedance amplifier, transimpedance gain of the transimpedance amplifier, and the central frequency and bandwidth of the analogue band-pass filters, show a good match (within 1%) with the circuit simulations. With modulated light source and integrated lock-in detection the sensor effectively suppresses the interference from ambient light and 1/f noise. In a breath hold and release experiment the single chip sensor demonstrates consistent and comparable performance to commercial pulse oximetry devices with a mean of 1.2% difference. The single-chip sensor enables a compact and robust design solution that offers a route towards wearable devices for health monitoring.

Automated asteroseismic peak detections

DEFF Research Database (Denmark)

de Montellano, Andres Garcia Saravia Ortiz; Hekker, S.; Themessl, N.

2018-01-01

Space observatories such as Kepler have provided data that can potentially revolutionize our understanding of stars. Through detailed asteroseismic analyses we are capable of determining fundamental stellar parameters and reveal the stellar internal structure with unprecedented accuracy. However......, such detailed analyses, known as peak bagging, have so far been obtained for only a small percentage of the observed stars while most of the scientific potential of the available data remains unexplored. One of the major challenges in peak bagging is identifying how many solar-like oscillation modes are visible...... of detected oscillation modes. The algorithm presented here opens the possibility for detailed and automated peak bagging of the thousands of solar-like oscillators observed by Kepler....
Application of single-chip microcomputer in radiation detection

International Nuclear Information System (INIS)

Zhang Songshou

1993-01-01

The single-chip microcomputer has some advantages in many aspects for example the strong function, the small volume, the low-power, firmed and reliable. It is used widely in the control of industry, instrument, communication and machine, etc.. The paper introduces that the single-chip microcomputer is used in radiation detection, mostly including the use of control, linear, compensation, calculation, prefabricated change, improving precision and training
Optimal use of tandem biotin and V5 tags in ChIP assays

NARCIS (Netherlands)

K.E. Kolodziej (Katarzyna); F. Pourfarzad, F. (Farzin); E. de Boer (Ernie); S. Krpic (Sanja); F.G. Grosveld (Frank); J. Strouboulis (John)

2009-01-01

textabstractBackground: Chromatin immunoprecipitation (ChIP) assays coupled to genome arrays (Chip-on-chip) or massive parallel sequencing (ChIP-seq) lead to the genome wide identification of binding sites of chromatin associated proteins. However, the highly variable quality of antibodies and the
Single-Cell mRNA-Seq Using the Fluidigm C1 System and Integrated Fluidics Circuits.

Science.gov (United States)

Gong, Haibiao; Do, Devin; Ramakrishnan, Ramesh

2018-01-01

Single-cell mRNA-seq is a valuable tool to dissect expression profiles and to understand the regulatory network of genes. Microfluidics is well suited for single-cell analysis owing both to the small volume of the reaction chambers and easiness of automation. Here we describe the workflow of single-cell mRNA-seq using C1 IFC, which can isolate and process up to 96 cells. Both on-chip procedure (lysis, reverse transcription, and preamplification PCR) and off-chip sequencing library preparation protocols are described. The workflow generates full-length mRNA information, which is more valuable compared to 3' end counting method for many applications.
A Miniaturized On-Chip Colorimeter for Detecting NPK Elements.

Science.gov (United States)

Liu, Rui-Tao; Tao, Lu-Qi; Liu, Bo; Tian, Xiang-Guang; Mohammad, Mohammad Ali; Yang, Yi; Ren, Tian-Ling

2016-08-04

Recently, precision agriculture has become a globally attractive topic. As one of the most important factors, the soil nutrients play an important role in estimating the development of precision agriculture. Detecting the content of nitrogen, phosphorus and potassium (NPK) elements more efficiently is one of the key issues. In this paper, a novel chip-level colorimeter was fabricated to detect the NPK elements for the first time. A light source-microchannel photodetector in a sandwich structure was designed to realize on-chip detection. Compared with a commercial colorimeter, all key parts are based on MEMS (Micro-Electro-Mechanical System) technology so that the volume of this on-chip colorimeter can be minimized. Besides, less error and high precision are achieved. The cost of this colorimeter is two orders of magnitude less than that of a commercial one. All these advantages enable a low-cost and high-precision sensing operation in a monitoring network. The colorimeter developed herein has bright prospects for environmental and biological applications.
PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data.

Science.gov (United States)

Zhang, Yanju; Lameijer, Eric-Wubbo; 't Hoen, Peter A C; Ning, Zemin; Slagboom, P Eline; Ye, Kai

2012-02-15

RNA-seq is a powerful technology for the study of transcriptome profiles that uses deep-sequencing technologies. Moreover, it may be used for cellular phenotyping and help establishing the etiology of diseases characterized by abnormal splicing patterns. In RNA-Seq, the exact nature of splicing events is buried in the reads that span exon-exon boundaries. The accurate and efficient mapping of these reads to the reference genome is a major challenge. We developed PASSion, a pattern growth algorithm-based pipeline for splice site detection in paired-end RNA-Seq reads. Comparing the performance of PASSion to three existing RNA-Seq analysis pipelines, TopHat, MapSplice and HMMSplicer, revealed that PASSion is competitive with these packages. Moreover, the performance of PASSion is not affected by read length and coverage. It performs better than the other three approaches when detecting junctions in highly abundant transcripts. PASSion has the ability to detect junctions that do not have known splicing motifs, which cannot be found by the other tools. Of the two public RNA-Seq datasets, PASSion predicted ≈ 137,000 and 173,000 splicing events, of which on average 82 are known junctions annotated in the Ensembl transcript database and 18% are novel. In addition, our package can discover differential and shared splicing patterns among multiple samples. The code and utilities can be freely downloaded from https://trac.nbic.nl/passion and ftp://ftp.sanger.ac.uk/pub/zn1/passion.
Rapid, highly sensitive and highly specific gene detection by combining enzymatic amplification and DNA chip detection simultaneously

Directory of Open Access Journals (Sweden)

Koji Hashimoto

2016-05-01

Full Text Available We have developed a novel gene detection method based on the loop-mediated isothermal amplification (LAMP reaction and the DNA dissociation reaction on the same DNA chip surface to achieve a lower detection limit, broader dynamic range and faster detection time than are attainable with a conventional DNA chip. Both FAM- and thiol-labeled DNA probe bound to the complementary sequence accompanying Dabcyl was immobilized on the gold surface via Au/thiol bond. The LAMP reaction was carried out on the DNA probe fixed gold surface. At first, Dabcyl molecules quenched the FAM fluorescence. According to the LAMP reaction, the complementary sequence with Dabcyl was competitively reacted with the amplified targeted sequence. As a result, the FAM fluorescence increased owing to dissociation of the complementary sequence from the DNA probe. The simultaneous reaction of LAMP and DNA chip detection was achieved, and 103 copies of the targeted gene were detected within an hour by measuring fluorescence intensity of the DNA probe. Keywords: Biosensor, DNA chip, Loop-mediated isothermal amplification (LAMP, Fluorescence detection, Gold substrate, Au/thiol bond
A statistical method for the detection of alternative splicing using RNA-seq.

Directory of Open Access Journals (Sweden)

Liguo Wang

2010-01-01

Full Text Available Deep sequencing of transcriptome (RNA-seq provides unprecedented opportunity to interrogate plausible mRNA splicing patterns by mapping RNA-seq reads to exon junctions (thereafter junction reads. In most previous studies, exon junctions were detected by using the quantitative information of junction reads. The quantitative criterion (e.g. minimum of two junction reads, although is straightforward and widely used, usually results in high false positive and false negative rates, owning to the complexity of transcriptome. Here, we introduced a new metric, namely Minimal Match on Either Side of exon junction (MMES, to measure the quality of each junction read, and subsequently implemented an empirical statistical model to detect exon junctions. When applied to a large dataset (>200M reads consisting of mouse brain, liver and muscle mRNA sequences, and using independent transcripts databases as positive control, our method was proved to be considerably more accurate than previous ones, especially for detecting junctions originated from low-abundance transcripts. Our results were also confirmed by real time RT-PCR assay. The MMES metric can be used either in this empirical statistical model or in other more sophisticated classifiers, such as logistic regression.
A compact imaging spectroscopic system for biomolecular detections on plasmonic chips.

Science.gov (United States)

Lo, Shu-Cheng; Lin, En-Hung; Wei, Pei-Kuen; Tsai, Wan-Shao

2016-10-17

In this study, we demonstrate a compact imaging spectroscopic system for high-throughput detection of biomolecular interactions on plasmonic chips, based on a curved grating as the key element of light diffraction and light focusing. Both the curved grating and the plasmonic chips are fabricated on flexible plastic substrates using a gas-assisted thermal-embossing method. A fiber-coupled broadband light source and a camera are included in the system. Spectral resolution within 1 nm is achieved in sensing environmental index solutions and protein bindings. The detected sensitivities of the plasmonic chip are comparable with a commercial spectrometer. An extra one-dimensional scanning stage enables high-throughput detection of protein binding on a designed plasmonic chip consisting of several nanoslit arrays with different periods. The detected resonance wavelengths match well with the grating equation under an air environment. Wavelength shifts between 1 and 9 nm are detected for antigens of various concentrations binding with antibodies. A simple, mass-productive and cost-effective method has been demonstrated on the imaging spectroscopic system for real-time, label-free, highly sensitive and high-throughput screening of biomolecular interactions.
Variable threshold method for ECG R-peak detection.

Science.gov (United States)

Kew, Hsein-Ping; Jeong, Do-Un

2011-10-01

In this paper, a wearable belt-type ECG electrode worn around the chest by measuring the real-time ECG is produced in order to minimize the inconvenient in wearing. ECG signal is detected using a potential instrument system. The measured ECG signal is transmits via an ultra low power consumption wireless data communications unit to personal computer using Zigbee-compatible wireless sensor node. ECG signals carry a lot of clinical information for a cardiologist especially the R-peak detection in ECG. R-peak detection generally uses the threshold value which is fixed. There will be errors in peak detection when the baseline changes due to motion artifacts and signal size changes. Preprocessing process which includes differentiation process and Hilbert transform is used as signal preprocessing algorithm. Thereafter, variable threshold method is used to detect the R-peak which is more accurate and efficient than fixed threshold value method. R-peak detection using MIT-BIH databases and Long Term Real-Time ECG is performed in this research in order to evaluate the performance analysis.
Experiment list: SRX142526 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available source_name=C2C12 || biomaterial_provider=Barbara Wold lab || lab=Caltech-m || lab description=Wold - Califonia Institute of Technolo...gy || datatype=ChipSeq || datatype description=Chromatin
Bayesian approach for peak detection in two-dimensional chromatography

NARCIS (Netherlands)

Vivó-Truyols, G.

2012-01-01

A new method for peak detection in two-dimensional chromatography is presented. In a first step, the method starts with a conventional one-dimensional peak detection algorithm to detect modulated peaks. In a second step, a sophisticated algorithm is constructed to decide which of the individual
Experiment list: SRX620297 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available body=Pol II (Santa Cruz Biotechnology, N20, sc-899) http://dbarchive.biosciencedb...IP-Seq source_name=NIH3T3 fibroblasts || culture condition=continuous culture || chemicals=DMSO || chip anti
Experiment list: SRX142520 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Califonia Institute of Technology || datatype=ChipSeq || datatype description=Ch...t 24hr source_name=C2C12 || biomaterial_provider=Barbara Wold lab || lab=Caltech-m || lab description=Wold -
Experiment list: SRX143619 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Califonia Institute of Technology || datatype=ChipSeq || datatype description=Ch...t 24hr source_name=C2C12 || biomaterial_provider=Barbara Wold lab || lab=Caltech-m || lab description=Wold -
Experiment list: SRX142522 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Califonia Institute of Technology || datatype=ChipSeq || datatype description=Ch...t 60hr source_name=C2C12 || biomaterial_provider=Barbara Wold lab || lab=Caltech-m || lab description=Wold -
SignalSpider: Probabilistic pattern discovery on multiple normalized ChIP-Seq signal profiles

KAUST Repository

Wong, Kachun; Li, Yue; Peng, Chengbin; Zhang, Zhaolei

2014-01-01

Motivation: Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-Seq) measures the genome-wide occupancy of transcription factors in vivo. Different combinations of DNA-binding protein occupancies may result in a gene
Aiding the Detection of QRS Complex in ECG Signals by Detecting S Peaks Independently.

Science.gov (United States)

Sabherwal, Pooja; Singh, Latika; Agrawal, Monika

2018-03-30

In this paper, a novel algorithm for the accurate detection of QRS complex by combining the independent detection of R and S peaks, using fusion algorithm is proposed. R peak detection has been extensively studied and is being used to detect the QRS complex. Whereas, S peaks, which is also part of QRS complex can be independently detected to aid the detection of QRS complex. In this paper, we suggest a method to first estimate S peak from raw ECG signal and then use them to aid the detection of QRS complex. The amplitude of S peak in ECG signal is relatively weak than corresponding R peak, which is traditionally used for the detection of QRS complex, therefore, an appropriate digital filter is designed to enhance the S peaks. These enhanced S peaks are then detected by adaptive thresholding. The algorithm is validated on all the signals of MIT-BIH arrhythmia database and noise stress database taken from physionet.org. The algorithm performs reasonably well even for the signals highly corrupted by noise. The algorithm performance is confirmed by sensitivity and positive predictivity of 99.99% and the detection accuracy of 99.98% for QRS complex detection. The number of false positives and false negatives resulted while analysis has been drastically reduced to 80 and 42 against the 98 and 84 the best results reported so far.
Experiment list: SRX655691 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available ; Mus musculus; ChIP-Seq source_name=MEFs cells knockout MED23 || cell type=mouse embryonic fibroblast || ge...notype/variation=MED23 knockout || chip antibody=H2Bub http://dbarchive.bioscienc
Experiment list: SRX191071 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Mus musculus; ChIP-Seq source_name=Kdm2b knockdown mouse ES cells || chip antibody=Flag || antibody manufact... || cell type=embryonbic stem cells || genotype=Kdm2b knockdown http://dbarchive.

Simultaneous Detection of Genetically Modified Organisms in a Mixture by Multiplex PCR-Chip Capillary Electrophoresis.

Science.gov (United States)

Patwardhan, Supriya; Dasari, Srikanth; Bhagavatula, Krishna; Mueller, Steffen; Deepak, Saligrama Adavigowda; Ghosh, Sudip; Basak, Sanjay

2015-01-01

An efficient PCR-based method to trace genetically modified food and feed products is in demand due to regulatory requirements and contaminant issues in India. However, post-PCR detection with conventional methods has limited sensitivity in amplicon separation that is crucial in multiplexing. The study aimed to develop a sensitive post-PCR detection method by using PCR-chip capillary electrophoresis (PCR-CCE) to detect and identify specific genetically modified organisms in their genomic DNA mixture by targeting event-specific nucleotide sequences. Using the PCR-CCE approach, novel multiplex methods were developed to detect MON531 cotton, EH 92-527-1 potato, Bt176 maize, GT73 canola, or GA21 maize simultaneously when their genomic DNAs in mixtures were amplified using their primer mixture. The repeatability RSD (RSDr) of the peak migration time was 0.06 and 3.88% for the MON531 and Bt176, respectively. The RSD (RSDR) of the Cry1Ac peak ranged from 0.12 to 0.40% in multiplex methods. The method was sensitive in resolving amplicon of size difference up to 4 bp. The PCR-CCE method is suitable to detect multiple genetically modified events in a composite DNA sample by tagging their event specific sequences.
An electrochromatography chip with integrated waveguides for UV absorbance detection

International Nuclear Information System (INIS)

Gustafsson, O; Mogensen, K B; Ohlsson, P D; Kutter, J P; Liu, Y; Jacobson, S C

2008-01-01

A silicon-based microchip for electrochromatographic separations is presented. Apart from a microfluidic network, the microchip has integrated UV-transparent waveguides for detection and integrated couplers for optical fibers on the chip, yielding the most complete chromatography microchip to date in terms of the integration of optical components. The microfluidic network and the optical components are fabricated in a single etching step in silicon and subsequently thermally oxidized. The separation column consists of a regular array of microfabricated solid support structures with a monolayer of an octylsilane covalently bonded to the surfaces to provide chromatographic interaction. The chip features a 1 mm long U-shaped detection cell and planar silicon dioxide waveguides that couple light to and from the detection cell. Microfabricated on-chip fiber couplers assure perfect alignment of optical fibers to the waveguides. The entire oxidized silicon microchip structure is sealed with a glass lid. Reversed phase electrochromatographic separation of three neutral compounds is demonstrated using UV absorbance detection at 254 nm. Baseline separation of the analytes is achieved in less than two minutes
Experiment list: SRX620294 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available body=Pol II (Santa Cruz Biotechnology, N20, sc-899) http://dbarchive.biosciencedb...s; ChIP-Seq source_name=NIH3T3 fibroblasts || culture condition=serum starved || chemicals=DMSO || chip anti
Experiment list: SRX891837 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available denocarcinoma || chip antibody=none (input) http://dbarc...ut, treated, replicate 2; Homo sapiens; ChIP-Seq source_name=MDA-MB-231 || cell line=MDA-MB-231 || cell type=triple negative breast a
Experiment list: SRX185908 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available epton 1; Homo sapiens; ChIP-Seq source_name=MCF-7 breast adenocarcinoma cells, thiostrepton, FOXM1 ChIP || c...ell_line=MCF-7 || cell_type=ER-positive breast adenocarcinoma cells || treatment=
Experiment list: SRX185916 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available on 4; Homo sapiens; ChIP-Seq source_name=MCF-7 breast adenocarcinoma cells, thiostrepton, FOXM1 ChIP || cell..._line=MCF-7 || cell_type=ER-positive breast adenocarcinoma cells || treatment=thi
Experiment list: SRX745835 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available d Pol II; Homo sapiens; ChIP-Seq source_name=Breast cancer cells || cell line=MCF7 || treatment=untreated || sample type=Pleural effu...sion || passages=14-17 || chip antibody=Homemade Anti-Po
Prototype detection unit for the CHIPS experiment

Science.gov (United States)

Pfützner, Maciej M.

2017-09-01

CHIPS (CHerenkov detectors In mine PitS) is an R&D project aiming to develop novel cost-effective neutrino detectors, focused on measuring the CP-violating neutrino mixing phase (δ CP). A single detector module, containing an enclosed volume of purified water, would be submerged in an existing lake, located in a neutrino beam. A staged approach is proposed with first detectors deployed in a flooded mine pit in Northern Minnesota, 7 mrad off-axis from the existing NuMI beam. A small proof-of-principle model (CHIPS-M) has already been tested and the first stage of a fully functional 10 kt module (CHIPS-10) is planned for 2018. One of the instruments submerged on board of CHIPS-M in autumn 2015 was a prototype detection unit, constructed at Nikhef. The unit contains hardware borrowed from the KM3NeT experiment, including 16 3 inch photomultiplier tubes and readout electronics. In addition to testing the mechanical design and data acquisition, the detector was used to record a large sample of cosmic ray muon events. The collected data is valuable for characterising the cosmic muon background and validating a Monte Carlo simulation used to optimise future designs. This paper introduces the CHIPS project, describes the design of the prototype unit, and presents the results of a preliminary data analysis.
Experiment list: SRX143851 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available lance, and learn motor skills. 57796523,71.5,23.1,31516 GSM918759: LICR ChipSeq Cerebellum CTCF adult-8wks s...cerebellar nuclei. Its function is to coordinate voluntary movements, maintain ba
Experiment list: SRX185910 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available ton 2; Homo sapiens; ChIP-Seq source_name=MCF-7 breast adenocarcinoma cells, thiostrepton, FOXM1 ChIP || cel...l_line=MCF-7 || cell_type=ER-positive breast adenocarcinoma cells || treatment=th
Experiment list: SRX185918 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available ton 7; Homo sapiens; ChIP-Seq source_name=MCF-7 breast adenocarcinoma cells, thiostrepton, FOXM1 ChIP || cel...l_line=MCF-7 || cell_type=ER-positive breast adenocarcinoma cells || treatment=th
Experiment list: SRX286394 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 3: AR Cast1 [kidney, castrated+vehicle]; Mus musculus; ChIP-Seq source_name=AR_Cast1 || strain=wild type ICR... || tissue=kidney || age=8-12 weeks old || treatment=castrated+vehicle || chip an
Experiment list: SRX1165098 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available tibody=CREB1 Santa Cruz Biotechnology, sc-240 http://dbarchive.biosciencedbc.jp/k...apiens; ChIP-Seq source_name=HepG2 cells || cell line=HepG2 || cell type=Hepatocellular Carcinoma || chip an
Experiment list: SRX115969 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available ; ChIP-Seq source_name=Breast cancer cells || cell lines=MCF-7 || agent=E2 || time=24 hr || chip antibody=ERα, Santa Cruz Biotechnolo...gy, sc-8005 X http://dbarchive.biosciencedbc.jp/kyushu-u
Experiment list: SRX1427025 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available pring produced at one birth by a viviparous animal. 32763382,74.3,19.7,747 GSM1937508: SHP ChIP-seq with vehicle...week || genotype=wildtype || treatment=vehicle || chip antibody=SHP (sc-30169) ht
Experiment list: SRX655689 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 8698: pol2 KO ChIPSeq; Mus musculus; ChIP-Seq source_name=MEFs cells knockout MED23 || cell type=mouse embry...onic fibroblast || genotype/variation=MED23 knockout || chip antibody=Pol II http
Experiment list: SRX190193 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available rce_name=HL-60 || biomaterial_provider=ATCC || datatype=ChipSeq || datatype description=Chromatin IP Sequencing || antibody antibody...description=Mouse monoclonal to RNA polymerase II CTD repeat YSPTSPS antibody... (4H8) - ChIP Grade. Antibody Target: POL2 || antibody targetdescription=This gene encod...es the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes || antibody... vendorname=abcam || antibody vendorid=ab5408 || controlid=SL
Experiment list: SRX100504 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available .1 source_name=U87 || biomaterial_provider=ATCC || datatype=ChipSeq || datatype description=Chromatin IP Sequencing || antibody antib...odydescription=Mouse monoclonal to RNA polymerase II CTD repeat YSPTSPS antibody... (4H8) - ChIP Grade. Antibody Target: POL2 || antibody targetdescription=This gene e...ncodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes || antibody... vendorname=abcam || antibody vendorid=ab5408 || controli
Experiment list: SRX100529 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available aterial_provider=WiCell Research Institute || datatype=ChipSeq || datatype description=Chromatin IP Sequencing || antibody antibody...description=Mouse monoclonal to RNA polymerase II CTD repeat YSPTSPS antibody... (4H8) - ChIP Grade. Antibody Target: POL2 || antibody targetdescription=This gene encode...s the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes || antibody... vendorname=abcam || antibody vendorid=ab5408 || controlid=SL9
HMCan: A method for detecting chromatin modifications in cancer samples using ChIP-seq data

KAUST Repository

Ashoor, Haitham

2013-09-09

Motivation: Cancer cells are often characterized by epigenetic changes, which include aberrant histone modifications. In particular, local or regional epigenetic silencing is a common mechanism in cancer for silencing expression of tumor suppressor genes. Though several tools have been created to enable detection of histone marks in ChIP-seq data from normal samples, it is unclear whether these tools can be efficiently applied to ChIP-seq data generated from cancer samples. Indeed, cancer genomes are often characterized by frequent copy number alterations: gains and losses of large regions of chromosomal material. Copy number alterations may create a substantial statistical bias in the evaluation of histone mark signal enrichment and result in underdetection of the signal in the regions of loss and overdetection of the signal in the regions of gain. Results: We present HMCan (Histone modifications in cancer), a tool specially designed to analyze histone modification ChIP-seq data produced from cancer genomes. HMCan corrects for the GC-content and copy number bias and then applies Hidden Markov Models to detect the signal from the corrected data. On simulated data, HMCan outperformed several commonly used tools developed to analyze histone modification data produced from genomes without copy number alterations. HMCan also showed superior results on a ChIP-seq dataset generated for the repressive histone mark H3K27me3 in a bladder cancer cell line. HMCan predictions matched well with experimental data (qPCR validated regions) and included, for example, the previously detected H3K27me3 mark in the promoter of the DLEC1 gene, missed by other tools we tested. The Author 2013. Published by Oxford University Press. All rights reserved.

Experiment list: SRX150451 [Chip-atlas[Archive

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Full Text Available is=Leukemia Chronic Myelogenous 39880346,54.9,7.2,2209 GSM935371: Harvard ChipSeq K562 SIRT6 std source_name...=K562 || biomaterial_provider=ATCC || lab=Harvard || lab description=Struhl - Harvard University || datatype
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Full Text Available is=Leukemia Chronic Myelogenous 38544300,59.2,11.1,1031 GSM935392: Harvard ChipSeq K562 NELFe std source_nam...e=K562 || biomaterial_provider=ATCC || lab=Harvard || lab description=Struhl - Harvard University || datatyp
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Full Text Available us; ChIP-Seq source_name=Kdm2b knockdown mouse ES cells || chip antibody=Ezh2 || antibody manufacturer=Cell ...ine=E14 || cell type=embryonbic stem cells || genotype=Kdm2b knockdown http://dba
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Full Text Available ChIPSeq; Mus musculus; ChIP-Seq source_name=MEFs cells knockout MED23 || cell type=mouse embryonic fibroblas...t || genotype/variation=MED23 knockout || chip antibody=H3K4me3 http://dbarchive.
Experiment list: SRX248443 [Chip-atlas[Archive

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Full Text Available n PolII rep; Homo sapiens; ChIP-Seq source_name=Breast cancer cells || cell line=MCF7 || time point=40 min || cell type=Pleural effus...ion || passages=14-17 || chip antibody=Homemade Anti-Pol
Experiment list: SRX248446 [Chip-atlas[Archive

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Full Text Available usion || passages=14-17 || chip antibody=Homemade Anti-P...in PolII rep; Homo sapiens; ChIP-Seq source_name=Breast cancer cells || cell line=MCF7 || time point=320 min || cell type=Pleural eff
Experiment list: SRX248445 [Chip-atlas[Archive

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Full Text Available usion || passages=14-17 || chip antibody=Homemade Anti-P...in PolII rep; Homo sapiens; ChIP-Seq source_name=Breast cancer cells || cell line=MCF7 || time point=160 min || cell type=Pleural eff
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Full Text Available n PolII rep; Homo sapiens; ChIP-Seq source_name=Breast cancer cells || cell line=MCF7 || time point=20 min || cell type=Pleural effus...ion || passages=14-17 || chip antibody=Homemade Anti-Pol
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Full Text Available n PolII rep; Homo sapiens; ChIP-Seq source_name=Breast cancer cells || cell line=MCF7 || time point=80 min || cell type=Pleural effus...ion || passages=14-17 || chip antibody=Homemade Anti-Pol
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Full Text Available n PolII rep; Homo sapiens; ChIP-Seq source_name=Breast cancer cells || cell line=MCF7 || time point=10 min || cell type=Pleural effus...ion || passages=14-17 || chip antibody=Homemade Anti-Pol
Chip-to-chip SnO2 nanowire network sensors for room temperature H2 detection

Science.gov (United States)

Köck, A.; Brunet, E.; Mutinati, G. C.; Maier, T.; Steinhauer, S.

2012-06-01

The employment of nanowires is a very powerful strategy to improve gas sensor performance. We demonstrate a gas sensor device, which is based on silicon chip-to-chip synthesis of ultralong tin oxide (SnO2) nanowires. The sensor device employs an interconnected SnO2 nanowire network configuration, which exhibits a huge surface-to-volume ratio and provides full access of the target gas to the nanowires. The chip-to-chip SnO2 nanowire device is able to detect a H2 concentration of only 20 ppm in synthetic air with ~ 60% relative humidity at room temperature. At an operating temperature of 300°C a concentration of 50 ppm H2 results in a sensitivity of 5%. At this elevated temperature the sensor shows a linear response in a concentration range between 10 ppm and 100 ppm H2. The SnO2-nanowire fabrication procedure based on spray pyrolysis and subsequent annealing is performed at atmospheric pressure, requires no vacuum and allows upscale of the substrate to a wafer size. 3D-integration with CMOS chips is proposed as viable way for practical realization of smart nanowire based gas sensor devices for the consumer market.
Evaluation of different time domain peak models using extreme learning machine-based peak detection for EEG signal.

Science.gov (United States)

Adam, Asrul; Ibrahim, Zuwairie; Mokhtar, Norrima; Shapiai, Mohd Ibrahim; Cumming, Paul; Mubin, Marizan

2016-01-01

Various peak models have been introduced to detect and analyze peaks in the time domain analysis of electroencephalogram (EEG) signals. In general, peak model in the time domain analysis consists of a set of signal parameters, such as amplitude, width, and slope. Models including those proposed by Dumpala, Acir, Liu, and Dingle are routinely used to detect peaks in EEG signals acquired in clinical studies of epilepsy or eye blink. The optimal peak model is the most reliable peak detection performance in a particular application. A fair measure of performance of different models requires a common and unbiased platform. In this study, we evaluate the performance of the four different peak models using the extreme learning machine (ELM)-based peak detection algorithm. We found that the Dingle model gave the best performance, with 72 % accuracy in the analysis of real EEG data. Statistical analysis conferred that the Dingle model afforded significantly better mean testing accuracy than did the Acir and Liu models, which were in the range 37-52 %. Meanwhile, the Dingle model has no significant difference compared to Dumpala model.
Experiment list: SRX150623 [Chip-atlas[Archive

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Full Text Available is=Leukemia Chronic Myelogenous 34396876,78.6,11.1,16076 GSM935544: Harvard ChipSeq K562 HMGN3 std source_na...me=K562 || biomaterial_provider=ATCC || lab=Harvard || lab description=Struhl - Harvard University || dataty
Experiment list: SRX150471 [Chip-atlas[Archive

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Full Text Available s=Leukemia Chronic Myelogenous 34337514,69.2,8.6,1665 GSM935391: Harvard ChipSeq K562 ATF3 std source_name=K...562 || biomaterial_provider=ATCC || lab=Harvard || lab description=Struhl - Harvard University || datatype=C
Experiment list: SRX150423 [Chip-atlas[Archive

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Full Text Available sis=Leukemia Chronic Myelogenous 19694334,54.9,12.8,4256 GSM935343: Harvard ChipSeq K562 TFIIIC-110 std sour...ce_name=K562 || biomaterial_provider=ATCC || lab=Harvard || lab description=Struhl - Harvard University || d
Experiment list: SRX150474 [Chip-atlas[Archive

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Full Text Available is=Leukemia Chronic Myelogenous 16833014,69.7,4.8,2339 GSM935394: Harvard ChipSeq K562 GTF2B std source_name...=K562 || biomaterial_provider=ATCC || lab=Harvard || lab description=Struhl - Harvard University || datatype
Experiment list: SRX150452 [Chip-atlas[Archive

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Full Text Available s=Leukemia Chronic Myelogenous 17157530,93.1,18.0,2344 GSM935372: Harvard ChipSeq K562 RPC155 std source_nam...e=K562 || biomaterial_provider=ATCC || lab=Harvard || lab description=Struhl - Harvard University || datatyp
Experiment list: SRX185912 [Chip-atlas[Archive

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Full Text Available MB-231 foxm1 Thiostrepton 1; Homo sapiens; ChIP-Seq source_name=MDA-MB-231 breast adenocarcinoma cells, thio...strepton, FOXM1 ChIP || cell_line=MDA-MB-231 || cell_type=ER-negative breast adenocarcinoma
Experiment list: SRX185911 [Chip-atlas[Archive

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Full Text Available B-231 foxm1 DMSO 1; Homo sapiens; ChIP-Seq source_name=MDA-MB-231 breast adenocarcinoma cells, control, FOXM...1 ChIP || cell_line=MDA-MB-231 || cell_type=ER-negative breast adenocarcinoma cel
Experiment list: SRX185914 [Chip-atlas[Archive

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Full Text Available B-231 foxm1 Thiostrepton 2; Homo sapiens; ChIP-Seq source_name=MDA-MB-231 breast adenocarcinoma cells, thios...trepton, FOXM1 ChIP || cell_line=MDA-MB-231 || cell_type=ER-negative breast adenocarcinoma

Experiment list: SRX172567 [Chip-atlas[Archive

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Full Text Available P-Seq source_name=Embryonic Stem Cell || background mouse strain=129SvJae/C57BL/6 || chip antibody=streptavidin beads... || antibody vendor/catalog=Invitrogen 656-01 Dynabeads® MyOne? Streptavidin T1 || genotype/variati
Experiment list: SRX191073 [Chip-atlas[Archive

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Full Text Available ulus; ChIP-Seq source_name=Kdm2b knockdown mouse ES cells || chip antibody=Ring1b || antibody manufacturer=C...ll line=E14 || cell type=embryonbic stem cells || genotype=Kdm2b knockdown http:/
Experiment list: SRX998277 [Chip-atlas[Archive

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Full Text Available ial decompensation with sepsis || postmortem delay=4.2 hrs || experiment type=ChIP-Seq || chip antibody=H3K2...n female occipital pole tissue || tissue=Occipital pole || gender=female || age=68 || Cause of death=Myocard
Low-complexity R-peak detection for ambulatory fetal monitoring

International Nuclear Information System (INIS)

Rooijakkers, Michael J; Rabotti, Chiara; Mischi, Massimo; Oei, S Guid

2012-01-01

Non-invasive fetal health monitoring during pregnancy is becoming increasingly important because of the increasing number of high-risk pregnancies. Despite recent advances in signal-processing technology, which have enabled fetal monitoring during pregnancy using abdominal electrocardiogram (ECG) recordings, ubiquitous fetal health monitoring is still unfeasible due to the computational complexity of noise-robust solutions. In this paper, an ECG R-peak detection algorithm for ambulatory R-peak detection is proposed, as part of a fetal ECG detection algorithm. The proposed algorithm is optimized to reduce computational complexity, without reducing the R-peak detection performance compared to the existing R-peak detection schemes. Validation of the algorithm is performed on three manually annotated datasets. With a detection error rate of 0.23%, 1.32% and 9.42% on the MIT/BIH Arrhythmia and in-house maternal and fetal databases, respectively, the detection rate of the proposed algorithm is comparable to the best state-of-the-art algorithms, at a reduced computational complexity. (paper)
Low-complexity R-peak detection for ambulatory fetal monitoring.

Science.gov (United States)

Rooijakkers, Michael J; Rabotti, Chiara; Oei, S Guid; Mischi, Massimo

2012-07-01

Non-invasive fetal health monitoring during pregnancy is becoming increasingly important because of the increasing number of high-risk pregnancies. Despite recent advances in signal-processing technology, which have enabled fetal monitoring during pregnancy using abdominal electrocardiogram (ECG) recordings, ubiquitous fetal health monitoring is still unfeasible due to the computational complexity of noise-robust solutions. In this paper, an ECG R-peak detection algorithm for ambulatory R-peak detection is proposed, as part of a fetal ECG detection algorithm. The proposed algorithm is optimized to reduce computational complexity, without reducing the R-peak detection performance compared to the existing R-peak detection schemes. Validation of the algorithm is performed on three manually annotated datasets. With a detection error rate of 0.23%, 1.32% and 9.42% on the MIT/BIH Arrhythmia and in-house maternal and fetal databases, respectively, the detection rate of the proposed algorithm is comparable to the best state-of-the-art algorithms, at a reduced computational complexity.
Experiment list: SRX150674 [Chip-atlas[Archive

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Full Text Available s=Leukemia Chronic Myelogenous 18469470,89.4,7.1,725 GSM935595: Harvard ChipSeq K562 BRF1 std source_name=K5...62 || biomaterial_provider=ATCC || lab=Harvard || lab description=Struhl - Harvard University || datatype=Ch
Experiment list: SRX150569 [Chip-atlas[Archive

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Full Text Available s=Leukemia Chronic Myelogenous 51487836,63.2,7.7,861 GSM935490: Harvard ChipSeq K562 BRF2 std source_name=K5...62 || biomaterial_provider=ATCC || lab=Harvard || lab description=Struhl - Harvard University || datatype=Ch
Experiment list: SRX891827 [Chip-atlas[Archive

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Full Text Available d, replicate 2; Homo sapiens; ChIP-Seq source_name=MDA-MB-231 || cell line=MDA-MB-231 || cell type=triple negative breast adenocarcin...oma || chip antibody=H3K9ac, Millipore #07-352, Lot 2388
Experiment list: SRX185913 [Chip-atlas[Archive

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Full Text Available MB-231 foxm1 DMSO 2; Homo sapiens; ChIP-Seq source_name=MDA-MB-231 breast adenocarcinoma cells, control, FOX...M1 ChIP || cell_line=MDA-MB-231 || cell_type=ER-negative breast adenocarcinoma ce
Experiment list: SRX891826 [Chip-atlas[Archive

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Full Text Available ed, replicate 1; Homo sapiens; ChIP-Seq source_name=MDA-MB-231 || cell line=MDA-MB-231 || cell type=triple negative breast adenocarci...noma || chip antibody=H3K9ac, Millipore #07-352, Lot 238
Experiment list: SRX810435 [Chip-atlas[Archive

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Full Text Available idity in Shneider S2 Drosophila medium(Gibco) supplement...ster; ChIP-Seq source_name=Cell culture || cell line=S2 || chip antibody=none || growth protocol=S2 cells were grown in 24°C, 95% hum
Experiment list: SRX810433 [Chip-atlas[Archive

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Full Text Available er; ChIP-Seq source_name=Cell culture || cell line=S2 || chip antibody=none || growth protocol=S2 cells were grown in 24°C, 95% humid...ity in Shneider S2 Drosophila medium(Gibco) supplemented
Experiment list: SRX810434 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available idity in Shneider S2 Drosophila medium(Gibco) supplement...ster; ChIP-Seq source_name=Cell culture || cell line=S2 || chip antibody=none || growth protocol=S2 cells were grown in 24°C, 95% hum
Experiment list: SRX172568 [Chip-atlas[Archive

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Full Text Available us; ChIP-Seq source_name=Embryonic Stem Cell || background mouse strain=129SvJae/C57BL/6 || chip antibody=streptavidin beads... || antibody vendor/catalog=Invitrogen 656-01 Dynabeads® MyOne? Streptavidin T1 || genotype/
Experiment list: SRX643466 [Chip-atlas[Archive

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Full Text Available itory cortex) || chip antibody=input || tissue=Female Brain: medial superior temporal gyrus (secondary audit...,725 GSM1423167: Area 13 Brain1 input; Homo sapiens; ChIP-Seq source_name=Female Brain: medial superior temporal gyrus (secondary aud
Experiment list: SRX1427026 [Chip-atlas[Archive

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Full Text Available of offspring produced at one birth by a viviparous animal. 22029930,97.6,9.8,279 GSM1937509: Input for SHP ChIP-seq with vehicle...ver || age=8-12 week || genotype=wildtype || treatment=vehicle || chip antibody=n
Method and apparatus for current-output peak detection

Science.gov (United States)

De Geronimo, Gianluigi

2017-01-24

A method and apparatus for a current-output peak detector. A current-output peak detector circuit is disclosed and works in two phases. The peak detector circuit includes switches to switch the peak detector circuit from the first phase to the second phase upon detection of the peak voltage of an input voltage signal. The peak detector generates a current output with a high degree of accuracy in the second phase.
An integrated micro-chip for rapid detection of magnetic particles

KAUST Repository

Gooneratne, Chinthaka P.; Liang, Cai; Giouroudi, Ioanna; Kosel, Jü rgen

2012-01-01

This paper proposes an integrated micro-chip for the manipulation and detection of magnetic particles (MPs). A conducting ring structure is used to manipulate MPs toward giant magnetoresistance(GMR) sensing elements for rapid detection
Experiment list: SRX190244 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 1610.1 source_name=PANC-1 || biomaterial_provider=ATCC || datatype=ChipSeq || datatype description=Chromatin IP Sequencing || antibod...y antibodydescription=Mouse monoclonal to RNA polymerase... II CTD repeat YSPTSPS antibody (4H8) - ChIP Grade. Antibody Target: POL2 || antibody targetdescription=This...r RNA in eukaryotes || antibody vendorname=abcam || antibody vendorid=ab5408 || c...ontrolid=SL2340 || labexpid=SL2343,SL5609 || softwareversion=MACS || cell sex=M || antibody=Pol2-4H8 || antibody antibody
Practical guidelines for the comprehensive analysis of ChIP-seq data.

Directory of Open Access Journals (Sweden)

Timothy Bailey

Full Text Available Mapping the chromosomal locations of transcription factors, nucleosomes, histone modifications, chromatin remodeling enzymes, chaperones, and polymerases is one of the key tasks of modern biology, as evidenced by the Encyclopedia of DNA Elements (ENCODE Project. To this end, chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq is the standard methodology. Mapping such protein-DNA interactions in vivo using ChIP-seq presents multiple challenges not only in sample preparation and sequencing but also for computational analysis. Here, we present step-by-step guidelines for the computational analysis of ChIP-seq data. We address all the major steps in the analysis of ChIP-seq data: sequencing depth selection, quality checking, mapping, data normalization, assessment of reproducibility, peak calling, differential binding analysis, controlling the false discovery rate, peak annotation, visualization, and motif analysis. At each step in our guidelines we discuss some of the software tools most frequently used. We also highlight the challenges and problems associated with each step in ChIP-seq data analysis. We present a concise workflow for the analysis of ChIP-seq data in Figure 1 that complements and expands on the recommendations of the ENCODE and modENCODE projects. Each step in the workflow is described in detail in the following sections.

Detection and classification of ebola on microfluidic chips

Science.gov (United States)

Lin, Xue; Jin, Xiangyu; Fan, Yunqian; Huang, Qin; Kou, Yue; Zu, Guo; Huang, Shiguang; Liu, Xiaosheng; Huang, Guoliang

2016-10-01

Point-of-care testing (POCT) for an infectious diseases is the prerequisite to control of the disease and limitation of its spread. A microfluidic chip for detection and classification of four strains of Ebola virus was developed and evaluated. This assay was based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) and specific primers for Ebola Zaire virus, Ebola Sudan virus, Ebola Tai Forest virus and Ebola Bundibugyo virus were designed. The sensitivity of the microfluidic chip was under 103 copies per milliliter, as determined by ten repeated tests. This assay is unique in its ability to enable diagnosis of the Ebola infections and simultaneous typing of Ebola virus on a single chip. It offers short reaction time, ease of use and high specificity. These features should enable POCT in remote area during outbreaks of Ebola virus.
Experiment list: SRX150720 [Chip-atlas[Archive

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Full Text Available sue Diagnosis=Fibrocystic Disease 71490650,87.2,15.5,1356 GSM935641: Harvard ChipSeq MCF10A-Er-Src Input std... source_name=MCF10A-Er-Src || biomaterial_provider=Struhl laboratory || lab=Harvard || lab description=Struhl - Harvard
Experiment list: SRX150587 [Chip-atlas[Archive

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Full Text Available is=Adenocarcinoma 32859626,93.1,16.6,6448 GSM935508: Harvard ChipSeq HeLa-S3 NF-YA IgG-rab source_name=HeLa-...S3 || biomaterial_provider=ATCC || lab=Harvard || lab description=Struhl - Harvard University || datatype=Ch
Experiment list: SRX100563 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available s=Leukemia Chronic Myelogenous 39078535,86.0,20.8,1302 GSM803518: HudsonAlpha ChipSeq K562 BCL3 PCR1x source..._name=K562 || biomaterial_provider=ATCC || lab=HudsonAlpha || lab description=Myers - Hudson Alpha Institute
Experiment list: SRX100430 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available s=Leukemia Chronic Myelogenous 47818475,79.5,9.7,26072 GSM803385: HudsonAlpha ChipSeq K562 HEY1 PCR1x source..._name=K562 || biomaterial_provider=ATCC || lab=HudsonAlpha || lab description=Myers - Hudson Alpha Institute
Experiment list: SRX286381 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 7,533 GSM1146460: AR Cast1b [prostate, castrated+vehicle]; Mus musculus; ChIP-Seq source_name=AR_Cast1b || s...train=wild type ICR || tissue=prostate || age=8-12 weeks old || treatment=castrated+vehicle || chip antibody
Experiment list: SRX286380 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 2,497 GSM1146459: AR Cast1a [prostate, castrated+vehicle]; Mus musculus; ChIP-Seq source_name=AR_Cast1a || s...train=wild type ICR || tissue=prostate || age=8-12 weeks old || treatment=castrated+vehicle || chip antibody
Experiment list: SRX286386 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 60.2,17474 GSM1146465: FoxA1 Cast [prostate, castrated+vehicle]; Mus musculus; ChIP-Seq source_name=FoxA1_Ca...st || strain=wild type ICR || tissue=prostate || age=8-12 weeks old || treatment=castrated+vehicle || chip a
Experiment list: SRX471838 [Chip-atlas[Archive

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Full Text Available : ChIPseq GS WT Bmi1; Mus musculus; ChIP-Seq source_name=Cultured germline stem cells || genotype/variation=...Wild-type || strain=CD1 x C57BL/6 || cell type=Cultured germline stem cells || chip antibody=Mouse anti-Bmi1
Experiment list: SRX471836 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 0: ChIPseq GS WT Scml2; Mus musculus; ChIP-Seq source_name=Cultured germline stem cells || genotype/variatio...n=Wild-type || strain=CD1 x C57BL/6 || cell type=Cultured germline stem cells || chip antibody=Rabbit anti-S
Experiment list: SRX100493 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available is=Carcinoma Hepatocellular 67635839,78.1,18.6,34708 GSM803448: HudsonAlpha ChipSeq HepG2 HEY1 v041610.1 sou...rce_name=HepG2 || biomaterial_provider=ATCC || lab=HudsonAlpha || lab description=Myers - Hudson Alpha Insti
Experiment list: SRX1084162 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 0 GSM1811344: P2 HA ChIPSeq; Drosophila melanogaster; ChIP-Seq source_name=Female whole animal_paraquat || tissue=whole animal || gen...der=female || age=1-3 days || genotype=k6801/k6801;gHA-KDM5 || chip antibody=HA htt
Experiment list: SRX212457 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available apiens; ChIP-Seq source_name=CD4+CD25+CD45RA- expanded memory regulatory T cells || donor=C || cell type=CD4...+CD25+CD45RA- expanded memory regulatory T cells || chip antibody=H3K27ac (abcam
Experiment list: SRX212463 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available sapiens; ChIP-Seq source_name=CD4+CD25-CD45RA- expanded memory conventional T cells || donor=C || cell type...=CD4+CD25-CD45RA- expanded memory conventional T cells || chip antibody=H3K4me1 (
Experiment list: SRX203399 [Chip-atlas[Archive

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Full Text Available r lymph. (Rosen et al., Dictionary of Immunology, 1989, p169 & Abbas et al., Cellular and Molecular Immuno...logy, 2d ed, p20) 30508063,94.1,4.3,15496 GSM1033764: MM.1S RNAPII JQ1 JL ChipSeq;
Experiment list: SRX1084161 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available tissue=whole animal || gender=female || age=1-3 days || genotype=k6801/k6801;gHA-KDM5 || chip antibody=HA ht...,0 GSM1811343: P1 HA ChIPSeq; Drosophila melanogaster; ChIP-Seq source_name=Female whole animal_paraquat ||
Experiment list: SRX837357 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available ource_name=ChIP-Seq with MyoD antibody 6975 in mouse P19 cells transduced with MD(ND2bHLH) chimera || cell l...ine=P19 || transduction=MD(ND2bHLH) chimera || chip antibody=MyoD antibody 6975 h
Experiment list: SRX837356 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available ource_name=ChIP-Seq with MyoD antibody 6196 in mouse P19 cells transduced with MD(ND2bHLH) chimera || cell l...ine=P19 || transduction=MD(ND2bHLH) chimera || chip antibody=MyoD antibody 6196 h
Experiment list: SRX192254 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available f offspring produced at one birth by a viviparous animal. 84324878,97.5,12.5,559 GSM1016423: A INPUT vehicle... donor1024; Mus musculus; ChIP-Seq source_name=whole liver extract || age=29-32 days || chip antibody=INPUT || treament=vehicle
Experiment list: SRX192258 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available f offspring produced at one birth by a viviparous animal. 20609955,77.1,6.7,117 GSM1016427: B INPUT vehicle ...donor1; Mus musculus; ChIP-Seq source_name=whole liver extract || age=29-32 days || chip antibody=INPUT || treament=vehicle

Experiment list: SRX192259 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available f offspring produced at one birth by a viviparous animal. 15402183,74.5,5.4,117 GSM1016428: B INPUT vehicle ...donor7; Mus musculus; ChIP-Seq source_name=whole liver extract || age=29-32 days || chip antibody=INPUT || treament=vehicle
Experiment list: SRX192267 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available f offspring produced at one birth by a viviparous animal. 28874920,80.3,4.9,183 GSM1016436: C INPUT vehicle ...donor10; Mus musculus; ChIP-Seq source_name=whole liver extract || age=29-32 days || chip antibody=INPUT || treament=vehicle
Experiment list: SRX192266 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available f offspring produced at one birth by a viviparous animal. 25871870,71.5,4.2,143 GSM1016435: C INPUT vehicle ...donor5; Mus musculus; ChIP-Seq source_name=whole liver extract || age=29-32 days || chip antibody=INPUT || treament=vehicle
Experiment list: SRX192253 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available f offspring produced at one birth by a viviparous animal. 106959657,97.4,12.9,578 GSM1016422: A INPUT vehicle... donor1021; Mus musculus; ChIP-Seq source_name=whole liver extract || age=29-32 days || chip antibody=INPUT || treament=vehicle
Probabilistic peak detection for first-order chromatographic data.

Science.gov (United States)

Lopatka, M; Vivó-Truyols, G; Sjerps, M J

2014-03-19

We present a novel algorithm for probabilistic peak detection in first-order chromatographic data. Unlike conventional methods that deliver a binary answer pertaining to the expected presence or absence of a chromatographic peak, our method calculates the probability of a point being affected by such a peak. The algorithm makes use of chromatographic information (i.e. the expected width of a single peak and the standard deviation of baseline noise). As prior information of the existence of a peak in a chromatographic run, we make use of the statistical overlap theory. We formulate an exhaustive set of mutually exclusive hypotheses concerning presence or absence of different peak configurations. These models are evaluated by fitting a segment of chromatographic data by least-squares. The evaluation of these competing hypotheses can be performed as a Bayesian inferential task. We outline the potential advantages of adopting this approach for peak detection and provide several examples of both improved performance and increased flexibility afforded by our approach. Copyright © 2014 Elsevier B.V. All rights reserved.
Bayesian approach for peak detection in two-dimensional chromatography.

Science.gov (United States)

Vivó-Truyols, Gabriel

2012-03-20

A new method for peak detection in two-dimensional chromatography is presented. In a first step, the method starts with a conventional one-dimensional peak detection algorithm to detect modulated peaks. In a second step, a sophisticated algorithm is constructed to decide which of the individual one-dimensional peaks have been originated from the same compound and should then be arranged in a two-dimensional peak. The merging algorithm is based on Bayesian inference. The user sets prior information about certain parameters (e.g., second-dimension retention time variability, first-dimension band broadening, chromatographic noise). On the basis of these priors, the algorithm calculates the probability of myriads of peak arrangements (i.e., ways of merging one-dimensional peaks), finding which of them holds the highest value. Uncertainty in each parameter can be accounted by adapting conveniently its probability distribution function, which in turn may change the final decision of the most probable peak arrangement. It has been demonstrated that the Bayesian approach presented in this paper follows the chromatographers' intuition. The algorithm has been applied and tested with LC × LC and GC × GC data and takes around 1 min to process chromatograms with several thousands of peaks.
A low-cost 2D fluorescence detection system for mm sized beads on-chip

NARCIS (Netherlands)

Segerink, Loes Irene; Koster, Maarten J.; Sprenkels, A.J.; van den Berg, Albert

2012-01-01

In this paper we describe a compact fluorescence detection system for on-chip analysis of beads, comprising a low-cost optical HD-DVD pickup. The complete system consists of a fluorescence detection unit, a control unit and a microfluidic chip containing microchannels and optical markers. With these
Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins

NARCIS (Netherlands)

Teytelman, L.; Thurtle, D.M.; Rine, J.; van Oudenaarden, A.

2013-01-01

Chromatin immunoprecipitation (ChIP) is the gold-standard technique for localizing nuclear proteins in the genome. We used ChIP, in combination with deep sequencing (Seq), to study the genome-wide distribution of the Silent information regulator (Sir) complex in Saccharomyces cerevisiae. We analyzed
A ChIP-Seq benchmark shows that sequence conservation mainly improves detection of strong transcription factor binding sites.

Directory of Open Access Journals (Sweden)

Tony Håndstad

Full Text Available BACKGROUND: Transcription factors are important controllers of gene expression and mapping transcription factor binding sites (TFBS is key to inferring transcription factor regulatory networks. Several methods for predicting TFBS exist, but there are no standard genome-wide datasets on which to assess the performance of these prediction methods. Also, it is believed that information about sequence conservation across different genomes can generally improve accuracy of motif-based predictors, but it is not clear under what circumstances use of conservation is most beneficial. RESULTS: Here we use published ChIP-seq data and an improved peak detection method to create comprehensive benchmark datasets for prediction methods which use known descriptors or binding motifs to detect TFBS in genomic sequences. We use this benchmark to assess the performance of five different prediction methods and find that the methods that use information about sequence conservation generally perform better than simpler motif-scanning methods. The difference is greater on high-affinity peaks and when using short and information-poor motifs. However, if the motifs are specific and information-rich, we find that simple motif-scanning methods can perform better than conservation-based methods. CONCLUSIONS: Our benchmark provides a comprehensive test that can be used to rank the relative performance of transcription factor binding site prediction methods. Moreover, our results show that, contrary to previous reports, sequence conservation is better suited for predicting strong than weak transcription factor binding sites.
Sensitivity of the ViroSeq HIV-1 Genotyping System for Detection of the K103N Resistance Mutation in HIV-1 Subtypes A, C, and D

Science.gov (United States)

Church, Jessica D.; Jones, Dana; Flys, Tamara; Hoover, Donald; Marlowe, Natalia; Chen, Shu; Shi, Chanjuan; Eshleman, James R.; Guay, Laura A.; Jackson, J. Brooks; Kumwenda, Newton; Taha, Taha E.; Eshleman, Susan H.

2006-01-01

The US Food and Drug Administration-cleared ViroSeq HIV-1 Genotyping System (ViroSeq) and other population sequencing-based human immunodeficiency virus type 1 (HIV-1) genotyping methods detect antiretroviral drug resistance mutations present in the major viral population of a test sample. These assays also detect some mutations in viral variants that are present as mixtures. We compared detection of the K103N nevirapine resistance mutation using ViroSeq and a sensitive, quantitative point mutation assay, LigAmp. The LigAmp assay measured the percentage of K103N-containing variants in the viral population (percentage of K103N). We analyzed 305 samples with HIV-1 subtypes A, C, and D collected from African women after nevirapine administration. ViroSeq detected K103N in 100% of samples with >20% K103N, 77.8% of samples with 10 to 20% K103N, 71.4% of samples with 5 to 10% K103N, and 16.9% of samples with 1 to 5% K103N. The sensitivity of ViroSeq for detection of K103N was similar for subtypes A, C, and D. These data indicate that the ViroSeq system reliably detects the K103N mutation at levels above 20% and frequently detects the mutation at lower levels. Further studies are needed to compare the sensitivity of different assays for detection of HIV-1 drug resistance mutations and to determine the clinical relevance of HIV-1 minority variants. PMID:16931582
Experiment list: SRX212459 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available o sapiens; ChIP-Seq source_name=CD4+CD25-CD45RA- expanded memory conventional T cells || donor=C || cell typ...e=CD4+CD25-CD45RA- expanded memory conventional T cells || chip antibody=H3K27ac
Experiment list: SRX212458 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available sapiens; ChIP-Seq source_name=CD4+CD25+CD45RA- expanded memory regulatory T cells || donor=D || cell type=C...D4+CD25+CD45RA- expanded memory regulatory T cells || chip antibody=H3K27ac (abca
Experiment list: SRX212464 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available o sapiens; ChIP-Seq source_name=CD4+CD25-CD45RA- expanded memory conventional T cells || donor=D || cell typ...e=CD4+CD25-CD45RA- expanded memory conventional T cells || chip antibody=H3K4me1
Experiment list: SRX212460 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available o sapiens; ChIP-Seq source_name=CD4+CD25-CD45RA- expanded memory conventional T cells || donor=D || cell typ...e=CD4+CD25-CD45RA- expanded memory conventional T cells || chip antibody=H3K27ac
Experiment list: SRX212462 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available sapiens; ChIP-Seq source_name=CD4+CD25+CD45RA- expanded memory regulatory T cells || donor=D || cell type=C...D4+CD25+CD45RA- expanded memory regulatory T cells || chip antibody=H3K4me1 (abca
Experiment list: SRX286391 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available 7,47.9,41.3,666 GSM1146470: rIgG1a [prostate, castrated+vehicle]; Mus musculus; ChIP-Seq source_name=rIgG1a ...|| strain=wild type ICR || tissue=prostate || age=8-12 weeks old || treatment=castrated+vehicle || chip anti
Experiment list: SRX590292 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available -rep1; Mus musculus; ChIP-Seq source_name=R-Ctrl-Flag ChIP || strain background=C57BL/6 || genotype/variation=Foxd3 conditional knock...out || cell type=embryonic stem cells (ESCs; R cells) || cell line of origin=Foxd3 conditional knock
Experiment list: SRX542620 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available sculus; ChIP-Seq source_name=Embryonic Stem Cells || time point=NA || treatment=no treatment || strain=129 X C57bl/6 || cell type=Par...ental mouse ES(KH2) cells || chip antibody=MacroH2A2 antibody, Abcam ab4173 http://
ICPD-a new peak detection algorithm for LC/MS.

Science.gov (United States)

Zhang, Jianqiu; Haskins, William

2010-12-01

The identification and quantification of proteins using label-free Liquid Chromatography/Mass Spectrometry (LC/MS) play crucial roles in biological and biomedical research. Increasing evidence has shown that biomarkers are often low abundance proteins. However, LC/MS systems are subject to considerable noise and sample variability, whose statistical characteristics are still elusive, making computational identification of low abundance proteins extremely challenging. As a result, the inability of identifying low abundance proteins in a proteomic study is the main bottleneck in protein biomarker discovery. In this paper, we propose a new peak detection method called Information Combining Peak Detection (ICPD ) for high resolution LC/MS. In LC/MS, peptides elute during a certain time period and as a result, peptide isotope patterns are registered in multiple MS scans. The key feature of the new algorithm is that the observed isotope patterns registered in multiple scans are combined together for estimating the likelihood of the peptide existence. An isotope pattern matching score based on the likelihood probability is provided and utilized for peak detection. The performance of the new algorithm is evaluated based on protein standards with 48 known proteins. The evaluation shows better peak detection accuracy for low abundance proteins than other LC/MS peak detection methods.
Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis.

Science.gov (United States)

Yang, Chao; He, Zengyou; Yu, Weichuan

2009-01-06

In mass spectrometry (MS) based proteomic data analysis, peak detection is an essential step for subsequent analysis. Recently, there has been significant progress in the development of various peak detection algorithms. However, neither a comprehensive survey nor an experimental comparison of these algorithms is yet available. The main objective of this paper is to provide such a survey and to compare the performance of single spectrum based peak detection methods. In general, we can decompose a peak detection procedure into three consequent parts: smoothing, baseline correction and peak finding. We first categorize existing peak detection algorithms according to the techniques used in different phases. Such a categorization reveals the differences and similarities among existing peak detection algorithms. Then, we choose five typical peak detection algorithms to conduct a comprehensive experimental study using both simulation data and real MALDI MS data. The results of comparison show that the continuous wavelet-based algorithm provides the best average performance.

Impact of artefact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data.

Directory of Open Access Journals (Sweden)

Thomas Samuel Carroll

2014-04-01

Full Text Available With the advent of ChIP-seq multiplexing technologies and the subsequent increase in ChIP-seq throughput, the development of working standards for the quality assessment of ChIP-seq studies has received significant attention. The ENCODE consortium’s large scale analysis of transcription factor binding and epigenetic marks as well as concordant work on ChIP-seq by other laboratories has established a new generation of ChIP-seq quality control measures. The use of these metrics alongside common processing steps has however not been evaluated. In this study, we investigate the effects of blacklisting and removal of duplicated reads on established metrics of ChIP-seq quality and show that the interpretation of these metrics is highly dependent on the ChIP-seq preprocessing steps applied. Further to this we perform the first investigation of the use of these metrics for ChIP-exo data and make recommendations for the adaptation of the NSC statistic to allow for the assessment of ChIP-exo efficiency.
Nebula--a web-server for advanced ChIP-seq data analysis.

Science.gov (United States)

Boeva, Valentina; Lermine, Alban; Barette, Camille; Guillouf, Christel; Barillot, Emmanuel

2012-10-01

ChIP-seq consists of chromatin immunoprecipitation and deep sequencing of the extracted DNA fragments. It is the technique of choice for accurate characterization of the binding sites of transcription factors and other DNA-associated proteins. We present a web service, Nebula, which allows inexperienced users to perform a complete bioinformatics analysis of ChIP-seq data. Nebula was designed for both bioinformaticians and biologists. It is based on the Galaxy open source framework. Galaxy already includes a large number of functionalities for mapping reads and peak calling. We added the following to Galaxy: (i) peak calling with FindPeaks and a module for immunoprecipitation quality control, (ii) de novo motif discovery with ChIPMunk, (iii) calculation of the density and the cumulative distribution of peak locations relative to gene transcription start sites, (iv) annotation of peaks with genomic features and (v) annotation of genes with peak information. Nebula generates the graphs and the enrichment statistics at each step of the process. During Steps 3-5, Nebula optionally repeats the analysis on a control dataset and compares these results with those from the main dataset. Nebula can also incorporate gene expression (or gene modulation) data during these steps. In summary, Nebula is an innovative web service that provides an advanced ChIP-seq analysis pipeline providing ready-to-publish results. Nebula is available at http://nebula.curie.fr/ Supplementary data are available at Bioinformatics online.
Experiment list: SRX150670 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available gnosis=Fibrocystic Disease 53773968,83.9,44.3,13035 GSM935591: Harvard ChipSeq MCF10A-Er-Src EtOH 0.01pct ST...AT3 std source_name=MCF10A-Er-Src || biomaterial_provider=Struhl laboratory || lab=Harvard || lab description=Struhl - Harvard
Experiment list: SRX150630 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available gnosis=Fibrocystic Disease 42446970,82.6,25.1,47688 GSM935551: Harvard ChipSeq MCF10A-Er-Src EtOH 0.01pct 12...hr STAT3 std source_name=MCF10A-Er-Src || biomaterial_provider=Struhl laboratory || lab=Harvard || lab description=Struhl - Harvard
Experiment list: SRX100511 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available ,37.1,107266 GSM803466: HudsonAlpha ChipSeq H1-hESC Rad21 v041610.2 source_name=H1-hESC || biomaterial_provi...SRX100511 hg19 TFs and others RAD21 Pluripotent stem cell hESC H1 NA 109287919,77.2
Experiment list: SRX153145 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available ast adenocarcinoma cell-line MCF7 || cell-line=MCF7 || passage=5 || chip antibody=H...n=Pleura|Tissue Diagnosis=Adenocarcinoma 93237597,98.2,8.2,1358 GSM946849: MCF7 H3K4me1; Homo sapiens; ChIP-Seq source_name=Human bre
Experiment list: SRX212461 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available iens; ChIP-Seq source_name=CD4+CD25+CD45RA- expanded memory regulatory T cells || donor=C || cell type=CD4+CD25+CD45RA- expanded memo...ry regulatory T cells || chip antibody=H3K4me1 (abcam ab
Experiment list: SRX713898 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available -D567 || agent=Ethanol (vehicle control) || chip antibody=AR -N20 (Santa Cruz, SC-816 lot B1012) || biologic...5527: R1D567 Eth ARv567es rep2; Homo sapiens; ChIP-Seq source_name=prostate cancer cell line || cell type=R1
Experiment list: SRX713899 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available D567 || agent=Ethanol (vehicle control) || chip antibody=AR -N20 (Santa Cruz, SC-816 lot B1012) || biologica...528: R1D567 Eth ARv567es rep3; Homo sapiens; ChIP-Seq source_name=prostate cancer cell line || cell type=R1-
Global mapping of cell type-specific open chromatin by FAIRE-seq reveals the regulatory role of the NFI family in adipocyte differentiation.

Directory of Open Access Journals (Sweden)

Hironori Waki

2011-10-01

Full Text Available Identification of regulatory elements within the genome is crucial for understanding the mechanisms that govern cell type-specific gene expression. We generated genome-wide maps of open chromatin sites in 3T3-L1 adipocytes (on day 0 and day 8 of differentiation and NIH-3T3 fibroblasts using formaldehyde-assisted isolation of regulatory elements coupled with high-throughput sequencing (FAIRE-seq. FAIRE peaks at the promoter were associated with active transcription and histone modifications of H3K4me3 and H3K27ac. Non-promoter FAIRE peaks were characterized by H3K4me1+/me3-, the signature of enhancers, and were largely located in distal regions. The non-promoter FAIRE peaks showed dynamic change during differentiation, while the promoter FAIRE peaks were relatively constant. Functionally, the adipocyte- and preadipocyte-specific non-promoter FAIRE peaks were, respectively, associated with genes up-regulated and down-regulated by differentiation. Genes highly up-regulated during differentiation were associated with multiple clustered adipocyte-specific FAIRE peaks. Among the adipocyte-specific FAIRE peaks, 45.3% and 11.7% overlapped binding sites for, respectively, PPARγ and C/EBPα, the master regulators of adipocyte differentiation. Computational motif analyses of the adipocyte-specific FAIRE peaks revealed enrichment of a binding motif for nuclear family I (NFI transcription factors. Indeed, ChIP assay showed that NFI occupy the adipocyte-specific FAIRE peaks and/or the PPARγ binding sites near PPARγ, C/EBPα, and aP2 genes. Overexpression of NFIA in 3T3-L1 cells resulted in robust induction of these genes and lipid droplet formation without differentiation stimulus. Overexpression of dominant-negative NFIA or siRNA-mediated knockdown of NFIA or NFIB significantly suppressed both induction of genes and lipid accumulation during differentiation, suggesting a physiological function of these factors in the adipogenic program. Together, our
Experiment list: SRX150497 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available sue Diagnosis=Fibrocystic Disease 30305817,89.0,5.1,579 GSM935418: Harvard ChipSeq MCF10A-Er-Src EtOH 0.01pc...t 4hr Input std source_name=MCF10A-Er-Src || biomaterial_provider=Struhl laboratory || lab=Harvard || lab description=Struhl - Harvar
Experiment list: SRX100495 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available SRX100495 hg19 TFs and others TAF1 Pluripotent stem cell hESC H1 NA 40640767,80.2,12.3,29488 GSM803450: Huds...onAlpha ChipSeq H1-hESC TAF1 v041610.2 source_name=H1-hESC || biomaterial_provider=
Experiment list: SRX100469 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available SRX100469 hg19 TFs and others GABPA Pluripotent stem cell hESC H1 NA 59698055,78.1,10.0,16884 GSM803424: Hud...sonAlpha ChipSeq H1-hESC GABP PCR1x source_name=H1-hESC || biomaterial_provider=WiC
Experiment list: SRX100587 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available SRX100587 hg19 TFs and others EP300 Pluripotent stem cell hESC H1 NA 46380456,87.7,10.1,18476 GSM803542: Hud...sonAlpha ChipSeq H1-hESC p300 v041610.2 source_name=H1-hESC || biomaterial_provider
Genome-wide ChIP-seq analysis of human TOP2B occupancy in MCF7 breast cancer epithelial cells

Directory of Open Access Journals (Sweden)

Catriona M. Manville

2015-11-01

Full Text Available We report the whole genome ChIP seq for human TOP2B from MCF7 cells. Using three different peak calling methods, regions of binding were identified in the presence or absence of the nuclear hormone estradiol, as TOP2B has been reported to play a role in ligand-induced transcription. TOP2B peaks were found across the whole genome, 50% of the peaks fell either within a gene or within 5 kb of a transcription start site. TOP2B peaks coincident with gene promoters were less frequently associated with epigenetic features marking active promoters in estradiol treated than in untreated cells. Significantly enriched transcription factor motifs within the DNA sequences underlying the peaks were identified. These included SP1, KLF4, TFAP2A, MYF, REST, CTCF, ESR1 and ESR2. Gene ontology analysis of genes associated with TOP2B peaks found neuronal development terms including axonogenesis and axon guidance were significantly enriched. In the absence of functional TOP2B there are errors in axon guidance in the zebrafish eye. Specific heparin sulphate structures are involved in retinal axon targeting. The glycosaminoglycan biosynthesis–heparin sulphate/heparin pathway is significantly enriched in the TOP2B gene ontology analysis, suggesting changes in this pathway in the absence of TOP2B may cause the axon guidance faults.
Chemiluminescence generation and detection in a capillary-driven microfluidic chip

Science.gov (United States)

Ramon, Charlotte; Temiz, Yuksel; Delamarche, Emmanuel

2017-02-01

The use of microfluidic technology represents a strong opportunity for providing sensitive, low-cost and rapid diagnosis at the point-of-care and such a technology might therefore support better, faster and more efficient diagnosis and treatment of patients at home and in healthcare settings both in developed and developing countries. In this work, we consider luminescence-based assays as an alternative to well-established fluorescence-based systems because luminescence does not require a light source or expensive optical components and is therefore a promising detection method for point-of-care applications. Here, we show a proof-of-concept of chemiluminescence (CL) generation and detection in a capillary-driven microfluidic chip for potential immunoassay applications. We employed a commercial acridan-based reaction, which is catalyzed by horseradish peroxidase (HRP). We investigated CL generation under flow conditions using a simplified immunoassay model where HRP is used instead of the complete sandwich immunocomplex. First, CL signals were generated in a capillary microfluidic chip by immobilizing HRP on a polydimethylsiloxane (PDMS) sealing layer using stencil deposition and flowing CL substrate through the hydrophilic channels. CL signals were detected using a compact (only 5×5×2.5 cm3) and custom-designed scanner, which was assembled for less than $30 and comprised a 128×1 photodiode array, a mini stepper motor, an Arduino microcontroller, and a 3D-printed housing. In addition, microfluidic chips having specific 30-μm-deep structures were fabricated and used to immobilize ensembles of 4.50 μm beads functionalized with HRP so as to generate high CL signals from capillary-driven chips.
Detecting a single molecule using a micropore-nanopore hybrid chip.

Science.gov (United States)

Liu, Lei; Zhu, Lizhong; Ni, Zhonghua; Chen, Yunfei

2013-11-21

Nanopore-based DNA sequencing and biomolecule sensing have attracted more and more attention. In this work, novel sensing devices were built on the basis of the chips containing nanopore arrays in polycarbonate (PC) membranes and micropores in Si3N4 films. Using the integrated chips, the transmembrane ionic current induced by biomolecule's translocation was recorded and analyzed, which suggested that the detected current did not change linearly as commonly expected with increasing biomolecule concentration. On the other hand, detailed translocation information (such as translocation gesture) was also extracted from the discrete current blockages in basic current curves. These results indicated that the nanofluidic device based on the chips integrated by micropores and nanopores possessed comparative potentials in biomolecule sensing.
[An automatic peak detection method for LIBS spectrum based on continuous wavelet transform].

Science.gov (United States)

Chen, Peng-Fei; Tian, Di; Qiao, Shu-Jun; Yang, Guang

2014-07-01

Spectrum peak detection in the laser-induced breakdown spectroscopy (LIBS) is an essential step, but the presence of background and noise seriously disturb the accuracy of peak position. The present paper proposed a method applied to automatic peak detection for LIBS spectrum in order to enhance the ability of overlapping peaks searching and adaptivity. We introduced the ridge peak detection method based on continuous wavelet transform to LIBS, and discussed the choice of the mother wavelet and optimized the scale factor and the shift factor. This method also improved the ridge peak detection method with a correcting ridge method. The experimental results show that compared with other peak detection methods (the direct comparison method, derivative method and ridge peak search method), our method had a significant advantage on the ability to distinguish overlapping peaks and the precision of peak detection, and could be be applied to data processing in LIBS.
Simultaneous detection of lactate and glucose by integrated printed circuit board based array sensing chip

Energy Technology Data Exchange (ETDEWEB)

Li, Xuelian [Institute for Clean Energy and Advanced Materials, Southwest University, Chongqing 400715 (China); School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China); Zang, Jianfeng [Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708 (United States); Liu, Yingshuai; Lu, Zhisong [Institute for Clean Energy and Advanced Materials, Southwest University, Chongqing 400715 (China); Li, Qing, E-mail: Qli@swu.edu.cn [School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China); Li, Chang Ming, E-mail: ecmli@swu.edu.cn [Institute for Clean Energy and Advanced Materials, Southwest University, Chongqing 400715 (China)

2013-04-10

Highlights: ► An integrated printed circuit board (PCB) based array sensing chip was developed. ► Simultaneous detection of lactate and glucose in serum has been demonstrated. ► The array electronic biochip has high signal to noise ratio and high sensitivity. ► Additional electrodes were designed on the chip to correct interferences. -- Abstract: An integrated printed circuit board (PCB) based array sensing chip was developed to simultaneously detect lactate and glucose in mouse serum. The novelty of the chip relies on a concept demonstration of inexpensive high-throughput electronic biochip, a chip design for high signal to noise ratio and high sensitivity by construction of positively charged chitosan/redox polymer Polyvinylimidazole-Os (PVI-Os)/carbon nanotube (CNT) composite sensing platform, in which the positively charged chitosan/PVI-Os is mediator and electrostatically immobilizes the negatively charged enzyme, while CNTs function as an essential cross-linker to network PVI-Os and chitosan due to its negative charged nature. Additional electrodes on the chip with the same sensing layer but without enzymes were prepared to correct the interferences for high specificity. Low detection limits of 0.6 μM and 5 μM were achieved for lactate and glucose, respectively. This work could be extended to inexpensive array sensing chips with high sensitivity, good specificity and high reproducibility for various sensor applications.
Experiment list: SRX100473 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available SRX100473 hg19 TFs and others SIN3A Pluripotent stem cell hESC H1 NA 48520029,77.7,11.0,14690 GSM803428: Hud...sonAlpha ChipSeq H1-hESC Sin3Ak-20 PCR1x source_name=H1-hESC || biomaterial_provide

Experiment list: SRX524970 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available SRX524970 hg19 Input control Input control Uterus Endometrial stromal cells NA 3525...5109,88.2,37.7,339 GSM1372862: Input case1 control; Homo sapiens; ChIP-Seq source_name=Human endometrial stromal cells || tissue=Endo...metrial stromal cells || condition=control (without any induction) || chip antibody
Experiment list: SRX524980 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available SRX524980 hg19 Input control Input control Uterus Endometrial stromal cells NA 2708...7271,98.6,31.8,308 GSM1372876: Input case2 control; Homo sapiens; ChIP-Seq source_name=Human endometrial stromal cells || tissue=Endo...metrial stromal cells || condition=control (without any induction) || chip antibody
Experiment list: SRX192270 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available produced at one birth by a viviparous animal. 29213160,79.3,3.6,131 GSM1016439: C H3K27me3 vehicle donor5; ...Mus musculus; ChIP-Seq source_name=whole liver extract || age=29-32 days || chip antibody=H3K27me3 || treament=vehicle
Experiment list: SRX192271 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available produced at one birth by a viviparous animal. 29600718,81.2,4.5,188 GSM1016440: C H3K27me3 vehicle donor10;... Mus musculus; ChIP-Seq source_name=whole liver extract || age=29-32 days || chip antibody=H3K27me3 || treament=vehicle
Probabilistic peak detection for first-order chromatographic data

NARCIS (Netherlands)

Lopatka, M.; Vivó-Truyols, G.; Sjerps, M.J.

2014-01-01

We present a novel algorithm for probabilistic peak detection in first-order chromatographic data. Unlike conventional methods that deliver a binary answer pertaining to the expected presence or absence of a chromatographic peak, our method calculates the probability of a point being affected by
A volumetric meter chip for point-of-care quantitative detection of bovine catalase for food safety control.

Science.gov (United States)

Cui, Xingye; Hu, Jie; Choi, Jane Ru; Huang, Yalin; Wang, Xuemin; Lu, Tian Jian; Xu, Feng

2016-09-07

A volumetric meter chip was developed for quantitative point-of-care (POC) analysis of bovine catalase, a bioindicator of bovine mastitis, in milk samples. The meter chip displays multiplexed quantitative results by presenting the distance of ink bar advancement that is detectable by the naked eye. The meter chip comprises a poly(methyl methacrylate) (PMMA) layer, a double-sided adhesive (DSA) layer and a glass slide layer fabricated by the laser-etching method, which is typically simple, rapid (∼3 min per chip), and cost effective (∼$0.2 per chip). Specially designed "U shape" reaction cells are covered by an adhesive tape that serves as an on-off switch, enabling the simple operation of the assay. As a proof of concept, we employed the developed meter chip for the quantification of bovine catalase in raw milk samples to detect catalase concentrations as low as 20 μg/mL. The meter chip has great potential to detect various target analytes for a wide range of POC applications. Copyright © 2016 Elsevier B.V. All rights reserved.
Immuno-capture and in situ detection of Salmonella typhimurium on a novel microfluidic chip

Energy Technology Data Exchange (ETDEWEB)

Wang, Renjie, E-mail: 1058464972@qq.com [College of Chemistry and Chemical Engineering, Chongqing University, No. 174, St. Shazheng, Shapingba District, Chongqing (China); Ni, Yanan, E-mail: 468885029@qq.com [College of Chemistry and Chemical Engineering, Chongqing University, No. 174, St. Shazheng, Shapingba District, Chongqing (China); Xu, Yi, E-mail: xuyibbd@sina.com [College of Chemistry and Chemical Engineering, Chongqing University, No. 174, St. Shazheng, Shapingba District, Chongqing (China); National Center for International Research of Micro/Nano-System and New Material Technology, No. 174, St. Shazhengjie, Shapingba District, Chongqing (China); Key Laboratory of Fundamental Science of Micro/Nano-Device and System Technology for National Defense, Chongqing (China); Jiang, Yan, E-mail: 919865356@qq.com [College of Chemistry and Chemical Engineering, Chongqing University, No. 174, St. Shazheng, Shapingba District, Chongqing (China); Dong, Chunyan, E-mail: 774176325@qq.com [College of Chemistry and Chemical Engineering, Chongqing University, No. 174, St. Shazheng, Shapingba District, Chongqing (China); Chuan, Na, E-mail: 814859441@qq.com [College of Chemistry and Chemical Engineering, Chongqing University, No. 174, St. Shazheng, Shapingba District, Chongqing (China)

2015-01-01

Highlights: • A novel microfluidic chip and a LIF microsystem were designed and fabricated. • Salmonella typhimurium was captured and labeled by specific immuno-capture on chip. • CdSe/ZnS quantum dots-labeled bacteria were detected by in situ analysis using LIF microsystem. • The proposed method has potential application in practice. - Abstract: The new method presented in this article achieved the goal of capturing Salmonella typhimurium via immunoreaction and rapid in situ detection of the CdSe/ZnS quantum dots (QDs) labeled S. typhimurium by self-assembly light-emitting diode-induced fluorescence detection (LIF) microsystem on a specially designed multichannel microfluidic chip. CdSe/ZnS QDs were used as fluorescent markers improving detection sensitivity. The microfluidic chip developed in this study was composed of 12 sample channels, 3 mixing zones, and 6 immune reaction zones, which also acted as fluorescence detection zones. QDs–IgG–primary antibody complexes were generated by mixing CdSe/ZnS QDs conjugated secondary antibody (QDs–IgG) and S. typhimurium antibody (primary antibody) in mixing zones. Then, the complexes went into immune reaction zones to label previously captured S. typhimurium in the sandwich mode. The capture rate of S. typhimurium in each detection zone was up to 70%. The enriched QDs-labeled S. typhimurium was detected using a self-assembly LIF microsystem. A good linear relationship was obtained in the range from 3.7 × 10 to 3.7 × 10{sup 5} cfu mL{sup −1} using the equation I = 0.1739 log (C) − 0.1889 with R{sup 2} = 0.9907, and the detection limit was down to 37 cfu mL{sup −1}. The proposed method of online immunolabeling with QDs for in situ fluorescence detection on the designed multichannel microfluidic chip had been successfully used to detect S. typhimurium in pork sample, and it has shown potential advantages in practice.
QRS peak detection for heart rate monitoring on Android smartphone

Science.gov (United States)

Pambudi Utomo, Trio; Nuryani, Nuryani; Darmanto

2017-11-01

In this study, Android smartphone is used for heart rate monitoring and displaying electrocardiogram (ECG) graph. Heart rate determination is based on QRS peak detection. Two methods are studied to detect the QRS complex peak; they are Peak Threshold and Peak Filter. The acquisition of ECG data is utilized by AD8232 module from Analog Devices, three electrodes, and Microcontroller Arduino UNO R3. To record the ECG data from a patient, three electrodes are attached to particular body’s surface of a patient. Patient’s heart activity which is recorded by AD8232 module is decoded by Arduino UNO R3 into analog data. Then, the analog data is converted into a voltage value (mV) and is processed to get the QRS complex peak. Heart rate value is calculated by Microcontroller Arduino UNO R3 uses the QRS complex peak. Voltage, heart rate, and the QRS complex peak are sent to Android smartphone by Bluetooth HC-05. ECG data is displayed as the graph by Android smartphone. To evaluate the performance of QRS complex peak detection method, three parameters are used; they are positive predictive, accuracy and sensitivity. Positive predictive, accuracy, and sensitivity of Peak Threshold method is 92.39%, 70.30%, 74.62% and for Peak Filter method are 98.38%, 82.47%, 83.61%, respectively.
A volumetric meter chip for point-of-care quantitative detection of bovine catalase for food safety control

International Nuclear Information System (INIS)

Cui, Xingye; Hu, Jie; Choi, Jane Ru; Huang, Yalin; Wang, Xuemin; Lu, Tian Jian; Xu, Feng

2016-01-01

A volumetric meter chip was developed for quantitative point-of-care (POC) analysis of bovine catalase, a bioindicator of bovine mastitis, in milk samples. The meter chip displays multiplexed quantitative results by presenting the distance of ink bar advancement that is detectable by the naked eye. The meter chip comprises a poly(methyl methacrylate) (PMMA) layer, a double-sided adhesive (DSA) layer and a glass slide layer fabricated by the laser-etching method, which is typically simple, rapid (∼3 min per chip), and cost effective (∼$0.2 per chip). Specially designed “U shape” reaction cells are covered by an adhesive tape that serves as an on-off switch, enabling the simple operation of the assay. As a proof of concept, we employed the developed meter chip for the quantification of bovine catalase in raw milk samples to detect catalase concentrations as low as 20 μg/mL. The meter chip has great potential to detect various target analytes for a wide range of POC applications. - Highlights: • The meter chip is a standalone point-of-care diagnostic tool with visible readouts of quantification results. • A fast and low cost fabrication protocol (~3 min and ~$0.2 per chip) of meter chip was proposed. • The chip may hold the potential for rapid scaning of bovine mastitis in cattle farms for food safety control.
A volumetric meter chip for point-of-care quantitative detection of bovine catalase for food safety control

Energy Technology Data Exchange (ETDEWEB)

Cui, Xingye; Hu, Jie; Choi, Jane Ru; Huang, Yalin; Wang, Xuemin [The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi' an Jiaotong University, Xi' an, 710049 (China); Bioinspired Engineering and Biomechanics Center (BEBC), Xi' an Jiaotong University, Xi' an, 710049 (China); Lu, Tian Jian, E-mail: tjlu@mail.xjtu.edu.cn [Bioinspired Engineering and Biomechanics Center (BEBC), Xi' an Jiaotong University, Xi' an, 710049 (China); Xu, Feng, E-mail: fengxu@mail.xjtu.edu.cn [The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi' an Jiaotong University, Xi' an, 710049 (China); Bioinspired Engineering and Biomechanics Center (BEBC), Xi' an Jiaotong University, Xi' an, 710049 (China)

2016-09-07

A volumetric meter chip was developed for quantitative point-of-care (POC) analysis of bovine catalase, a bioindicator of bovine mastitis, in milk samples. The meter chip displays multiplexed quantitative results by presenting the distance of ink bar advancement that is detectable by the naked eye. The meter chip comprises a poly(methyl methacrylate) (PMMA) layer, a double-sided adhesive (DSA) layer and a glass slide layer fabricated by the laser-etching method, which is typically simple, rapid (∼3 min per chip), and cost effective (∼$0.2 per chip). Specially designed “U shape” reaction cells are covered by an adhesive tape that serves as an on-off switch, enabling the simple operation of the assay. As a proof of concept, we employed the developed meter chip for the quantification of bovine catalase in raw milk samples to detect catalase concentrations as low as 20 μg/mL. The meter chip has great potential to detect various target analytes for a wide range of POC applications. - Highlights: • The meter chip is a standalone point-of-care diagnostic tool with visible readouts of quantification results. • A fast and low cost fabrication protocol (~3 min and ~$0.2 per chip) of meter chip was proposed. • The chip may hold the potential for rapid scaning of bovine mastitis in cattle farms for food safety control.
Comparative analysis of peak-detection techniques for comprehensive two-dimensional chromatography.

Science.gov (United States)

Latha, Indu; Reichenbach, Stephen E; Tao, Qingping

2011-09-23

Comprehensive two-dimensional gas chromatography (GC×GC) is a powerful technology for separating complex samples. The typical goal of GC×GC peak detection is to aggregate data points of analyte peaks based on their retention times and intensities. Two techniques commonly used for two-dimensional peak detection are the two-step algorithm and the watershed algorithm. A recent study [4] compared the performance of the two-step and watershed algorithms for GC×GC data with retention-time shifts in the second-column separations. In that analysis, the peak retention-time shifts were corrected while applying the two-step algorithm but the watershed algorithm was applied without shift correction. The results indicated that the watershed algorithm has a higher probability of erroneously splitting a single two-dimensional peak than the two-step approach. This paper reconsiders the analysis by comparing peak-detection performance for resolved peaks after correcting retention-time shifts for both the two-step and watershed algorithms. Simulations with wide-ranging conditions indicate that when shift correction is employed with both algorithms, the watershed algorithm detects resolved peaks with greater accuracy than the two-step method. Copyright © 2011 Elsevier B.V. All rights reserved.
Experiment list: SRX192263 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available produced at one birth by a viviparous animal. 19707029,78.6,5.0,577 GSM1016432: B H3K4me2 vehicle donor7; Mu...s musculus; ChIP-Seq source_name=whole liver extract || age=29-32 days || chip antibody=H3K4me2 || treament=vehicle
Experiment list: SRX192262 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available produced at one birth by a viviparous animal. 13178340,75.6,7.8,715 GSM1016431: B H3K4me2 vehicle donor1; Mu...s musculus; ChIP-Seq source_name=whole liver extract || age=29-32 days || chip antibody=H3K4me2 || treament=vehicle
Experiment list: SRX192250 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available produced at one birth by a viviparous animal. 98336587,96.8,24.1,627 GSM1016419: A H3K36me3 vehicle donor10...24; Mus musculus; ChIP-Seq source_name=whole liver extract || age=29-32 days || chip antibody=H3K36me3 || treament=vehicle
Experiment list: SRX192257 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available produced at one birth by a viviparous animal. 73877067,96.7,23.5,560 GSM1016426: A H3K36me3 vehicle donor10...21; Mus musculus; ChIP-Seq source_name=whole liver extract || age=29-32 days || chip antibody=H3K36me3 || treament=vehicle
Experiment list: SRX190205 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available labexpid=SL7110,SL8075 || softwareversion=MACS || cell sex=M || antibody=NRSF ||...ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) || controlid=SL6021 || labexpid=SL7110,SL8075 || replicate=1,2 || softw...areversion=MACS http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/eachData/bw/SRX1902
Bayesian Peptide Peak Detection for High Resolution TOF Mass Spectrometry.

Science.gov (United States)

Zhang, Jianqiu; Zhou, Xiaobo; Wang, Honghui; Suffredini, Anthony; Zhang, Lin; Huang, Yufei; Wong, Stephen

2010-11-01

In this paper, we address the issue of peptide ion peak detection for high resolution time-of-flight (TOF) mass spectrometry (MS) data. A novel Bayesian peptide ion peak detection method is proposed for TOF data with resolution of 10 000-15 000 full width at half-maximum (FWHW). MS spectra exhibit distinct characteristics at this resolution, which are captured in a novel parametric model. Based on the proposed parametric model, a Bayesian peak detection algorithm based on Markov chain Monte Carlo (MCMC) sampling is developed. The proposed algorithm is tested on both simulated and real datasets. The results show a significant improvement in detection performance over a commonly employed method. The results also agree with expert's visual inspection. Moreover, better detection consistency is achieved across MS datasets from patients with identical pathological condition.
Experiment list: SRX1056357 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available || cell type=ES cells || treated with=2.5 µM tamoxifen (Tam) || chip antibody=none http://dbarchive.bioscien...tiate into specialized cells. 35337197,98.9,19.2,224 GSM1708671: input DNA +Tam R...2; Mus musculus; ChIP-Seq source_name=input DNA_+Tam || strain=J1 || genotype/variation=inducible SetDB1 KO
Experiment list: SRX026424 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available SRX026424 mm9 RNA polymerase RNA Polymerase II Neural Cerebellum MeSH Description=T..., maintain balance, and learn motor skills. 15567107,93.1,10.8,650 GSM587797: P5 Cerebellum RNAP-II ChIP-Seq... source_name=PostNatal-Day5_Cerebellum || strain=CD1 || age=postnatal day 5 || tissue=cerebellum || chip-ant
Multiplexed ChIP-Seq Using Direct Nucleosome Barcoding: A Tool for High-Throughput Chromatin Analysis.

Science.gov (United States)

Chabbert, Christophe D; Adjalley, Sophie H; Steinmetz, Lars M; Pelechano, Vicent

2018-01-01

Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) or microarray hybridization (ChIP-on-chip) are standard methods for the study of transcription factor binding sites and histone chemical modifications. However, these approaches only allow profiling of a single factor or protein modification at a time.In this chapter, we present Bar-ChIP, a higher throughput version of ChIP-Seq that relies on the direct ligation of molecular barcodes to chromatin fragments. Bar-ChIP enables the concurrent profiling of multiple DNA-protein interactions and is therefore amenable to experimental scale-up, without the need for any robotic instrumentation.

On-Chip Magnetic Bead Manipulation and Detection Using a Magnetoresistive Sensor-Based Micro-Chip: Design Considerations and Experimental Characterization

KAUST Repository

Gooneratne, Chinthaka Pasan; Kodzius, Rimantas; Li, Fuquan; Foulds, Ian G.; Kosel, Jü rgen

2016-01-01

The remarkable advantages micro-chip platforms offer over cumbersome, time-consuming equipment currently in use for bio-analysis are well documented. In this research, a micro-chip that includes a unique magnetic actuator (MA) for the manipulation of superparamagnetic beads (SPBs), and a magnetoresistive sensor for the detection of SPBs is presented. A design methodology, which takes into account the magnetic volume of SPBs, diffusion and heat transfer phenomena, is presented with the aid of numerical analysis to optimize the parameters of the MA. The MA was employed as a magnetic flux generator and experimental analysis with commercially available COMPEL™ and Dynabeads® demonstrated the ability of the MA to precisely transport a small number of SPBs over long distances and concentrate SPBs to a sensing site for detection. Moreover, the velocities of COMPEL™ and Dynabead® SPBs were correlated to their magnetic volumes and were in good agreement with numerical model predictions. We found that 2.8 μm Dynabeads® travel faster, and can be attracted to a magnetic source from a longer distance, than 6.2 μm COMPEL™ beads at magnetic flux magnitudes of less than 10 mT. The micro-chip system could easily be integrated with electronic circuitry and microfluidic functions, paving the way for an on-chip biomolecule quantification device
On-Chip Magnetic Bead Manipulation and Detection Using a Magnetoresistive Sensor-Based Micro-Chip: Design Considerations and Experimental Characterization

KAUST Repository

Gooneratne, Chinthaka Pasan

2016-08-26

The remarkable advantages micro-chip platforms offer over cumbersome, time-consuming equipment currently in use for bio-analysis are well documented. In this research, a micro-chip that includes a unique magnetic actuator (MA) for the manipulation of superparamagnetic beads (SPBs), and a magnetoresistive sensor for the detection of SPBs is presented. A design methodology, which takes into account the magnetic volume of SPBs, diffusion and heat transfer phenomena, is presented with the aid of numerical analysis to optimize the parameters of the MA. The MA was employed as a magnetic flux generator and experimental analysis with commercially available COMPEL™ and Dynabeads® demonstrated the ability of the MA to precisely transport a small number of SPBs over long distances and concentrate SPBs to a sensing site for detection. Moreover, the velocities of COMPEL™ and Dynabead® SPBs were correlated to their magnetic volumes and were in good agreement with numerical model predictions. We found that 2.8 μm Dynabeads® travel faster, and can be attracted to a magnetic source from a longer distance, than 6.2 μm COMPEL™ beads at magnetic flux magnitudes of less than 10 mT. The micro-chip system could easily be integrated with electronic circuitry and microfluidic functions, paving the way for an on-chip biomolecule quantification device
On-Chip Magnetic Bead Manipulation and Detection Using a Magnetoresistive Sensor-Based Micro-Chip: Design Considerations and Experimental Characterization

Directory of Open Access Journals (Sweden)

Chinthaka P. Gooneratne

2016-08-01

Full Text Available The remarkable advantages micro-chip platforms offer over cumbersome, time-consuming equipment currently in use for bio-analysis are well documented. In this research, a micro-chip that includes a unique magnetic actuator (MA for the manipulation of superparamagnetic beads (SPBs, and a magnetoresistive sensor for the detection of SPBs is presented. A design methodology, which takes into account the magnetic volume of SPBs, diffusion and heat transfer phenomena, is presented with the aid of numerical analysis to optimize the parameters of the MA. The MA was employed as a magnetic flux generator and experimental analysis with commercially available COMPEL™ and Dynabeads® demonstrated the ability of the MA to precisely transport a small number of SPBs over long distances and concentrate SPBs to a sensing site for detection. Moreover, the velocities of COMPEL™ and Dynabead® SPBs were correlated to their magnetic volumes and were in good agreement with numerical model predictions. We found that 2.8 μm Dynabeads® travel faster, and can be attracted to a magnetic source from a longer distance, than 6.2 μm COMPEL™ beads at magnetic flux magnitudes of less than 10 mT. The micro-chip system could easily be integrated with electronic circuitry and microfluidic functions, paving the way for an on-chip biomolecule quantification device.
Integrated three-dimensional optical MEMS for chip-based fluorescence detection

Science.gov (United States)

Hung, Kuo-Yung; Tseng, Fan-Gang; Khoo, Hwa-Seng

2009-04-01

This paper presents a novel fluorescence sensing chip for parallel protein microarray detection in the context of a 3-in-1 protein chip system. This portable microchip consists of a monolithic integration of CMOS-based avalanche photo diodes (APDs) combined with a polymer micro-lens, a set of three-dimensional (3D) inclined mirrors for separating adjacent light signals and a low-noise transformer-free dc-dc boost mini-circuit to power the APDs (ripple below 1.28 mV, 0-5 V input, 142 V and 12 mA output). We fabricated our APDs using the planar CMOS process so as to facilitate the post-CMOS integration of optical MEMS components such as the lenses. The APD arrays were arranged in unique circular patterns appropriate for detecting the specific fluorescently labelled protein spots in our study. The array-type APDs were designed so as to compensate for any alignment error as detected by a positional error signal algorithm. The condenser lens was used as a structure for light collection to enhance the fluorescent signals by about 25%. This element also helped to reduce the light loss due to surface absorption. We fabricated an inclined mirror to separate two adjacent fluorescent signals from different specimens. Excitation using evanescent waves helped reduce the interference of the excitation light source. This approach also reduced the number of required optical lenses and minimized the complexity of the structural design. We achieved detection floors for anti-rabbit IgG and Cy5 fluorescent dye as low as 0.5 ng/µl (~3.268 nM). We argue that the intrinsic nature of point-to-point and batch-detection methods as showcased in our chip offers advantages over the serial-scanning approach used in traditional scanner systems. In addition, our system is low cost and lightweight.
Experiment list: SRX886445 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available hIP-Seq source_name=Colorectal adenocarcinoma cells || cell line=Caco2 || antibody=FOXA2 (Santa-Cruz sc-6554...) || style parameter used for peak calling=factor || input used for peak calling=Caco2
Experiment list: SRX886446 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available hIP-Seq source_name=Colorectal adenocarcinoma cells || cell line=Caco2 || antibody=FOXA2 (Santa-Cruz sc-6554...) || style parameter used for peak calling=factor || input used for peak calling=Caco2
From benchmarking HITS-CLIP peak detection programs to a new method for identification of miRNA-binding sites from Ago2-CLIP data.

Science.gov (United States)

Bottini, Silvia; Hamouda-Tekaya, Nedra; Tanasa, Bogdan; Zaragosi, Laure-Emmanuelle; Grandjean, Valerie; Repetto, Emanuela; Trabucchi, Michele

2017-05-19

Experimental evidence indicates that about 60% of miRNA-binding activity does not follow the canonical rule about the seed matching between miRNA and target mRNAs, but rather a non-canonical miRNA targeting activity outside the seed or with a seed-like motifs. Here, we propose a new unbiased method to identify canonical and non-canonical miRNA-binding sites from peaks identified by Ago2 Cross-Linked ImmunoPrecipitation associated to high-throughput sequencing (CLIP-seq). Since the quality of peaks is of pivotal importance for the final output of the proposed method, we provide a comprehensive benchmarking of four peak detection programs, namely CIMS, PIPE-CLIP, Piranha and Pyicoclip, on four publicly available Ago2-HITS-CLIP datasets and one unpublished in-house Ago2-dataset in stem cells. We measured the sensitivity, the specificity and the position accuracy toward miRNA binding sites identification, and the agreement with TargetScan. Secondly, we developed a new pipeline, called miRBShunter, to identify canonical and non-canonical miRNA-binding sites based on de novo motif identification from Ago2 peaks and prediction of miRNA::RNA heteroduplexes. miRBShunter was tested and experimentally validated on the in-house Ago2-dataset and on an Ago2-PAR-CLIP dataset in human stem cells. Overall, we provide guidelines to choose a suitable peak detection program and a new method for miRNA-target identification. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.
A Miniaturized On-Chip Colorimeter for Detecting NPK Elements

OpenAIRE

Liu, Rui-Tao; Tao, Lu-Qi; Liu, Bo; Tian, Xiang-Guang; Mohammad, Mohammad Ali; Yang, Yi; Ren, Tian-Ling

2016-01-01

Recently, precision agriculture has become a globally attractive topic. As one of the most important factors, the soil nutrients play an important role in estimating the development of precision agriculture. Detecting the content of nitrogen, phosphorus and potassium (NPK) elements more efficiently is one of the key issues. In this paper, a novel chip-level colorimeter was fabricated to detect the NPK elements for the first time. A light source–microchannel photodetector in a sandwich structu...
Adaptive Fourier decomposition based R-peak detection for noisy ECG Signals.

Science.gov (United States)

Ze Wang; Chi Man Wong; Feng Wan

2017-07-01

An adaptive Fourier decomposition (AFD) based R-peak detection method is proposed for noisy ECG signals. Although lots of QRS detection methods have been proposed in literature, most detection methods require high signal quality. The proposed method extracts the R waves from the energy domain using the AFD and determines the R-peak locations based on the key decomposition parameters, achieving the denoising and the R-peak detection at the same time. Validated by clinical ECG signals in the MIT-BIH Arrhythmia Database, the proposed method shows better performance than the Pan-Tompkin (PT) algorithm in both situations of a native PT and the PT with a denoising process.
R Peak Detection Method Using Wavelet Transform and Modified Shannon Energy Envelope.

Science.gov (United States)

Park, Jeong-Seon; Lee, Sang-Woong; Park, Unsang

2017-01-01

Rapid automatic detection of the fiducial points-namely, the P wave, QRS complex, and T wave-is necessary for early detection of cardiovascular diseases (CVDs). In this paper, we present an R peak detection method using the wavelet transform (WT) and a modified Shannon energy envelope (SEE) for rapid ECG analysis. The proposed WTSEE algorithm performs a wavelet transform to reduce the size and noise of ECG signals and creates SEE after first-order differentiation and amplitude normalization. Subsequently, the peak energy envelope (PEE) is extracted from the SEE. Then, R peaks are estimated from the PEE, and the estimated peaks are adjusted from the input ECG. Finally, the algorithm generates the final R features by validating R-R intervals and updating the extracted R peaks. The proposed R peak detection method was validated using 48 first-channel ECG records of the MIT-BIH arrhythmia database with a sensitivity of 99.93%, positive predictability of 99.91%, detection error rate of 0.16%, and accuracy of 99.84%. Considering the high detection accuracy and fast processing speed due to the wavelet transform applied before calculating SEE, the proposed method is highly effective for real-time applications in early detection of CVDs.
A nanofluidic bioarray chip for fast and high-throughput detection of antibodies in biological fluids

Science.gov (United States)

Lee, Jonathan; Gulzar, Naveed; Scott, Jamie K.; Li, Paul C. H.

2012-10-01

Immunoassays have become a standard in secretome analysis in clinical and research analysis. In this field there is a need for a high throughput method that uses low sample volumes. Microfluidics and nanofluidics have been developed for this purpose. Our lab has developed a nanofluidic bioarray (NBA) chip with the goal being a high throughput system that assays low sample volumes against multiple probes. A combination of horizontal and vertical channels are produced to create an array antigens on the surface of the NBA chip in one dimension that is probed by flowing in the other dimension antibodies from biological fluids. We have tested the NBA chip by immobilizing streptavidin and then biotinylated peptide to detect the presence of a mouse monoclonal antibody (MAb) that is specific for the peptide. Bound antibody is detected by an AlexaFluor 647 labeled goat (anti-mouse IgG) polyclonal antibody. Using the NBA chip, we have successfully detected peptide binding by small-volume (0.5 μl) samples containing 50 attomoles (100 pM) MAb.
A prototype pixel readout chip for asynchronous detection applications

International Nuclear Information System (INIS)

Raymond, D.M.; Hall, G.; Lewis, A.J.; Sharp, P.H.

1991-01-01

A two-dimensional array of amplifier cells has been fabricated as a prototype readout system for a matching array of silicon diode detectors. Each cell contains a preamplifier, shaping amplifier, comparator and analogue signal storage in an area of 300 μmx320 μm using 3 μm CMOS technology. Full size chips will be bump bonded to pixel detector arrays. Low noise and asynchronous operation are novel design features. With noise levels of less than 250 rms electrons for input capacitances up to 600 fF, pixel detectors will be suitable for autoradiography, synchrotron X-ray and high energy particle detection applications. The design of the prototype chip is presented and future developments and prospects for applications are discussed. (orig.)
Chip-Oriented Fluorimeter Design and Detection System Development for DNA Quantification in Nano-Liter Volumes

Directory of Open Access Journals (Sweden)

Da-Sheng Lee

2009-12-01

Full Text Available The chip-based polymerase chain reaction (PCR system has been developed in recent years to achieve DNA quantification. Using a microstructure and miniature chip, the volume consumption for a PCR can be reduced to a nano-liter. With high speed cycling and a low reaction volume, the time consumption of one PCR cycle performed on a chip can be reduced. However, most of the presented prototypes employ commercial fluorimeters which are not optimized for fluorescence detection of such a small quantity sample. This limits the performance of DNA quantification, especially low experiment reproducibility. This study discusses the concept of a chip-oriented fluorimeter design. Using the analytical model, the current study analyzes the sensitivity and dynamic range of the fluorimeter to fit the requirements for detecting fluorescence in nano-liter volumes. Through the optimized processes, a real-time PCR on a chip system with only one nano-liter volume test sample is as sensitive as the commercial real-time PCR machine using the sample with twenty micro-liter volumes. The signal to noise (S/N ratio of a chip system for DNA quantification with hepatitis B virus (HBV plasmid samples is 3 dB higher. DNA quantification by the miniature chip shows higher reproducibility compared to the commercial machine with respect to samples of initial concentrations from 103 to 105 copies per reaction.
Recent Developments in Optical Detection Technologies in Lab-on-a-Chip Devices for Biosensing Applications

Directory of Open Access Journals (Sweden)

Nuno Miguel Matos Pires

2014-08-01

Full Text Available The field of microfluidics has yet to develop practical devices that provide real clinical value. One of the main reasons for this is the difficulty in realizing low-cost, sensitive, reproducible, and portable analyte detection microfluidic systems. Previous research has addressed two main approaches for the detection technologies in lab-on-a-chip devices: (a study of the compatibility of conventional instrumentation with microfluidic structures, and (b integration of innovative sensors contained within the microfluidic system. Despite the recent advances in electrochemical and mechanical based sensors, their drawbacks pose important challenges to their application in disposable microfluidic devices. Instead, optical detection remains an attractive solution for lab-on-a-chip devices, because of the ubiquity of the optical methods in the laboratory. Besides, robust and cost-effective devices for use in the field can be realized by integrating proper optical detection technologies on chips. This review examines the recent developments in detection technologies applied to microfluidic biosensors, especially addressing several optical methods, including fluorescence, chemiluminescence, absorbance and surface plasmon resonance.
Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching.

Science.gov (United States)

Du, Pan; Kibbe, Warren A; Lin, Simon M

2006-09-01

A major problem for current peak detection algorithms is that noise in mass spectrometry (MS) spectra gives rise to a high rate of false positives. The false positive rate is especially problematic in detecting peaks with low amplitudes. Usually, various baseline correction algorithms and smoothing methods are applied before attempting peak detection. This approach is very sensitive to the amount of smoothing and aggressiveness of the baseline correction, which contribute to making peak detection results inconsistent between runs, instrumentation and analysis methods. Most peak detection algorithms simply identify peaks based on amplitude, ignoring the additional information present in the shape of the peaks in a spectrum. In our experience, 'true' peaks have characteristic shapes, and providing a shape-matching function that provides a 'goodness of fit' coefficient should provide a more robust peak identification method. Based on these observations, a continuous wavelet transform (CWT)-based peak detection algorithm has been devised that identifies peaks with different scales and amplitudes. By transforming the spectrum into wavelet space, the pattern-matching problem is simplified and in addition provides a powerful technique for identifying and separating the signal from the spike noise and colored noise. This transformation, with the additional information provided by the 2D CWT coefficients can greatly enhance the effective signal-to-noise ratio. Furthermore, with this technique no baseline removal or peak smoothing preprocessing steps are required before peak detection, and this improves the robustness of peak detection under a variety of conditions. The algorithm was evaluated with SELDI-TOF spectra with known polypeptide positions. Comparisons with two other popular algorithms were performed. The results show the CWT-based algorithm can identify both strong and weak peaks while keeping false positive rate low. The algorithm is implemented in R and will be
Screening DNA chip and event-specific multiplex PCR detection methods for biotech crops.

Science.gov (United States)

Lee, Seong-Hun

2014-11-01

There are about 80 biotech crop events that have been approved by safety assessment in Korea. They have been controlled by genetically modified organism (GMO) and living modified organism (LMO) labeling systems. The DNA-based detection method has been used as an efficient scientific management tool. Recently, the multiplex polymerase chain reaction (PCR) and DNA chip have been developed as simultaneous detection methods for several biotech crops' events. The event-specific multiplex PCR method was developed to detect five biotech maize events: MIR604, Event 3272, LY 038, MON 88017 and DAS-59122-7. The specificity was confirmed and the sensitivity was 0.5%. The screening DNA chip was developed from four endogenous genes of soybean, maize, cotton and canola respectively along with two regulatory elements and seven genes: P35S, tNOS, pat, bar, epsps1, epsps2, pmi, cry1Ac and cry3B. The specificity was confirmed and the sensitivity was 0.5% for four crops' 12 events: one soybean, six maize, three cotton and two canola events. The multiplex PCR and DNA chip can be available for screening, gene-specific and event-specific analysis of biotech crops as efficient detection methods by saving on workload and time. © 2014 Society of Chemical Industry. © 2014 Society of Chemical Industry.
Lab-on-a-chip for rapid electrochemical detection of nerve agent Sarin

DEFF Research Database (Denmark)

Tan, Hsih-Yin; Loke, Weng Keong; Nguyen, Nam-Trung

2014-01-01

This paper reports a lab-on-a-chip for the detection of Sarin nerve agent based on rapid electrochemical detection. The chemical warfare agent Sarin (C4H10FO2P, O-isopropyl methylphosphonofluoridate) is a highly toxic organophosphate that induces rapid respiratory depression, seizures and death...
SNP discovery in the bovine milk transcriptome using RNA-Seq technology.

Science.gov (United States)

Cánovas, Angela; Rincon, Gonzalo; Islas-Trejo, Alma; Wickramasinghe, Saumya; Medrano, Juan F

2010-12-01

High-throughput sequencing of RNA (RNA-Seq) was developed primarily to analyze global gene expression in different tissues. However, it also is an efficient way to discover coding SNPs. The objective of this study was to perform a SNP discovery analysis in the milk transcriptome using RNA-Seq. Seven milk samples from Holstein cows were analyzed by sequencing cDNAs using the Illumina Genome Analyzer system. We detected 19,175 genes expressed in milk samples corresponding to approximately 70% of the total number of genes analyzed. The SNP detection analysis revealed 100,734 SNPs in Holstein samples, and a large number of those corresponded to differences between the Holstein breed and the Hereford bovine genome assembly Btau4.0. The number of polymorphic SNPs within Holstein cows was 33,045. The accuracy of RNA-Seq SNP discovery was tested by comparing SNPs detected in a set of 42 candidate genes expressed in milk that had been resequenced earlier using Sanger sequencing technology. Seventy of 86 SNPs were detected using both RNA-Seq and Sanger sequencing technologies. The KASPar Genotyping System was used to validate unique SNPs found by RNA-Seq but not observed by Sanger technology. Our results confirm that analyzing the transcriptome using RNA-Seq technology is an efficient and cost-effective method to identify SNPs in transcribed regions. This study creates guidelines to maximize the accuracy of SNP discovery and prevention of false-positive SNP detection, and provides more than 33,000 SNPs located in coding regions of genes expressed during lactation that can be used to develop genotyping platforms to perform marker-trait association studies in Holstein cattle.
Evaluation of tools for highly variable gene discovery from single-cell RNA-seq data.

Science.gov (United States)

Yip, Shun H; Sham, Pak Chung; Wang, Junwen

2018-02-21

Traditional RNA sequencing (RNA-seq) allows the detection of gene expression variations between two or more cell populations through differentially expressed gene (DEG) analysis. However, genes that contribute to cell-to-cell differences are not discoverable with RNA-seq because RNA-seq samples are obtained from a mixture of cells. Single-cell RNA-seq (scRNA-seq) allows the detection of gene expression in each cell. With scRNA-seq, highly variable gene (HVG) discovery allows the detection of genes that contribute strongly to cell-to-cell variation within a homogeneous cell population, such as a population of embryonic stem cells. This analysis is implemented in many software packages. In this study, we compare seven HVG methods from six software packages, including BASiCS, Brennecke, scLVM, scran, scVEGs and Seurat. Our results demonstrate that reproducibility in HVG analysis requires a larger sample size than DEG analysis. Discrepancies between methods and potential issues in these tools are discussed and recommendations are made.
Peptide Peak Detection for Low Resolution MALDI-TOF Mass Spectrometry.

Science.gov (United States)

Yao, Jingwen; Utsunomiya, Shin-Ichi; Kajihara, Shigeki; Tabata, Tsuyoshi; Aoshima, Ken; Oda, Yoshiya; Tanaka, Koichi

2014-01-01

A new peak detection method has been developed for rapid selection of peptide and its fragment ion peaks for protein identification using tandem mass spectrometry. The algorithm applies classification of peak intensities present in the defined mass range to determine the noise level. A threshold is then given to select ion peaks according to the determined noise level in each mass range. This algorithm was initially designed for the peak detection of low resolution peptide mass spectra, such as matrix-assisted laser desorption/ionization Time-of-Flight (MALDI-TOF) mass spectra. But it can also be applied to other type of mass spectra. This method has demonstrated obtaining a good rate of number of real ions to noises for even poorly fragmented peptide spectra. The effect of using peak lists generated from this method produces improved protein scores in database search results. The reliability of the protein identifications is increased by finding more peptide identifications. This software tool is freely available at the Mass++ home page (http://www.first-ms3d.jp/english/achievement/software/).

An RNA-Seq strategy to detect the complete coding and non-coding transcriptome including full-length imprinted macro ncRNAs.

Directory of Open Access Journals (Sweden)

Ru Huang

Full Text Available Imprinted macro non-protein-coding (nc RNAs are cis-repressor transcripts that silence multiple genes in at least three imprinted gene clusters in the mouse genome. Similar macro or long ncRNAs are abundant in the mammalian genome. Here we present the full coding and non-coding transcriptome of two mouse tissues: differentiated ES cells and fetal head using an optimized RNA-Seq strategy. The data produced is highly reproducible in different sequencing locations and is able to detect the full length of imprinted macro ncRNAs such as Airn and Kcnq1ot1, whose length ranges between 80-118 kb. Transcripts show a more uniform read coverage when RNA is fragmented with RNA hydrolysis compared with cDNA fragmentation by shearing. Irrespective of the fragmentation method, all coding and non-coding transcripts longer than 8 kb show a gradual loss of sequencing tags towards the 3' end. Comparisons to published RNA-Seq datasets show that the strategy presented here is more efficient in detecting known functional imprinted macro ncRNAs and also indicate that standardization of RNA preparation protocols would increase the comparability of the transcriptome between different RNA-Seq datasets.
Sentence‐Chain Based Seq2seq Model for Corpus Expansion

Directory of Open Access Journals (Sweden)

Euisok Chung

2017-08-01

Full Text Available This study focuses on a method for sequential data augmentation in order to alleviate data sparseness problems. Specifically, we present corpus expansion techniques for enhancing the coverage of a language model. Recent recurrent neural network studies show that a seq2seq model can be applied for addressing language generation issues; it has the ability to generate new sentences from given input sentences. We present a method of corpus expansion using a sentence‐chain based seq2seq model. For training the seq2seq model, sentence chains are used as triples. The first two sentences in a triple are used for the encoder of the seq2seq model, while the last sentence becomes a target sequence for the decoder. Using only internal resources, evaluation results show an improvement of approximately 7.6% relative perplexity over a baseline language model of Korean text. Additionally, from a comparison with a previous study, the sentence chain approach reduces the size of the training data by 38.4% while generating 1.4‐times the number of n‐grams with superior performance for English text.
ReliefSeq: a gene-wise adaptive-K nearest-neighbor feature selection tool for finding gene-gene interactions and main effects in mRNA-Seq gene expression data.

Directory of Open Access Journals (Sweden)

Brett A McKinney

Full Text Available Relief-F is a nonparametric, nearest-neighbor machine learning method that has been successfully used to identify relevant variables that may interact in complex multivariate models to explain phenotypic variation. While several tools have been developed for assessing differential expression in sequence-based transcriptomics, the detection of statistical interactions between transcripts has received less attention in the area of RNA-seq analysis. We describe a new extension and assessment of Relief-F for feature selection in RNA-seq data. The ReliefSeq implementation adapts the number of nearest neighbors (k for each gene to optimize the Relief-F test statistics (importance scores for finding both main effects and interactions. We compare this gene-wise adaptive-k (gwak Relief-F method with standard RNA-seq feature selection tools, such as DESeq and edgeR, and with the popular machine learning method Random Forests. We demonstrate performance on a panel of simulated data that have a range of distributional properties reflected in real mRNA-seq data including multiple transcripts with varying sizes of main effects and interaction effects. For simulated main effects, gwak-Relief-F feature selection performs comparably to standard tools DESeq and edgeR for ranking relevant transcripts. For gene-gene interactions, gwak-Relief-F outperforms all comparison methods at ranking relevant genes in all but the highest fold change/highest signal situations where it performs similarly. The gwak-Relief-F algorithm outperforms Random Forests for detecting relevant genes in all simulation experiments. In addition, Relief-F is comparable to the other methods based on computational time. We also apply ReliefSeq to an RNA-Seq study of smallpox vaccine to identify gene expression changes between vaccinia virus-stimulated and unstimulated samples. ReliefSeq is an attractive tool for inclusion in the suite of tools used for analysis of mRNA-Seq data; it has power to
Fully automated pipeline for detection of sex linked genes using RNA-Seq data.

Science.gov (United States)

Michalovova, Monika; Kubat, Zdenek; Hobza, Roman; Vyskot, Boris; Kejnovsky, Eduard

2015-03-11

Sex chromosomes present a genomic region which to some extent, differs between the genders of a single species. Reliable high-throughput methods for detection of sex chromosomes specific markers are needed, especially in species where genome information is limited. Next generation sequencing (NGS) opens the door for identification of unique sequences or searching for nucleotide polymorphisms between datasets. A combination of classical genetic segregation analysis along with RNA-Seq data can present an ideal tool to map and identify sex chromosome-specific expressed markers. To address this challenge, we established genetic cross of dioecious plant Rumex acetosa and generated RNA-Seq data from both parental generation and male and female offspring. We present a pipeline for detection of sex linked genes based on nucleotide polymorphism analysis. In our approach, tracking of nucleotide polymorphisms is carried out using a cross of preferably distant populations. For this reason, only 4 datasets are needed - reads from high-throughput sequencing platforms for parent generation (mother and father) and F1 generation (male and female progeny). Our pipeline uses custom scripts together with external assembly, mapping and variant calling software. Given the resource-intensive nature of the computation, servers with high capacity are a requirement. Therefore, in order to keep this pipeline easily accessible and reproducible, we implemented it in Galaxy - an open, web-based platform for data-intensive biomedical research. Our tools are present in the Galaxy Tool Shed, from which they can be installed to any local Galaxy instance. As an output of the pipeline, user gets a FASTA file with candidate transcriptionally active sex-linked genes, sorted by their relevance. At the same time, a BAM file with identified genes and alignment of reads is also provided. Thus, polymorphisms following segregation pattern can be easily visualized, which significantly enhances primer design
Highly specific detection of genetic modification events using an enzyme-linked probe hybridization chip.

Science.gov (United States)

Zhang, M Z; Zhang, X F; Chen, X M; Chen, X; Wu, S; Xu, L L

2015-08-10

The enzyme-linked probe hybridization chip utilizes a method based on ligase-hybridizing probe chip technology, with the principle of using thio-primers for protection against enzyme digestion, and using lambda DNA exonuclease to cut multiple PCR products obtained from the sample being tested into single-strand chains for hybridization. The 5'-end amino-labeled probe was fixed onto the aldehyde chip, and hybridized with the single-stranded PCR product, followed by addition of a fluorescent-modified probe that was then enzymatically linked with the adjacent, substrate-bound probe in order to achieve highly specific, parallel, and high-throughput detection. Specificity and sensitivity testing demonstrated that enzyme-linked probe hybridization technology could be applied to the specific detection of eight genetic modification events at the same time, with a sensitivity reaching 0.1% and the achievement of accurate, efficient, and stable results.
A 3D Microfluidic Chip for Electrochemical Detection of Hydrolysed Nucleic Bases by a Modified Glassy Carbon Electrode

Directory of Open Access Journals (Sweden)

Jana Vlachova

2015-01-01

Full Text Available Modification of carbon materials, especially graphene-based materials, has wide applications in electrochemical detection such as electrochemical lab-on-chip devices. A glassy carbon electrode (GCE modified with chemically alternated graphene oxide was used as a working electrode (glassy carbon modified by graphene oxide with sulphur containing compounds and Nafion for detection of nucleobases in hydrolysed samples (HCl pH = 2.9, 100 °C, 1 h, neutralization by NaOH. It was found out that modification, especially with trithiocyanuric acid, increased the sensitivity of detection in comparison with pure GCE. All processes were finally implemented in a microfluidic chip formed with a 3D printer by fused deposition modelling technology. As a material for chip fabrication, acrylonitrile butadiene styrene was chosen because of its mechanical and chemical stability. The chip contained the one chamber for the hydrolysis of the nucleic acid and another for the electrochemical detection by the modified GCE. This chamber was fabricated to allow for replacement of the GCE.
A 3D microfluidic chip for electrochemical detection of hydrolysed nucleic bases by a modified glassy carbon electrode.

Science.gov (United States)

Vlachova, Jana; Tmejova, Katerina; Kopel, Pavel; Korabik, Maria; Zitka, Jan; Hynek, David; Kynicky, Jindrich; Adam, Vojtech; Kizek, Rene

2015-01-22

Modification of carbon materials, especially graphene-based materials, has wide applications in electrochemical detection such as electrochemical lab-on-chip devices. A glassy carbon electrode (GCE) modified with chemically alternated graphene oxide was used as a working electrode (glassy carbon modified by graphene oxide with sulphur containing compounds and Nafion) for detection of nucleobases in hydrolysed samples (HCl pH = 2.9, 100 °C, 1 h, neutralization by NaOH). It was found out that modification, especially with trithiocyanuric acid, increased the sensitivity of detection in comparison with pure GCE. All processes were finally implemented in a microfluidic chip formed with a 3D printer by fused deposition modelling technology. As a material for chip fabrication, acrylonitrile butadiene styrene was chosen because of its mechanical and chemical stability. The chip contained the one chamber for the hydrolysis of the nucleic acid and another for the electrochemical detection by the modified GCE. This chamber was fabricated to allow for replacement of the GCE.
ToNER: A tool for identifying nucleotide enrichment signals in feature-enriched RNA-seq data.

Directory of Open Access Journals (Sweden)

Yuttachon Promworn

Full Text Available Biochemical methods are available for enriching 5' ends of RNAs in prokaryotes, which are employed in the differential RNA-seq (dRNA-seq and the more recent Cappable-seq protocols. Computational methods are needed to locate RNA 5' ends from these data by statistical analysis of the enrichment. Although statistical-based analysis methods have been developed for dRNA-seq, they may not be suitable for Cappable-seq data. The more efficient enrichment method employed in Cappable-seq compared with dRNA-seq could affect data distribution and thus algorithm performance.We present Transformation of Nucleotide Enrichment Ratios (ToNER, a tool for statistical modeling of enrichment from RNA-seq data obtained from enriched and unenriched libraries. The tool calculates nucleotide enrichment scores and determines the global transformation for fitting to the normal distribution using the Box-Cox procedure. From the transformed distribution, sites of significant enrichment are identified. To increase power of detection, meta-analysis across experimental replicates is offered. We tested the tool on Cappable-seq and dRNA-seq data for identifying Escherichia coli transcript 5' ends and compared the results with those from the TSSAR tool, which is designed for analyzing dRNA-seq data. When combining results across Cappable-seq replicates, ToNER detects more known transcript 5' ends than TSSAR. In general, the transcript 5' ends detected by ToNER but not TSSAR occur in regions which cannot be locally modeled by TSSAR.ToNER uses a simple yet robust statistical modeling approach, which can be used for detecting RNA 5'ends from Cappable-seq data, in particular when combining information from experimental replicates. The ToNER tool could potentially be applied for analyzing other RNA-seq datasets in which enrichment for other structural features of RNA is employed. The program is freely available for download at ToNER webpage (http://www4a
ToNER: A tool for identifying nucleotide enrichment signals in feature-enriched RNA-seq data.

Science.gov (United States)

Promworn, Yuttachon; Kaewprommal, Pavita; Shaw, Philip J; Intarapanich, Apichart; Tongsima, Sissades; Piriyapongsa, Jittima

2017-01-01

Biochemical methods are available for enriching 5' ends of RNAs in prokaryotes, which are employed in the differential RNA-seq (dRNA-seq) and the more recent Cappable-seq protocols. Computational methods are needed to locate RNA 5' ends from these data by statistical analysis of the enrichment. Although statistical-based analysis methods have been developed for dRNA-seq, they may not be suitable for Cappable-seq data. The more efficient enrichment method employed in Cappable-seq compared with dRNA-seq could affect data distribution and thus algorithm performance. We present Transformation of Nucleotide Enrichment Ratios (ToNER), a tool for statistical modeling of enrichment from RNA-seq data obtained from enriched and unenriched libraries. The tool calculates nucleotide enrichment scores and determines the global transformation for fitting to the normal distribution using the Box-Cox procedure. From the transformed distribution, sites of significant enrichment are identified. To increase power of detection, meta-analysis across experimental replicates is offered. We tested the tool on Cappable-seq and dRNA-seq data for identifying Escherichia coli transcript 5' ends and compared the results with those from the TSSAR tool, which is designed for analyzing dRNA-seq data. When combining results across Cappable-seq replicates, ToNER detects more known transcript 5' ends than TSSAR. In general, the transcript 5' ends detected by ToNER but not TSSAR occur in regions which cannot be locally modeled by TSSAR. ToNER uses a simple yet robust statistical modeling approach, which can be used for detecting RNA 5'ends from Cappable-seq data, in particular when combining information from experimental replicates. The ToNER tool could potentially be applied for analyzing other RNA-seq datasets in which enrichment for other structural features of RNA is employed. The program is freely available for download at ToNER webpage (http://www4a.biotec.or.th/GI/tools/toner) and Git
Fast detection of genetic information by an optimized PCR in an interchangeable chip.

KAUST Repository

Wu, Jinbo

2012-02-01

In this paper, we report the construction of a polymerase chain reaction (PCR) device for fast amplification and detection of DNA. This device consists of an interchangeable PCR chamber, a temperature control component as well as an optical detection system. The DNA amplification happens on an interchangeable chip with the volumes as low as 1.25 μl, while the heating and cooling rate was as fast as 12.7°C/second ensuring that the total time needed of only 25 min to complete the 35 cycle PCR amplification. An optimized PCR with two-temperature approach for denaturing and annealing (Td and Ta) of DNA was also formulated with the PCR chip, with which the amplification of male-specific sex determining region Y (SRY) gene marker by utilizing raw saliva was successfully achieved and the genetic identification was in-situ detected right after PCR by the optical detection system.
FibroChip, a Functional DNA Microarray to Monitor Cellulolytic and Hemicellulolytic Activities of Rumen Microbiota

Directory of Open Access Journals (Sweden)

Sophie Comtet-Marre

2018-02-01

Full Text Available Ruminants fulfill their energy needs for growth primarily through microbial breakdown of plant biomass in the rumen. Several biotic and abiotic factors influence the efficiency of fiber degradation, which can ultimately impact animal productivity and health. To provide more insight into mechanisms involved in the modulation of fibrolytic activity, a functional DNA microarray targeting genes encoding key enzymes involved in cellulose and hemicellulose degradation by rumen microbiota was designed. Eight carbohydrate-active enzyme (CAZyme families (GH5, GH9, GH10, GH11, GH43, GH48, CE1, and CE6 were selected which represented 392 genes from bacteria, protozoa, and fungi. The DNA microarray, designated as FibroChip, was validated using targets of increasing complexity and demonstrated sensitivity and specificity. In addition, FibroChip was evaluated for its explorative and semi-quantitative potential. Differential expression of CAZyme genes was evidenced in the rumen bacterium Fibrobacter succinogenes S85 grown on wheat straw or cellobiose. FibroChip was used to identify the expressed CAZyme genes from the targeted families in the rumen of a cow fed a mixed diet based on grass silage. Among expressed genes, those encoding GH43, GH5, and GH10 families were the most represented. Most of the F. succinogenes genes detected by the FibroChip were also detected following RNA-seq analysis of RNA transcripts obtained from the rumen fluid sample. Use of the FibroChip also indicated that transcripts of fiber degrading enzymes derived from eukaryotes (protozoa and anaerobic fungi represented a significant proportion of the total microbial mRNA pool. FibroChip represents a reliable and high-throughput tool that enables researchers to monitor active members of fiber degradation in the rumen.
FibroChip, a Functional DNA Microarray to Monitor Cellulolytic and Hemicellulolytic Activities of Rumen Microbiota.

Science.gov (United States)

Comtet-Marre, Sophie; Chaucheyras-Durand, Frédérique; Bouzid, Ourdia; Mosoni, Pascale; Bayat, Ali R; Peyret, Pierre; Forano, Evelyne

2018-01-01

Ruminants fulfill their energy needs for growth primarily through microbial breakdown of plant biomass in the rumen. Several biotic and abiotic factors influence the efficiency of fiber degradation, which can ultimately impact animal productivity and health. To provide more insight into mechanisms involved in the modulation of fibrolytic activity, a functional DNA microarray targeting genes encoding key enzymes involved in cellulose and hemicellulose degradation by rumen microbiota was designed. Eight carbohydrate-active enzyme (CAZyme) families (GH5, GH9, GH10, GH11, GH43, GH48, CE1, and CE6) were selected which represented 392 genes from bacteria, protozoa, and fungi. The DNA microarray, designated as FibroChip, was validated using targets of increasing complexity and demonstrated sensitivity and specificity. In addition, FibroChip was evaluated for its explorative and semi-quantitative potential. Differential expression of CAZyme genes was evidenced in the rumen bacterium Fibrobacter succinogenes S85 grown on wheat straw or cellobiose. FibroChip was used to identify the expressed CAZyme genes from the targeted families in the rumen of a cow fed a mixed diet based on grass silage. Among expressed genes, those encoding GH43, GH5, and GH10 families were the most represented. Most of the F. succinogenes genes detected by the FibroChip were also detected following RNA-seq analysis of RNA transcripts obtained from the rumen fluid sample. Use of the FibroChip also indicated that transcripts of fiber degrading enzymes derived from eukaryotes (protozoa and anaerobic fungi) represented a significant proportion of the total microbial mRNA pool. FibroChip represents a reliable and high-throughput tool that enables researchers to monitor active members of fiber degradation in the rumen.
Experiment list: SRX143825 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available SRX143825 mm9 Input control Input control Neural Cerebellum MeSH Description=The pa...ntain balance, and learn motor skills. 38330550,73.2,10.7,868 GSM918733: LICR ChipSeq Cerebellum Input adult-8wks source_name=Cerebel...ption=Chromatin IP Sequencing || cell=Cerebellum || cell organism=mouse || cell description=Cerebellum || ce...lum || biomaterial_provider=1)LICR lab; 2)CSHL lab || lab=LICR-m || lab description
An Adaptive and Time-Efficient ECG R-Peak Detection Algorithm.

Science.gov (United States)

Qin, Qin; Li, Jianqing; Yue, Yinggao; Liu, Chengyu

2017-01-01

R-peak detection is crucial in electrocardiogram (ECG) signal analysis. This study proposed an adaptive and time-efficient R-peak detection algorithm for ECG processing. First, wavelet multiresolution analysis was applied to enhance the ECG signal representation. Then, ECG was mirrored to convert large negative R-peaks to positive ones. After that, local maximums were calculated by the first-order forward differential approach and were truncated by the amplitude and time interval thresholds to locate the R-peaks. The algorithm performances, including detection accuracy and time consumption, were tested on the MIT-BIH arrhythmia database and the QT database. Experimental results showed that the proposed algorithm achieved mean sensitivity of 99.39%, positive predictivity of 99.49%, and accuracy of 98.89% on the MIT-BIH arrhythmia database and 99.83%, 99.90%, and 99.73%, respectively, on the QT database. By processing one ECG record, the mean time consumptions were 0.872 s and 0.763 s for the MIT-BIH arrhythmia database and QT database, respectively, yielding 30.6% and 32.9% of time reduction compared to the traditional Pan-Tompkins method.
Photonics-on-a-chip: recent advances in integrated waveguides as enabling detection elements for real-world, lab-on-a-chip biosensing applications.

Science.gov (United States)

Washburn, Adam L; Bailey, Ryan C

2011-01-21

By leveraging advances in semiconductor microfabrication technologies, chip-integrated optical biosensors are poised to make an impact as scalable and multiplexable bioanalytical measurement tools for lab-on-a-chip applications. In particular, waveguide-based optical sensing technology appears to be exceptionally amenable to chip integration and miniaturization, and, as a result, the recent literature is replete with examples of chip-integrated waveguide sensing platforms developed to address a wide range of contemporary analytical challenges. As an overview of the most recent advances within this dynamic field, this review highlights work from the last 2-3 years in the areas of grating-coupled, interferometric, photonic crystal, and microresonator waveguide sensors. With a focus towards device integration, particular emphasis is placed on demonstrations of biosensing using these technologies within microfluidically controlled environments. In addition, examples of multiplexed detection and sensing within complex matrices--important features for real-world applicability--are given special attention.
ChIP-seq Analysis in R (CSAR): An R package for the statistical detection of protein-bound genomic regions

NARCIS (Netherlands)

Muino, J.M.; Kaufmann, K.; Ham, van R.C.H.J.; Angenent, G.C.; Krajewski, P.

2011-01-01

Background In vivo detection of protein-bound genomic regions can be achieved by combining chromatin-immunoprecipitation with next-generation sequencing technology (ChIP-seq). The large amount of sequence data produced by this method needs to be analyzed in a statistically proper and computationally
Detection of bovine mastitis pathogens by loop-mediated isothermal amplification and an electrochemical DNA chip.

Science.gov (United States)

Kawai, Kazuhiro; Inada, Mika; Ito, Keiko; Hashimoto, Koji; Nikaido, Masaru; Hata, Eiji; Katsuda, Ken; Kiku, Yoshio; Tagawa, Yuichi; Hayashi, Tomohito

2017-12-22

Bovine mastitis causes significant economic losses in the dairy industry. Effective prevention of bovine mastitis requires an understanding of the infection status of a pathogenic microorganism in a herd that has not yet shown clinical signs of mastitis and appropriate treatment specific for the pathogenic microorganism. However, bacterial identification by culture has drawbacks in that the sensitivity may be low and the procedure can be complex. In this study, we developed a genetic detection method to identify mastitis pathogens using a simple and highly sensitive electrochemical DNA chip which can specifically detect bacterial DNA in milk specimens. First, we selected microorganisms belonging to 12 families and/or genera associated with mastitis for which testing should be performed. Next, we optimized the conditions for amplifying microorganism DNA by loop-mediated isothermal amplification (LAMP) using 32 primers and the use of a DNA chip capable of measuring all pathogens simultaneously. Sample detection could be completed in just a few hours using this method. Comparison of the results obtained with our DNA chip method and those obtained by bacterial culture verified that when the culture method was set to 100%, the total positive concordance rate of the DNA chip was 85.0% and the total negative concordance rate was 86.9%. Furthermore, the proposed method allows both rapid and highly sensitive detection of mastitis pathogens. We believe that this method will contribute to the development of an effective mastitis control program.
An Electrochromatography Chip with Integrated Waveguides for UV Absorbance Detection

DEFF Research Database (Denmark)

Gustafsson, Omar; Mogensen, Klaus Bo; Ohlsson, Pelle Daniel

2008-01-01

A silicon-based microchip for electrochromatographic separations is presented. Apart from a microfluidic network, the microchip has integrated UV-transparent waveguides for detection and integrated couplers for optical fibers on the chip, yielding the most complete chromatography microchip to date...... to the waveguides. The entire oxidized silicon microchip structure is sealed with a glass lid. Reversed phase electrochromatographic separation of three neutral compounds is demonstrated using UV absorbance detection at 254 nm. Baseline separation of the analytes is achieved in less than two minutes....
Experiment list: SRX1056356 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available O || cell type=ES cells || treated with=2.5 µM tamoxifen (Tam) || chip antibody=H3K27me3 (Millipore: 07-449)...specialized cells. 43433717,97.9,45.2,1333 GSM1708670: H3K27me3 ChIPSeq+Tam R2; M...us musculus; ChIP-Seq source_name=H3K27me3_ChIPSeq+Tam || strain=J1 || genotype/variation=inducible SetDB1 K
Single nucleotide polymorphism discovery in bovine liver using RNA-seq technology

DEFF Research Database (Denmark)

Pareek, Chandra Shekhar; Błaszczyk, Paweł; Dziuba, Piotr

2017-01-01

Background RNA-seq is a useful next-generation sequencing (NGS) technology that has been widely used to understand mammalian transcriptome architecture and function. In this study, a breed-specific RNA-seq experiment was utilized to detect putative single nucleotide polymorphisms (SNPs) in liver...

Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP)

NARCIS (Netherlands)

Kaufmann, K.; Muiño, J.M.; Østerås, M.; Farinelli, L.; Krajewski, P.; Angenent, G.C.

2010-01-01

Chromatin immunoprecipitation (ChIP) is a powerful technique to study interactions between transcription factors (TFs) and DNA in vivo. For genome-wide de novo discovery of TF-binding sites, the DNA that is obtained in ChIP experiments needs to be processed for sequence identification. The sequences
Quantitative ChIP-Seq Normalization Reveals Global Modulation of the Epigenome

Directory of Open Access Journals (Sweden)

David A. Orlando

2014-11-01

Full Text Available Epigenomic profiling by chromatin immunoprecipitation coupled with massively parallel DNA sequencing (ChIP-seq is a prevailing methodology used to investigate chromatin-based regulation in biological systems such as human disease, but the lack of an empirical methodology to enable normalization among experiments has limited the precision and usefulness of this technique. Here, we describe a method called ChIP with reference exogenous genome (ChIP-Rx that allows one to perform genome-wide quantitative comparisons of histone modification status across cell populations using defined quantities of a reference epigenome. ChIP-Rx enables the discovery and quantification of dynamic epigenomic profiles across mammalian cells that would otherwise remain hidden using traditional normalization methods. We demonstrate the utility of this method for measuring epigenomic changes following chemical perturbations and show how reference normalization of ChIP-seq experiments enables the discovery of disease-relevant changes in histone modification occupancy.
SVM classifier on chip for melanoma detection.

Science.gov (United States)

Afifi, Shereen; GholamHosseini, Hamid; Sinha, Roopak

2017-07-01

Support Vector Machine (SVM) is a common classifier used for efficient classification with high accuracy. SVM shows high accuracy for classifying melanoma (skin cancer) clinical images within computer-aided diagnosis systems used by skin cancer specialists to detect melanoma early and save lives. We aim to develop a medical low-cost handheld device that runs a real-time embedded SVM-based diagnosis system for use in primary care for early detection of melanoma. In this paper, an optimized SVM classifier is implemented onto a recent FPGA platform using the latest design methodology to be embedded into the proposed device for realizing online efficient melanoma detection on a single system on chip/device. The hardware implementation results demonstrate a high classification accuracy of 97.9% and a significant acceleration factor of 26 from equivalent software implementation on an embedded processor, with 34% of resources utilization and 2 watts for power consumption. Consequently, the implemented system meets crucial embedded systems constraints of high performance and low cost, resources utilization and power consumption, while achieving high classification accuracy.
Integration of ATAC-seq and RNA-seq identifies human alpha cell and beta cell signature genes.

Science.gov (United States)

Ackermann, Amanda M; Wang, Zhiping; Schug, Jonathan; Naji, Ali; Kaestner, Klaus H

2016-03-01

Although glucagon-secreting α-cells and insulin-secreting β-cells have opposing functions in regulating plasma glucose levels, the two cell types share a common developmental origin and exhibit overlapping transcriptomes and epigenomes. Notably, destruction of β-cells can stimulate repopulation via transdifferentiation of α-cells, at least in mice, suggesting plasticity between these cell fates. Furthermore, dysfunction of both α- and β-cells contributes to the pathophysiology of type 1 and type 2 diabetes, and β-cell de-differentiation has been proposed to contribute to type 2 diabetes. Our objective was to delineate the molecular properties that maintain islet cell type specification yet allow for cellular plasticity. We hypothesized that correlating cell type-specific transcriptomes with an atlas of open chromatin will identify novel genes and transcriptional regulatory elements such as enhancers involved in α- and β-cell specification and plasticity. We sorted human α- and β-cells and performed the "Assay for Transposase-Accessible Chromatin with high throughput sequencing" (ATAC-seq) and mRNA-seq, followed by integrative analysis to identify cell type-selective gene regulatory regions. We identified numerous transcripts with either α-cell- or β-cell-selective expression and discovered the cell type-selective open chromatin regions that correlate with these gene activation patterns. We confirmed cell type-selective expression on the protein level for two of the top hits from our screen. The "group specific protein" (GC; or vitamin D binding protein) was restricted to α-cells, while CHODL (chondrolectin) immunoreactivity was only present in β-cells. Furthermore, α-cell- and β-cell-selective ATAC-seq peaks were identified to overlap with known binding sites for islet transcription factors, as well as with single nucleotide polymorphisms (SNPs) previously identified as risk loci for type 2 diabetes. We have determined the genetic landscape of
Genome-wide analysis of replication timing by next-generation sequencing with E/L Repli-seq.

Science.gov (United States)

Marchal, Claire; Sasaki, Takayo; Vera, Daniel; Wilson, Korey; Sima, Jiao; Rivera-Mulia, Juan Carlos; Trevilla-García, Claudia; Nogues, Coralin; Nafie, Ebtesam; Gilbert, David M

2018-05-01

This protocol is an extension to: Nat. Protoc. 6, 870-895 (2014); doi:10.1038/nprot.2011.328; published online 02 June 2011Cycling cells duplicate their DNA content during S phase, following a defined program called replication timing (RT). Early- and late-replicating regions differ in terms of mutation rates, transcriptional activity, chromatin marks and subnuclear position. Moreover, RT is regulated during development and is altered in diseases. Here, we describe E/L Repli-seq, an extension of our Repli-chip protocol. E/L Repli-seq is a rapid, robust and relatively inexpensive protocol for analyzing RT by next-generation sequencing (NGS), allowing genome-wide assessment of how cellular processes are linked to RT. Briefly, cells are pulse-labeled with BrdU, and early and late S-phase fractions are sorted by flow cytometry. Labeled nascent DNA is immunoprecipitated from both fractions and sequenced. Data processing leads to a single bedGraph file containing the ratio of nascent DNA from early versus late S-phase fractions. The results are comparable to those of Repli-chip, with the additional benefits of genome-wide sequence information and an increased dynamic range. We also provide computational pipelines for downstream analyses, for parsing phased genomes using single-nucleotide polymorphisms (SNPs) to analyze RT allelic asynchrony, and for direct comparison to Repli-chip data. This protocol can be performed in up to 3 d before sequencing, and requires basic cellular and molecular biology skills, as well as a basic understanding of Unix and R.
Autopiquer - a Robust and Reliable Peak Detection Algorithm for Mass Spectrometry.

Science.gov (United States)

Kilgour, David P A; Hughes, Sam; Kilgour, Samantha L; Mackay, C Logan; Palmblad, Magnus; Tran, Bao Quoc; Goo, Young Ah; Ernst, Robert K; Clarke, David J; Goodlett, David R

2017-02-01

We present a simple algorithm for robust and unsupervised peak detection by determining a noise threshold in isotopically resolved mass spectrometry data. Solving this problem will greatly reduce the subjective and time-consuming manual picking of mass spectral peaks and so will prove beneficial in many research applications. The Autopiquer approach uses autocorrelation to test for the presence of (isotopic) structure in overlapping windows across the spectrum. Within each window, a noise threshold is optimized to remove the most unstructured data, whilst keeping as much of the (isotopic) structure as possible. This algorithm has been successfully demonstrated for both peak detection and spectral compression on data from many different classes of mass spectrometer and for different sample types, and this approach should also be extendible to other types of data that contain regularly spaced discrete peaks. Graphical Abstract ᅟ.
Rapid antibiotic efficacy screening with aluminum oxide nanoporous membrane filter-chip and optical detection system.

Science.gov (United States)

Tsou, Pei-Hsiang; Sreenivasappa, Harini; Hong, Sungmin; Yasuike, Masayuki; Miyamoto, Hiroshi; Nakano, Keiyo; Misawa, Takeyuki; Kameoka, Jun

2010-09-15

We have developed a filter-chip and optical detection system for rapid antibiotic efficacy screening. The filter-chip consisted of a 1-mL reservoir and an anodic aluminum oxide (AAO) nanoporous membrane. Sample solution with liquid growth media, bacteria, and antibiotics was incubated in the reservoir for a specific period of time. The number of live bacteria on the surface of membrane was counted after the incubation with antibiotics and filtration. Using this biosensing system, we have demonstrated a 1-h antibiotic screening for patients' clinical samples, significantly faster than the conventional antibiotic susceptibility tests that typically take more than 24h. This rapid screening nature makes the filter-chip and detection system ideal for tailoring antibiotic treatment to individual patients by reducing the microbial antibiotic resistance, and improving the survival rate for patients suffering from postoperative infections. Published by Elsevier B.V.
RELIABILITY OF THE DETECTION OF THE BARYON ACOUSTIC PEAK

International Nuclear Information System (INIS)

MartInez, Vicent J.; Arnalte-Mur, Pablo; De la Cruz, Pablo; Saar, Enn; Tempel, Elmo; Pons-BorderIa, MarIa Jesus; Paredes, Silvestre; Fernandez-Soto, Alberto

2009-01-01

The correlation function of the distribution of matter in the universe shows, at large scales, baryon acoustic oscillations, which were imprinted prior to recombination. This feature was first detected in the correlation function of the luminous red galaxies of the Sloan Digital Sky Survey (SDSS). Recently, the final release (DR7) of the SDSS has been made available, and the useful volume is about two times bigger than in the old sample. We present here, for the first time, the redshift-space correlation function of this sample at large scales together with that for one shallower, but denser volume-limited subsample drawn from the Two-Degree Field Redshift Survey. We test the reliability of the detection of the acoustic peak at about 100 h -1 Mpc and the behavior of the correlation function at larger scales by means of careful estimation of errors. We confirm the presence of the peak in the latest data although broader than in previous detections.
VLSI Design of SVM-Based Seizure Detection System With On-Chip Learning Capability.

Science.gov (United States)

Feng, Lichen; Li, Zunchao; Wang, Yuanfa

2018-02-01

Portable automatic seizure detection system is very convenient for epilepsy patients to carry. In order to make the system on-chip trainable with high efficiency and attain high detection accuracy, this paper presents a very large scale integration (VLSI) design based on the nonlinear support vector machine (SVM). The proposed design mainly consists of a feature extraction (FE) module and an SVM module. The FE module performs the three-level Daubechies discrete wavelet transform to fit the physiological bands of the electroencephalogram (EEG) signal and extracts the time-frequency domain features reflecting the nonstationary signal properties. The SVM module integrates the modified sequential minimal optimization algorithm with the table-driven-based Gaussian kernel to enable efficient on-chip learning. The presented design is verified on an Altera Cyclone II field-programmable gate array and tested using the two publicly available EEG datasets. Experiment results show that the designed VLSI system improves the detection accuracy and training efficiency.
ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data.

Science.gov (United States)

Ou, Jianhong; Liu, Haibo; Yu, Jun; Kelliher, Michelle A; Castilla, Lucio H; Lawson, Nathan D; Zhu, Lihua Julie

2018-03-01

ATAC-seq (Assays for Transposase-Accessible Chromatin using sequencing) is a recently developed technique for genome-wide analysis of chromatin accessibility. Compared to earlier methods for assaying chromatin accessibility, ATAC-seq is faster and easier to perform, does not require cross-linking, has higher signal to noise ratio, and can be performed on small cell numbers. However, to ensure a successful ATAC-seq experiment, step-by-step quality assurance processes, including both wet lab quality control and in silico quality assessment, are essential. While several tools have been developed or adopted for assessing read quality, identifying nucleosome occupancy and accessible regions from ATAC-seq data, none of the tools provide a comprehensive set of functionalities for preprocessing and quality assessment of aligned ATAC-seq datasets. We have developed a Bioconductor package, ATACseqQC, for easily generating various diagnostic plots to help researchers quickly assess the quality of their ATAC-seq data. In addition, this package contains functions to preprocess aligned ATAC-seq data for subsequent peak calling. Here we demonstrate the utilities of our package using 25 publicly available ATAC-seq datasets from four studies. We also provide guidelines on what the diagnostic plots should look like for an ideal ATAC-seq dataset. This software package has been used successfully for preprocessing and assessing several in-house and public ATAC-seq datasets. Diagnostic plots generated by this package will facilitate the quality assessment of ATAC-seq data, and help researchers to evaluate their own ATAC-seq experiments as well as select high-quality ATAC-seq datasets from public repositories such as GEO to avoid generating hypotheses or drawing conclusions from low-quality ATAC-seq experiments. The software, source code, and documentation are freely available as a Bioconductor package at https://bioconductor.org/packages/release/bioc/html/ATACseqQC.html .
Peak Detection Method Evaluation for Ion Mobility Spectrometry by Using Machine Learning Approaches

DEFF Research Database (Denmark)

Hauschild, Anne-Christin; Kopczynski, Dominik; D'Addario, Marianna

2013-01-01

machine learning methods exist, an inevitable preprocessing step is reliable and robust peak detection without manual intervention. In this work we evaluate four state-of-the-art approaches for automated IMS-based peak detection: local maxima search, watershed transformation with IPHEx, region......-merging with VisualNow, and peak model estimation (PME).We manually generated Metabolites 2013, 3 278 a gold standard with the aid of a domain expert (manual) and compare the performance of the four peak calling methods with respect to two distinct criteria. We first utilize established machine learning methods...
Detection of Metallothionein in Javanese Medaka (Oryzias javanicus, Using a scFv-Immobilized Protein Chip

Directory of Open Access Journals (Sweden)

Euiyeon Lee

2018-04-01

Full Text Available Environmental pollution by various industrial chemicals and biological agents poses serious risks to human health. Especially, marine contamination by potentially toxic elements (PTEs has become a global concern in recent years. Many efforts have been undertaken to monitor the PTE contamination of the aquatic environment. However, there are few approaches available to assess the PTE exposure of aquatic organisms. In this research, we developed a strategy to evaluate the heavy metal exposure of marine organisms, by measuring the expression levels of metallothionein protein derived from Oryzias javanicus (OjaMT. OjaMT is a biomarker of heavy metal exposure because the expression level increases upon heavy metal exposure. The developed assay is based on a real-time, label-free surface plasmon resonance (SPR measurement. Anti-OjaMT antibody and anti-OjaMT single-chain fragment of variable region (scFv were used as detection probes. Two types of SPR sensor chips were fabricated, by immobilizing antibody or Cys3-tagged scFv (scFv-Cys3 in a controlled orientation and were tested for in situ label-free OjaMT detection. Compared to the antibody-presenting sensor chips, the scFv-presenting sensor chips showed improved performance, displaying enhanced sensitivity and enabling semi-quantitative detection. The portable SPR system combined with scFv-immobilized sensor chips is expected to provide an excellent point-of-care testing system that can monitor target biomarkers in real time.
Making the most of RNA-seq: Pre-processing sequencing data with Opossum for reliable SNP variant detection [version 2; referees: 2 approved, 1 approved with reservations

Directory of Open Access Journals (Sweden)

Laura Oikkonen

2017-03-01

Full Text Available Identifying variants from RNA-seq (transcriptome sequencing data is a cost-effective and versatile complement to whole-exome (WES and whole-genome sequencing (WGS analysis. RNA-seq (transcriptome sequencing is primarily considered a method of gene expression analysis but it can also be used to detect DNA variants in expressed regions of the genome. However, current variant callers do not generally behave well with RNA-seq data due to reads encompassing intronic regions. We have developed a software programme called Opossum to address this problem. Opossum pre-processes RNA-seq reads prior to variant calling, and although it has been designed to work specifically with Platypus, it can be used equally well with other variant callers such as GATK HaplotypeCaller. In this work, we show that using Opossum in conjunction with either Platypus or GATK HaplotypeCaller maintains precision and improves the sensitivity for SNP detection compared to the GATK Best Practices pipeline. In addition, using it in combination with Platypus offers a substantial reduction in run times compared to the GATK pipeline so it is ideal when there are only limited time or computational resources available.
Fast Metabolite Identification in Nuclear Magnetic Resonance Metabolomic Studies: Statistical Peak Sorting and Peak Overlap Detection for More Reliable Database Queries.

Science.gov (United States)

Hoijemberg, Pablo A; Pelczer, István

2018-01-05

A lot of time is spent by researchers in the identification of metabolites in NMR-based metabolomic studies. The usual metabolite identification starts employing public or commercial databases to match chemical shifts thought to belong to a given compound. Statistical total correlation spectroscopy (STOCSY), in use for more than a decade, speeds the process by finding statistical correlations among peaks, being able to create a better peak list as input for the database query. However, the (normally not automated) analysis becomes challenging due to the intrinsic issue of peak overlap, where correlations of more than one compound appear in the STOCSY trace. Here we present a fully automated methodology that analyzes all STOCSY traces at once (every peak is chosen as driver peak) and overcomes the peak overlap obstacle. Peak overlap detection by clustering analysis and sorting of traces (POD-CAST) first creates an overlap matrix from the STOCSY traces, then clusters the overlap traces based on their similarity and finally calculates a cumulative overlap index (COI) to account for both strong and intermediate correlations. This information is gathered in one plot to help the user identify the groups of peaks that would belong to a single molecule and perform a more reliable database query. The simultaneous examination of all traces reduces the time of analysis, compared to viewing STOCSY traces by pairs or small groups, and condenses the redundant information in the 2D STOCSY matrix into bands containing similar traces. The COI helps in the detection of overlapping peaks, which can be added to the peak list from another cross-correlated band. POD-CAST overcomes the generally overlooked and underestimated presence of overlapping peaks and it detects them to include them in the search of all compounds contributing to the peak overlap, enabling the user to accelerate the metabolite identification process with more successful database queries and searching all tentative
Detection of Golden apples' climacteric peak by laser biospeckle measurements.

Science.gov (United States)

Nassif, Rana; Nader, Christelle Abou; Afif, Charbel; Pellen, Fabrice; Le Brun, Guy; Le Jeune, Bernard; Abboud, Marie

2014-12-10

In this paper, we report a study in which a laser biospeckle technique is used to detect the climacteric peak indicating the optimal ripeness of fruits. We monitor two batches of harvested Golden apples going through the ripening phase in low- and room-temperature environments, determine speckle parameters, and measure the emitted ethylene concentration using gas chromatography as reference method. Speckle results are then correlated to the emitted ethylene concentration by a principal component analysis. From a practical point of view, this approach allows us to validate biospeckle as a noninvasive and alternative method to respiration rate and ethylene production for climacteric peak detection as a ripening index.
Inductively coupled plasma emission spectrometric detection of simulated high performance liquid chromatographic peaks

International Nuclear Information System (INIS)

Fraley, D.M.; Yates, D.; Manahan, S.E.

1979-01-01

Because of its multielement capability, element-specificity, and low detection limits, inductively coupled plasma optical emission spectrometry (ICP) is a very promising technique for the detection of specific elemental species separated by high performance liquid chromatography (HPLC). This paper evaluated ICP as a detector for HPLC peaks containing specific elements. Detection limits for a number of elements have been evaluated in terms of the minimum detectable concentration of the element at the chromatographic peak maximum. The elements studies were Al, As, B, Ba, Ca, Cd, Co, Cr, Cu, Fe, K, Li, Mg, Mn, Mo, Na, Ni, P, Pb, Sb, Se, Sr, Ti, V, and Zn. In addition, ICP was compared with atomic absorption spectrometry for the detection of HPLC peaks composed of EDTA and NTA chelates of copper. Furthermore, ICP was compared to uv solution absorption for the detection of copper chelates. 6 figures, 4 tables
Experiment list: SRX186751 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available | biomaterial_provider=Lonza || datatype=ChipSeq || datatype description=Chromatin IP Sequencing || antibody antibody...description=Rabbit polyclonal antibody raised against a peptide containi...ng K79 di-methylation. Antibody Target: H3K79me2 || antibody targetdescription=H3K79me2 is a mark of the tra...nscriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). || antibody... vendorname=Active Motif || antibody vendorid=39143 || co
Experiment list: SRX186750 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available l_provider=Lonza || datatype=ChipSeq || datatype description=Chromatin IP Sequencing || antibody antibodydes...cription=Rabbit polyclonal antibody raised against a peptide containing K79 di-me...thylation. Antibody Target: H3K79me2 || antibody targetdescription=H3K79me2 is a mark of the transcriptional... transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). || antibody... vendorname=Active Motif || antibody vendorid=39143 || controlid=wgEn
Experiment list: SRX186672 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available RC || datatype=ChipSeq || datatype description=Chromatin IP Sequencing || antibody antibody...description=Rabbit polyclonal antibody raised against a peptide corresponding to the C-terminus of... H2AZ. Antibody Target: H2AZ || antibody targetdescription=H2A.Z is a sequence variant of Histone H2A. || antibody... vendorname=Millipore || antibody vendorid=07-594 || controlid=wgEncodeEH00...3132 || replicate=1,2 || softwareversion=ScriptureVPaperR3 || cell sex=F || antibody=H2A.Z || antibody antibody
Dopamine-functionalized InP/ZnS quantum dots as fluorescence probes for the detection of adenosine in microfluidic chip.

Science.gov (United States)

Ankireddy, Seshadri Reddy; Kim, Jongsung

2015-01-01

Microbeads are frequently used as solid supports for biomolecules such as proteins and nucleic acids in heterogeneous microfluidic assays. Chip-based, quantum dot (QD)-bead-biomolecule probes have been used for the detection of various types of DNA. In this study, we developed dopamine (DA)-functionalized InP/ZnS QDs (QDs-DA) as fluorescence probes for the detection of adenosine in microfluidic chips. The photoluminescence (PL) intensity of the QDs-DA is quenched by Zn(2+) because of the strong coordination interactions. In the presence of adenosine, Zn(2+) cations preferentially bind to adenosine, and the PL intensity of the QDs-DA is recovered. A polydimethylsiloxane-based microfluidic chip was fabricated, and adenosine detection was confirmed using QDs-DA probes.

Dry Matter Losses and Greenhouse Gas Emissions From Outside Storage of Short Rotation Coppice Willow Chip.

Science.gov (United States)

Whittaker, Carly; Yates, Nicola E; Powers, Stephen J; Misselbrook, Tom; Shield, Ian

This study examined the dry matter losses and the greenhouse gas (GHG) concentrations within two short rotation coppice (SRC) willow wood chip storage heaps. One heap was built on a grassland area (East Midlands) and the other (Rothamsted) on a concrete hard standing. A series of 1- and 3-m probes were embedded in the heaps in order to retrieve gas samples for analysis, and pre-weighed net bags were positioned in the core of the heap to detect dry matter losses. The bagged samples showed dry matter losses of 18 and 19 % in the East Midlands and Rothamsted heaps after 210 and 97 days storage, respectively. The Rothamsted heap showed a whole-heap dry matter loss of 21 %. During this time, the wood chips dried from 54 to 39 % moisture content in the East Midlands heap and 50 to 43 % at Rothamsted. The results from analysing the whole Rothamsted heap indicated an overall loss of 1.5 GJ per tonne stored, although measurements from bagged samples in the core suggested that the chips dried sufficiently to have a minimal energy loss from storage. The process of mixing the heap, however, led to incorporation of wet outer layers and hence the average moisture content was higher in an average sample of chip. After establishment of the heaps, the temperature rose rapidly and this correlated with a peak in carbon dioxide (CO 2 ) concentration within the heap. A peak in methane (CH 4 ) concentration was also detected in both heaps, though more noticeably in the East Midlands heap after around 55 days. In both instances, the peak CH 4 concentration occurred as CO 2 concentrations dropped, suggesting that after an active period of aerobic decomposition in the first 2 months of storage, the conditions in the heap became anaerobic. The results from this study suggest that outside wood chip storage is not an efficient method of storing biomass, though this may be location-specific as there are some studies showing lower dry matter losses. It is necessary to explore other
Apparatus, System and Method for Fast Detection of Genetic Information by PCR in an Interchangeable Chip

KAUST Repository

Wen, Weijia

2011-03-03

A polymerase chain reaction (PCR) device for fast amplification and detection of DNA includes an interchangeable PCR chamber, a temperature control component, and an optical detection system. The DNA amplification is performed on an interchangeable chip with volumes as small as 1.25 µl, while the heating and cooling rate may be as fast as 12.7 °C/second ensuring that the total time needed of only 25 minutes to complete the 35 cycle PCR amplification. The PCR may be performed according to a two-temperature approach for denaturing and annealing (Td and Ta) of DNA with the PCR chip, with which the amplification of male-specific SRY gene marker by utilizing raw saliva may be achieved. The genetic identification may be in-situ detected after PCR by the optical detection system.
Seq2Ref: a web server to facilitate functional interpretation

Directory of Open Access Journals (Sweden)

Li Wenlin

2013-01-01

Full Text Available Abstract Background The size of the protein sequence database has been exponentially increasing due to advances in genome sequencing. However, experimentally characterized proteins only constitute a small portion of the database, such that the majority of sequences have been annotated by computational approaches. Current automatic annotation pipelines inevitably introduce errors, making the annotations unreliable. Instead of such error-prone automatic annotations, functional interpretation should rely on annotations of ‘reference proteins’ that have been experimentally characterized or manually curated. Results The Seq2Ref server uses BLAST to detect proteins homologous to a query sequence and identifies the reference proteins among them. Seq2Ref then reports publications with experimental characterizations of the identified reference proteins that might be relevant to the query. Furthermore, a plurality-based rating system is developed to evaluate the homologous relationships and rank the reference proteins by their relevance to the query. Conclusions The reference proteins detected by our server will lend insight into proteins of unknown function and provide extensive information to develop in-depth understanding of uncharacterized proteins. Seq2Ref is available at: http://prodata.swmed.edu/seq2ref.
Low-complexity R-peak detection in ECG signals: a preliminary step towards ambulatory fetal monitoring.

Science.gov (United States)

Rooijakkers, Michiel; Rabotti, Chiara; Bennebroek, Martijn; van Meerbergen, Jef; Mischi, Massimo

2011-01-01

Non-invasive fetal health monitoring during pregnancy has become increasingly important. Recent advances in signal processing technology have enabled fetal monitoring during pregnancy, using abdominal ECG recordings. Ubiquitous ambulatory monitoring for continuous fetal health measurement is however still unfeasible due to the computational complexity of noise robust solutions. In this paper an ECG R-peak detection algorithm for ambulatory R-peak detection is proposed, as part of a fetal ECG detection algorithm. The proposed algorithm is optimized to reduce computational complexity, while increasing the R-peak detection quality compared to existing R-peak detection schemes. Validation of the algorithm is performed on two manually annotated datasets, the MIT/BIH Arrhythmia database and an in-house abdominal database. Both R-peak detection quality and computational complexity are compared to state-of-the-art algorithms as described in the literature. With a detection error rate of 0.22% and 0.12% on the MIT/BIH Arrhythmia and in-house databases, respectively, the quality of the proposed algorithm is comparable to the best state-of-the-art algorithms, at a reduced computational complexity.
Nondestructive detection of zebra chip disease in potatoes using near-infrared spectroscopy

Science.gov (United States)

Near-Infrared (NIR) spectroscopy in the wavelength region from 900 nm to 2600 nm was evaluated as the basis for a rapid, non-destructive method for the detection of Zebra Chip disease in potatoes and the measurement of sugar concentrations in affected tubers. Using stepwise regression in conjunction...
A fast one-chip event-preprocessor and sequencer for the Simbol-X Low Energy Detector

Science.gov (United States)

Schanz, T.; Tenzer, C.; Maier, D.; Kendziorra, E.; Santangelo, A.

2010-12-01

We present an FPGA-based digital camera electronics consisting of an Event-Preprocessor (EPP) for on-board data preprocessing and a related Sequencer (SEQ) to generate the necessary signals to control the readout of the detector. The device has been originally designed for the Simbol-X low energy detector (LED). The EPP operates on 64×64 pixel images and has a real-time processing capability of more than 8000 frames per second. The already working releases of the EPP and the SEQ are now combined into one Digital-Camera-Controller-Chip (D3C).
A fast one-chip event-preprocessor and sequencer for the Simbol-X Low Energy Detector

Energy Technology Data Exchange (ETDEWEB)

Schanz, T., E-mail: schanz@astro.uni-tuebingen.d [Kepler Center for Astro- and Particlephysics, Institut fuer Astronomie und Astrophysik Tuebingen, Sand 1, 72076 Tuebingen (Germany); Tenzer, C., E-mail: tenzer@astro.uni-tuebingen.d [Kepler Center for Astro- and Particlephysics, Institut fuer Astronomie und Astrophysik Tuebingen, Sand 1, 72076 Tuebingen (Germany); Maier, D.; Kendziorra, E.; Santangelo, A. [Kepler Center for Astro- and Particlephysics, Institut fuer Astronomie und Astrophysik Tuebingen, Sand 1, 72076 Tuebingen (Germany)

2010-12-11

We present an FPGA-based digital camera electronics consisting of an Event-Preprocessor (EPP) for on-board data preprocessing and a related Sequencer (SEQ) to generate the necessary signals to control the readout of the detector. The device has been originally designed for the Simbol-X low energy detector (LED). The EPP operates on 64x64 pixel images and has a real-time processing capability of more than 8000 frames per second. The already working releases of the EPP and the SEQ are now combined into one Digital-Camera-Controller-Chip (D3C).
A fast one-chip event-preprocessor and sequencer for the Simbol-X Low Energy Detector

International Nuclear Information System (INIS)

Schanz, T.; Tenzer, C.; Maier, D.; Kendziorra, E.; Santangelo, A.

2010-01-01

We present an FPGA-based digital camera electronics consisting of an Event-Preprocessor (EPP) for on-board data preprocessing and a related Sequencer (SEQ) to generate the necessary signals to control the readout of the detector. The device has been originally designed for the Simbol-X low energy detector (LED). The EPP operates on 64x64 pixel images and has a real-time processing capability of more than 8000 frames per second. The already working releases of the EPP and the SEQ are now combined into one Digital-Camera-Controller-Chip (D3C).
Method and apparatus for clockless analog-to-digital conversion and peak detection

Science.gov (United States)

DeGeronimo, Gianluigi

2007-03-06

An apparatus and method for analog-to-digital conversion and peak detection includes at least one stage, which includes a first switch, second switch, current source or capacitor, and discriminator. The discriminator changes state in response to a current or charge associated with the input signal exceeding a threshold, thereby indicating whether the current or charge associated with the input signal is greater than the threshold. The input signal includes a peak or a charge, and the converter includes a peak or charge detect mode in which a state of the switch is retained in response to a decrease in the current or charge associated with the input signal. The state of the switch represents at least a portion of a value of the peak or of the charge.
Extraction, amplification and detection of DNA in microfluidic chip-based assays

KAUST Repository

Wu, Jinbo

2013-12-20

This review covers three aspects of PCR-based microfluidic chip assays: sample preparation, target amplification, and product detection. We also discuss the challenges related to the miniaturization and integration of each assay and make a comparison between conventional and microfluidic schemes. In order to accomplish these essential assays without human intervention between individual steps, the micro-components for fluid manipulation become critical. We therefore summarize and discuss components such as microvalves (for fluid regulation), pumps (for fluid driving) and mixers (for blending fluids). By combining the above assays and microcomponents, DNA testing of multi-step bio-reactions in microfluidic chips may be achieved with minimal external control. The combination of assay schemes with the use of micro-components also leads to rapid methods for DNA testing via multi-step bioreactions. Contains 259 references.
Modified automatic R-peak detection algorithm for patients with epilepsy using a portable electrocardiogram recorder.

Science.gov (United States)

Jeppesen, J; Beniczky, S; Fuglsang Frederiksen, A; Sidenius, P; Johansen, P

2017-07-01

Earlier studies have shown that short term heart rate variability (HRV) analysis of ECG seems promising for detection of epileptic seizures. A precise and accurate automatic R-peak detection algorithm is a necessity in a real-time, continuous measurement of HRV, in a portable ECG device. We used the portable CE marked ePatch® heart monitor to record the ECG of 14 patients, who were enrolled in the videoEEG long term monitoring unit for clinical workup of epilepsy. Recordings of the first 7 patients were used as training set of data for the R-peak detection algorithm and the recordings of the last 7 patients (467.6 recording hours) were used to test the performance of the algorithm. We aimed to modify an existing QRS-detection algorithm to a more precise R-peak detection algorithm to avoid the possible jitter Qand S-peaks can create in the tachogram, which causes error in short-term HRVanalysis. The proposed R-peak detection algorithm showed a high sensitivity (Se = 99.979%) and positive predictive value (P+ = 99.976%), which was comparable with a previously published QRS-detection algorithm for the ePatch® ECG device, when testing the same dataset. The novel R-peak detection algorithm designed to avoid jitter has very high sensitivity and specificity and thus is a suitable tool for a robust, fast, real-time HRV-analysis in patients with epilepsy, creating the possibility for real-time seizure detection for these patients.
RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome

Directory of Open Access Journals (Sweden)

Severin Andrew J

2010-08-01

Full Text Available Abstract Background Next generation sequencing is transforming our understanding of transcriptomes. It can determine the expression level of transcripts with a dynamic range of over six orders of magnitude from multiple tissues, developmental stages or conditions. Patterns of gene expression provide insight into functions of genes with unknown annotation. Results The RNA Seq-Atlas presented here provides a record of high-resolution gene expression in a set of fourteen diverse tissues. Hierarchical clustering of transcriptional profiles for these tissues suggests three clades with similar profiles: aerial, underground and seed tissues. We also investigate the relationship between gene structure and gene expression and find a correlation between gene length and expression. Additionally, we find dramatic tissue-specific gene expression of both the most highly-expressed genes and the genes specific to legumes in seed development and nodule tissues. Analysis of the gene expression profiles of over 2,000 genes with preferential gene expression in seed suggests there are more than 177 genes with functional roles that are involved in the economically important seed filling process. Finally, the Seq-atlas also provides a means of evaluating existing gene model annotations for the Glycine max genome. Conclusions This RNA-Seq atlas extends the analyses of previous gene expression atlases performed using Affymetrix GeneChip technology and provides an example of new methods to accommodate the increase in transcriptome data obtained from next generation sequencing. Data contained within this RNA-Seq atlas of Glycine max can be explored at http://www.soybase.org/soyseq.
Experiment list: SRX144529 [Chip-atlas[Archive

Lifescience Database Archive (English)

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Experiment list: SRX144528 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available -Seq source_name=IgG ChIP SFN treated || biomaterial_provider=Coriell; http://ccr....coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM06993 || biomaterial_provider=Coriell; http://ccr.cori...ell.org/Sections/Search/Search.aspx?PgId=165&q=GM07000 || biomaterial_provider=Coriell; http://ccr.coriell.o...rg/Sections/Search/Search.aspx?PgId=165&q=GM11882 || biomaterial_provider=Coriell...; http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM11992 || biomaterial_provider=Coriell; htt
Experiment list: SRX150477 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available osis=Fibrocystic Disease 70636654,97.7,24.3,106225 GSM935397: Harvard ChipSeq MCF10A-Er-Src 4OHTAM 1uM 4hr c-Fos Harvard... Control source_name=MCF10A-Er-Src || biomaterial_provider=Struhl laboratory || lab=Harvard || l... a leucine-zipper. || antibody vendorname=Santa Cruz Biotech || antibody vendorid=sc-7202 || control=Harvard..._Control || control description=input library was prepared at Harvard. || control=Harvard..._Control || control description=input library was prepared at Harvard. || controlid=wgEncodeEH002871
Experiment list: SRX150476 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available osis=Fibrocystic Disease 60050220,94.5,18.5,85444 GSM935396: Harvard ChipSeq MCF10A-Er-Src 4OHTAM 1uM 36hr c-Fos Harvard... Control source_name=MCF10A-Er-Src || biomaterial_provider=Struhl laboratory || lab=Harvard || l...is a leucine-zipper. || antibody vendorname=Santa Cruz Biotech || antibody vendorid=sc-7202 || control=Harvard..._Control || control description=input library was prepared at Harvard. || control=Harvard..._Control || control description=input library was prepared at Harvard. || controlid=wgEncodeEH0028
Experiment list: SRX186742 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available l_provider=ATCC || datatype=ChipSeq || datatype description=Chromatin IP Sequencing || antibody antibodydesc...ription=Rabbit polyclonal antibody raised against a peptide corresponding to the ...C-terminus of H2AZ. Antibody Target: H2AZ || antibody targetdescription=H2A.Z is a sequence variant of Histone H2A. || antibody... vendorname=Millipore || antibody vendorid=07-594 || controlid=wgEncodeEH003076 || replic...ate=1,2 || softwareversion=ScriptureVPaperR3 || cell sex=M || antibody=H2A.Z || antibody antibody
Experiment list: SRX186752 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available aterial_provider=Lonza || datatype=ChipSeq || datatype description=Chromatin IP Sequencing || antibody antibody...description=Rabbit polyclonal antibody raised against a peptide corresponding ...to the C-terminus of H2AZ. Antibody Target: H2AZ || antibody targetdescription=H2A.Z is a sequence variant of Histone H2A. || antibod...y vendorname=Millipore || antibody vendorid=07-594 || controlid=wgEncodeEH000060 ||... replicate=1,2 || softwareversion=ScriptureVPaperR3 || cell sex=U || antibody=H2A.Z || antibody antibody
Experiment list: SRX186726 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available rovider=Lonza || datatype=ChipSeq || datatype description=Chromatin IP Sequencing || antibody antibodydescri...terminus of H2AZ. Antibody Target: H2AZ || antibody targetdescription=H2A.Z is a sequence variant of Histone H2A. || antibody... vendorname=Millipore || antibody vendorid=07-594 || controlid=wgEncodeEH000105 || replicat...e=1,2 || softwareversion=ScriptureVPaperR3 || cell sex=U || antibody=H2A.Z || antibody antibody...description=Rabbit polyclonal antibody raised against a peptide corresponding to the C-terminu
Experiment list: SRX186723 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available K || biomaterial_provider=Lonza || datatype=ChipSeq || datatype description=Chromatin IP Sequencing || antibody antibody...description=Rabbit polyclonal antibody raised against a peptide conta...ining K79 di-methylation. Antibody Target: H3K79me2 || antibody targetdescription=H3K79me2 is a mark of the ...dy vendorname=Active Motif || antibody vendorid=39143 ||... controlid=wgEncodeEH000072 || replicate=1,2 || softwareversion=ScriptureVPaperR3 || cell sex=M || antibody=H3K79me2 || antibody anti

Experiment list: SRX190252 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available -1 || cell organism=human || cell description=pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a panc...SRX190252 hg19 Input control Input control Pancreas PANC-1 Tissue=Pancreas/Duct|Dis...ease=Epithelioid Carcinoma 117194289,90.9,30.1,1440 GSM1010796: HudsonAlpha ChipSeq PANC-1 RevXlinkChromatin...atin IP Sequencing || controlid=SL3776,SL2340 || labexpid=SL3776,SL2340 || cell=PANC...reatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old
Wide-field optical detection of nanoparticles using on-chip microscopy and self-assembled nanolenses

Science.gov (United States)

Mudanyali, Onur; McLeod, Euan; Luo, Wei; Greenbaum, Alon; Coskun, Ahmet F.; Hennequin, Yves; Allier, Cédric P.; Ozcan, Aydogan

2013-03-01

The direct observation of nanoscale objects is a challenging task for optical microscopy because the scattering from an individual nanoparticle is typically weak at optical wavelengths. Electron microscopy therefore remains one of the gold standard visualization methods for nanoparticles, despite its high cost, limited throughput and restricted field-of-view. Here, we describe a high-throughput, on-chip detection scheme that uses biocompatible wetting films to self-assemble aspheric liquid nanolenses around individual nanoparticles to enhance the contrast between the scattered and background light. We model the effect of the nanolens as a spatial phase mask centred on the particle and show that the holographic diffraction pattern of this effective phase mask allows detection of sub-100 nm particles across a large field-of-view of >20 mm2. As a proof-of-concept demonstration, we report on-chip detection of individual polystyrene nanoparticles, adenoviruses and influenza A (H1N1) viral particles.
Feature selection and classifier parameters estimation for EEG signals peak detection using particle swarm optimization.

Science.gov (United States)

Adam, Asrul; Shapiai, Mohd Ibrahim; Tumari, Mohd Zaidi Mohd; Mohamad, Mohd Saberi; Mubin, Marizan

2014-01-01

Electroencephalogram (EEG) signal peak detection is widely used in clinical applications. The peak point can be detected using several approaches, including time, frequency, time-frequency, and nonlinear domains depending on various peak features from several models. However, there is no study that provides the importance of every peak feature in contributing to a good and generalized model. In this study, feature selection and classifier parameters estimation based on particle swarm optimization (PSO) are proposed as a framework for peak detection on EEG signals in time domain analysis. Two versions of PSO are used in the study: (1) standard PSO and (2) random asynchronous particle swarm optimization (RA-PSO). The proposed framework tries to find the best combination of all the available features that offers good peak detection and a high classification rate from the results in the conducted experiments. The evaluation results indicate that the accuracy of the peak detection can be improved up to 99.90% and 98.59% for training and testing, respectively, as compared to the framework without feature selection adaptation. Additionally, the proposed framework based on RA-PSO offers a better and reliable classification rate as compared to standard PSO as it produces low variance model.
A Single-Chip CMOS Pulse Oximeter with On-Chip Lock-In Detection

OpenAIRE

Diwei He; Stephen P. Morgan; Dimitrios Trachanis; Jan van Hese; Dimitris Drogoudis; Franco Fummi; Francesco Stefanni; Valerio Guarnieri; Barrie R. Hayes-Gill

2015-01-01

Pulse oximetry is a noninvasive and continuous method for monitoring the blood oxygen saturation level. This paper presents the design and testing of a single-chip pulse oximeter fabricated in a 0.35 ?m CMOS process. The chip includes photodiode, transimpedance amplifier, analogue band-pass filters, analogue-to-digital converters, digital signal processor and LED timing control. The experimentally measured AC and DC characteristics of individual circuits including the DC output voltage of the...
Probabilistic peak detection in CE-LIF for STR DNA typing.

Science.gov (United States)

Woldegebriel, Michael; van Asten, Arian; Kloosterman, Ate; Vivó-Truyols, Gabriel

2017-07-01

In this work, we present a novel probabilistic peak detection algorithm based on a Bayesian framework for forensic DNA analysis. The proposed method aims at an exhaustive use of raw electropherogram data from a laser-induced fluorescence multi-CE system. As the raw data are informative up to a single data point, the conventional threshold-based approaches discard relevant forensic information early in the data analysis pipeline. Our proposed method assigns a posterior probability reflecting the data point's relevance with respect to peak detection criteria. Peaks of low intensity generated from a truly existing allele can thus constitute evidential value instead of fully discarding them and contemplating a potential allele drop-out. This way of working utilizes the information available within each individual data point and thus avoids making early (binary) decisions on the data analysis that can lead to error propagation. The proposed method was tested and compared to the application of a set threshold as is current practice in forensic STR DNA profiling. The new method was found to yield a significant improvement in the number of alleles identified, regardless of the peak heights and deviation from Gaussian shape. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
CLIP-seq analysis of multi-mapped reads discovers novel functional RNA regulatory sites in the human transcriptome.

Science.gov (United States)

Zhang, Zijun; Xing, Yi

2017-09-19

Crosslinking or RNA immunoprecipitation followed by sequencing (CLIP-seq or RIP-seq) allows transcriptome-wide discovery of RNA regulatory sites. As CLIP-seq/RIP-seq reads are short, existing computational tools focus on uniquely mapped reads, while reads mapped to multiple loci are discarded. We present CLAM (CLIP-seq Analysis of Multi-mapped reads). CLAM uses an expectation-maximization algorithm to assign multi-mapped reads and calls peaks combining uniquely and multi-mapped reads. To demonstrate the utility of CLAM, we applied it to a wide range of public CLIP-seq/RIP-seq datasets involving numerous splicing factors, microRNAs and m6A RNA methylation. CLAM recovered a large number of novel RNA regulatory sites inaccessible by uniquely mapped reads. The functional significance of these sites was demonstrated by consensus motif patterns and association with alternative splicing (splicing factors), transcript abundance (AGO2) and mRNA half-life (m6A). CLAM provides a useful tool to discover novel protein-RNA interactions and RNA modification sites from CLIP-seq and RIP-seq data, and reveals the significant contribution of repetitive elements to the RNA regulatory landscape of the human transcriptome. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.
Gene expression profiling of human breast tissue samples using SAGE-Seq.

Science.gov (United States)

Wu, Zhenhua Jeremy; Meyer, Clifford A; Choudhury, Sibgat; Shipitsin, Michail; Maruyama, Reo; Bessarabova, Marina; Nikolskaya, Tatiana; Sukumar, Saraswati; Schwartzman, Armin; Liu, Jun S; Polyak, Kornelia; Liu, X Shirley

2010-12-01

We present a powerful application of ultra high-throughput sequencing, SAGE-Seq, for the accurate quantification of normal and neoplastic mammary epithelial cell transcriptomes. We develop data analysis pipelines that allow the mapping of sense and antisense strands of mitochondrial and RefSeq genes, the normalization between libraries, and the identification of differentially expressed genes. We find that the diversity of cancer transcriptomes is significantly higher than that of normal cells. Our analysis indicates that transcript discovery plateaus at 10 million reads/sample, and suggests a minimum desired sequencing depth around five million reads. Comparison of SAGE-Seq and traditional SAGE on normal and cancerous breast tissues reveals higher sensitivity of SAGE-Seq to detect less-abundant genes, including those encoding for known breast cancer-related transcription factors and G protein-coupled receptors (GPCRs). SAGE-Seq is able to identify genes and pathways abnormally activated in breast cancer that traditional SAGE failed to call. SAGE-Seq is a powerful method for the identification of biomarkers and therapeutic targets in human disease.
Development and evaluation of a real-time fluorogenic loop-mediated isothermal amplification assay integrated on a microfluidic disc chip (on-chip LAMP) for rapid and simultaneous detection of ten pathogenic bacteria in aquatic animals.

Science.gov (United States)

Zhou, Qian-Jin; Wang, Lei; Chen, Jiong; Wang, Rui-Na; Shi, Yu-Hong; Li, Chang-Hong; Zhang, De-Min; Yan, Xiao-Jun; Zhang, Yan-Jun

2014-09-01

Rapid, low-cost, and user-friendly strategies are urgently needed for early disease diagnosis and timely treatment, particularly for on-site screening of pathogens in aquaculture. In this study, we successfully developed a real-time fluorogenic loop-mediated isothermal amplification assay integrated on a microfluidic disc chip (on-chip LAMP), which was capable of simultaneously detecting 10 pathogenic bacteria in aquatic animals, i.e., Nocardia seriolae, Pseudomonas putida, Streptococcus iniae, Vibrio alginolyticus, Vibrio anguillarum, Vibrio fluvialis, Vibrio harveyi, Vibrio parahaemolyticus, Vibrio rotiferianus, and Vibrio vulnificus. The assay provided a nearly-automated approach, with only a single pipetting step per chip for sample dispensing. This technique could achieve limits of detection (LOD) ranging from 0.40 to 6.42pg per 1.414μL reaction in less than 30 min. The robust reproducibility was demonstrated by a little variation among duplications for each bacterium with the coefficient of variation (CV) for time to positive (Tp) value less than 0.10. The clinical sensitivity and specificity of this on-chip LAMP assay in detecting field samples were 96.2% and 93.8% by comparison with conventional microbiological methods. Compared with other well-known techniques, on-chip LAMP assay provides low sample and reagent consumption, ease-of-use, accelerated analysis, multiple bacteria and on-site detection, and high reproducibility, indicating that such a technique would be applicable for on-site detection and routine monitoring of multiple pathogens in aquaculture. Copyright © 2014 Elsevier B.V. All rights reserved.
Ultra-Sensitive Lab-on-a-Chip Detection of Sudan I in Food using Plasmonics-Enhanced Diatomaceous Thin Film.

Science.gov (United States)

Kong, Xianming; Squire, Kenny; Chong, Xinyuan; Wang, Alan X

2017-09-01

Sudan I is a carcinogenic compound containing an azo group that has been illegally utilized as an adulterant in food products to impart a bright red color to foods. In this paper, we develop a facile lab-on-a-chip device for instant, ultra-sensitive detection of Sudan I from real food samples using plasmonics-enhanced diatomaceous thin film, which can simultaneously perform on-chip separation using thin layer chromatography (TLC) and highly specific sensing using surface-enhanced Raman scattering (SERS) spectroscopy. Diatomite is a kind of nature-created photonic crystal biosilica with periodic pores and was used both as the stationary phase of the TLC plate and photonic crystals to enhance the SERS sensitivity. The on-chip chromatography capability of the TLC plate was verified by isolating Sudan I in a mixture solution containing Rhodamine 6G, while SERS sensing was achieved by spraying gold colloidal nanoparticles into the sensing spot. Such plasmonics-enhanced diatomaceous film can effectively detect Sudan I with more than 10 times improvement of the Raman signal intensity than commercial silica gel TLC plates. We applied this lab-on-a-chip device for real food samples and successfully detected Sudan I in chili sauce and chili oil down to 1 ppm, or 0.5 ng/spot. This on-chip TLC-SERS biosensor based on diatomite biosilica can function as a cost-effective, ultra-sensitive, and reliable technology for screening Sudan I and many other illicit ingredients to enhance food safety.
Pixel detector readout chip

CERN Multimedia

1991-01-01

Close-up of a pixel detector readout chip. The photograph shows an aera of 1 mm x 2 mm containing 12 separate readout channels. The entire chip contains 1000 readout channels (around 80 000 transistors) covering a sensitive area of 8 mm x 5 mm. The chip has been mounted on a silicon detector to detect high energy particles.
DMS-Seq for In Vivo Genome-wide Mapping of Protein-DNA Interactions and Nucleosome Centers.

Science.gov (United States)

Umeyama, Taichi; Ito, Takashi

2017-10-03

Protein-DNA interactions provide the basis for chromatin structure and gene regulation. Comprehensive identification of protein-occupied sites is thus vital to an in-depth understanding of genome function. Dimethyl sulfate (DMS) is a chemical probe that has long been used to detect footprints of DNA-bound proteins in vitro and in vivo. Here, we describe a genomic footprinting method, dimethyl sulfate sequencing (DMS-seq), which exploits the cell-permeable nature of DMS to obviate the need for nuclear isolation. This feature makes DMS-seq simple in practice and removes the potential risk of protein re-localization during nuclear isolation. DMS-seq successfully detects transcription factors bound to cis-regulatory elements and non-canonical chromatin particles in nucleosome-free regions. Furthermore, an unexpected preference of DMS confers on DMS-seq a unique potential to directly detect nucleosome centers without using genetic manipulation. We expect that DMS-seq will serve as a characteristic method for genome-wide interrogation of in vivo protein-DNA interactions. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.
Joint modeling of ChIP-seq data via a Markov random field model

NARCIS (Netherlands)

Bao, Yanchun; Vinciotti, Veronica; Wit, Ernst; 't Hoen, Peter A C

Chromatin ImmunoPrecipitation-sequencing (ChIP-seq) experiments have now become routine in biology for the detection of protein-binding sites. In this paper, we present a Markov random field model for the joint analysis of multiple ChIP-seq experiments. The proposed model naturally accounts for
Rapid and label-free bioanalytical method of alpha fetoprotein detection using LSPR chip

Science.gov (United States)

Kim, Dongjoo; Kim, Jinwoon; Kwak, Cheol Hwan; Heo, Nam Su; Oh, Seo Yeong; Lee, Hoomin; Lee, Go-Woon; Vilian, A. T. Ezhil; Han, Young-Kyu; Kim, Woo-Sik; Kim, Gi-bum; Kwon, Soonjo; Huh, Yun Suk

2017-07-01

Alpha fetoprotein (AFP) is a cancer marker, particularly for hepatocellular carcinoma. Normal levels of AFP are less than 20 ng/mL; however, its levels can reach more than 400 ng/mL in patients with HCC. Enzyme linked immunosorbent assay (ELISA) and radioimmunoassay (RIA) have been employed for clinical diagnosis of AFP; however, these methods are time consuming and labor intensive. In this study, we developed a localized surface plasmon resonance (LSPR) based biosensor for simple and rapid detection of AFP. This biosensor consists of a UV-Vis spectrometer, a cuvette cell, and a biosensor chip nanopatterned with gold nanoparticles (AuNPs). In our LSPR biosensor, binding of AFP to the surface of the sensor chip led to an increasing magnitude of the LSPR signals, which was measured by an ultraviolet-visible (UV-Vis) spectrometer. Our LSPR biosensor showed sufficient detectability of AFP at concentrations of 1 ng/mL to 1 μg/mL. Moreover, the overall procedure for detection of AFP was completed within 20 min. This biosensor could also be utilized for a point of care test (POCT) by employing a portable UV-Vis spectrometer. Owing to the simplicity and rapidity of the detection process, our LSPR biosensor is expected to replace traditional diagnostic methods for the early detection of diseases.
Chemometric strategy for automatic chromatographic peak detection and background drift correction in chromatographic data.

Science.gov (United States)

Yu, Yong-Jie; Xia, Qiao-Ling; Wang, Sheng; Wang, Bing; Xie, Fu-Wei; Zhang, Xiao-Bing; Ma, Yun-Ming; Wu, Hai-Long

2014-09-12

Peak detection and background drift correction (BDC) are the key stages in using chemometric methods to analyze chromatographic fingerprints of complex samples. This study developed a novel chemometric strategy for simultaneous automatic chromatographic peak detection and BDC. A robust statistical method was used for intelligent estimation of instrumental noise level coupled with first-order derivative of chromatographic signal to automatically extract chromatographic peaks in the data. A local curve-fitting strategy was then employed for BDC. Simulated and real liquid chromatographic data were designed with various kinds of background drift and degree of overlapped chromatographic peaks to verify the performance of the proposed strategy. The underlying chromatographic peaks can be automatically detected and reasonably integrated by this strategy. Meanwhile, chromatograms with BDC can be precisely obtained. The proposed method was used to analyze a complex gas chromatography dataset that monitored quality changes in plant extracts during storage procedure. Copyright © 2014 Elsevier B.V. All rights reserved.
Experiment list: SRX150517 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available osis=Fibrocystic Disease 50667127,93.3,23.9,80828 GSM935438: Harvard ChipSeq MCF10A-Er-Src EtOH 0.01pct c-Fos Harvard... Control source_name=MCF10A-Er-Src || biomaterial_provider=Struhl laboratory || lab=Harvard || lab description=Struhl - Harv...me=Santa Cruz Biotech || antibody vendorid=sc-7202 || control=Harvard_Control || control description=input l...ibrary was prepared at Harvard. || control=Harvard_Control || control description...=input library was prepared at Harvard. || controlid=wgEncodeEH002871 || replicate=1 http://dbarchive.biosci
Experiment list: SRX150570 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available osis=Fibrocystic Disease 64692659,93.8,19.3,37417 GSM935491: Harvard ChipSeq MCF10A-Er-Src 4OHTAM 1uM 4hr c-Myc Harvard... Control source_name=MCF10A-Er-Src || biomaterial_provider=Struhl laboratory || lab=Harvard || la...ntibody vendorname=Santa Cruz Biotech || antibody vendorid=sc-764 || control=Harvard_Control || control desc...ription=input library was prepared at Harvard. || control=Harvard_Control || cont...rol description=input library was prepared at Harvard. || controlid=wgEncodeEH002871 || replicate=1 http://d
Experiment list: SRX186686 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available me=NH-A || biomaterial_provider=Lonza || datatype=ChipSeq || datatype description=Chromatin IP Sequencing || antibody antibody...description=Rabbit polyclonal antibody raised against a peptide... containing K79 di-methylation. Antibody Target: H3K79me2 || antibody targetdescription=H3K79me2 is a mark o...ation marks (K36me3). || antibody vendorname=Active Motif || antibody vendorid=39...143 || controlid=wgEncodeEH001027 || replicate=1,2 || softwareversion=ScriptureVPaperR3 || cell sex=U || antibody=H3K79me2 || antibod
Experiment list: SRX186696 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available nza || datatype=ChipSeq || datatype description=Chromatin IP Sequencing || antibody antibodydescription=Rabbit polyclonal antibody...f H2AZ. Antibody Target: H2AZ || antibody targetdescription=H2A.Z is a sequence variant of Histone H2A. || antibody... vendorname=Millipore || antibody vendorid=07-594 || controlid=wgEncodeEH000093 || replicate=1,2 || s...oftwareversion=ScriptureVPaperR3 || cell sex=U || antibody=H2A.Z || antibody antibody...description=Rabbit polyclonal antibody raised against a peptide corresponding to the C-terminus of H2AZ.
Experiment list: SRX186665 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available rovider=DSMZ || datatype=ChipSeq || datatype description=Chromatin IP Sequencing || antibody antibodydescrip...ation. Antibody Target: H3K79me2 || antibody targetdescription=H3K79me2 is a mark of the transcriptional tra...nsition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). || antibody... vendorname=Active Motif || antibody vendorid=39143 || controlid=wgEncode...EH002434 || replicate=1,2 || softwareversion=ScriptureVPaperR3 || cell sex=M || antibody=H3K79me2 || antibody antibody
Experiment list: SRX186661 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available r=DSMZ || datatype=ChipSeq || datatype description=Chromatin IP Sequencing || antibody antibodydescription=Rabbit polyclonal antibody...s of H2AZ. Antibody Target: H2AZ || antibody targetdescription=H2A.Z is a sequence variant of Histone H2A. || antibody... vendorname=Millipore || antibody vendorid=07-594 || controlid=wgEncodeEH002434 || replicate=1,2 |...| softwareversion=ScriptureVPaperR3 || cell sex=M || antibody=H2A.Z || antibody antibody...description=Rabbit polyclonal antibody raised against a peptide corresponding to the C-terminus of H2

Effect of background correction on peak detection and quantification in online comprehensive two-dimensional liquid chromatography using diode array detection.

Science.gov (United States)

Allen, Robert C; John, Mallory G; Rutan, Sarah C; Filgueira, Marcelo R; Carr, Peter W

2012-09-07

A singular value decomposition-based background correction (SVD-BC) technique is proposed for the reduction of background contributions in online comprehensive two-dimensional liquid chromatography (LC×LC) data. The SVD-BC technique was compared to simply subtracting a blank chromatogram from a sample chromatogram and to a previously reported background correction technique for one dimensional chromatography, which uses an asymmetric weighted least squares (AWLS) approach. AWLS was the only background correction technique to completely remove the background artifacts from the samples as evaluated by visual inspection. However, the SVD-BC technique greatly reduced or eliminated the background artifacts as well and preserved the peak intensity better than AWLS. The loss in peak intensity by AWLS resulted in lower peak counts at the detection thresholds established using standards samples. However, the SVD-BC technique was found to introduce noise which led to detection of false peaks at the lower detection thresholds. As a result, the AWLS technique gave more precise peak counts than the SVD-BC technique, particularly at the lower detection thresholds. While the AWLS technique resulted in more consistent percent residual standard deviation values, a statistical improvement in peak quantification after background correction was not found regardless of the background correction technique used. Copyright © 2012 Elsevier B.V. All rights reserved.
Strand-Specific RNA-Seq Analyses of Fruiting Body Development in Coprinopsis cinerea.

Directory of Open Access Journals (Sweden)

Hajime Muraguchi

Full Text Available The basidiomycete fungus Coprinopsis cinerea is an important model system for multicellular development. Fruiting bodies of C. cinerea are typical mushrooms, which can be produced synchronously on defined media in the laboratory. To investigate the transcriptome in detail during fruiting body development, high-throughput sequencing (RNA-seq was performed using cDNA libraries strand-specifically constructed from 13 points (stages/tissues with two biological replicates. The reads were aligned to 14,245 predicted transcripts, and counted for forward and reverse transcripts. Differentially expressed genes (DEGs between two adjacent points and between vegetative mycelium and each point were detected by Tag Count Comparison (TCC. To validate RNA-seq data, expression levels of selected genes were compared using RPKM values in RNA-seq data and qRT-PCR data, and DEGs detected in microarray data were examined in MA plots of RNA-seq data by TCC. We discuss events deduced from GO analysis of DEGs. In addition, we uncovered both transcription factor candidates and antisense transcripts that are likely to be involved in developmental regulation for fruiting.
Peaked signals from dark matter velocity structures in direct detection experiments

International Nuclear Information System (INIS)

Lang, Rafael F.; Weiner, Neal

2010-01-01

In direct dark matter detection experiments, conventional elastic scattering of WIMPs results in exponentially falling recoil spectra. In contrast, theories of WIMPs with excited states can lead to nuclear recoil spectra that peak at finite recoil energies E R . The peaks of such signals are typically fairly broad, with ΔE R /E peak ∼ 1. We show that in the presence of dark matter structures with low velocity dispersion, such as streams or clumps, peaks from up-scattering can become extremely narrow with FWHM of a few keV only. This differs dramatically from the conventionally expected WIMP spectrum and would, once detected, open the possibility to measure the dark matter velocity structure with high accuracy. As an intriguing example, we confront the observed cluster of 3 events near 42 keV from the CRESST commissioning run with this scenario. Inelastic dark matter particles with a wide range of parameters are capable of producing such a narrow peak. We calculate the possible signals at other experiments, and find that such particles could also give rise to the signal at DAMA, although not from the same stream. Over some range of parameters, a signal would be visible at xenon experiments. We show that such dark matter peaks are a very clear signal and can be easily disentangled from potential backgrounds, both terrestrial or due to WIMP down-scattering, by an enhanced annual modulation in both the amplitude of the signal and its spectral shape
Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads.

Science.gov (United States)

Sasagawa, Yohei; Danno, Hiroki; Takada, Hitomi; Ebisawa, Masashi; Tanaka, Kaori; Hayashi, Tetsutaro; Kurisaki, Akira; Nikaido, Itoshi

2018-03-09

High-throughput single-cell RNA-seq methods assign limited unique molecular identifier (UMI) counts as gene expression values to single cells from shallow sequence reads and detect limited gene counts. We thus developed a high-throughput single-cell RNA-seq method, Quartz-Seq2, to overcome these issues. Our improvements in the reaction steps make it possible to effectively convert initial reads to UMI counts, at a rate of 30-50%, and detect more genes. To demonstrate the power of Quartz-Seq2, we analyzed approximately 10,000 transcriptomes from in vitro embryonic stem cells and an in vivo stromal vascular fraction with a limited number of reads.
"Hook"-calibration of GeneChip-microarrays: Chip characteristics and expression measures

Directory of Open Access Journals (Sweden)

Krohn Knut

2008-08-01

Full Text Available Abstract Background Microarray experiments rely on several critical steps that may introduce biases and uncertainty in downstream analyses. These steps include mRNA sample extraction, amplification and labelling, hybridization, and scanning causing chip-specific systematic variations on the raw intensity level. Also the chosen array-type and the up-to-dateness of the genomic information probed on the chip affect the quality of the expression measures. In the accompanying publication we presented theory and algorithm of the so-called hook method which aims at correcting expression data for systematic biases using a series of new chip characteristics. Results In this publication we summarize the essential chip characteristics provided by this method, analyze special benchmark experiments to estimate transcript related expression measures and illustrate the potency of the method to detect and to quantify the quality of a particular hybridization. It is shown that our single-chip approach provides expression measures responding linearly on changes of the transcript concentration over three orders of magnitude. In addition, the method calculates a detection call judging the relation between the signal and the detection limit of the particular measurement. The performance of the method in the context of different chip generations and probe set assignments is illustrated. The hook method characterizes the RNA-quality in terms of the 3'/5'-amplification bias and the sample-specific calling rate. We show that the proper judgement of these effects requires the disentanglement of non-specific and specific hybridization which, otherwise, can lead to misinterpretations of expression changes. The consequences of modifying probe/target interactions by either changing the labelling protocol or by substituting RNA by DNA targets are demonstrated. Conclusion The single-chip based hook-method provides accurate expression estimates and chip-summary characteristics
An Integrated Approach for RNA-seq Data Normalization.

Science.gov (United States)

Yang, Shengping; Mercante, Donald E; Zhang, Kun; Fang, Zhide

2016-01-01

DNA copy number alteration is common in many cancers. Studies have shown that insertion or deletion of DNA sequences can directly alter gene expression, and significant correlation exists between DNA copy number and gene expression. Data normalization is a critical step in the analysis of gene expression generated by RNA-seq technology. Successful normalization reduces/removes unwanted nonbiological variations in the data, while keeping meaningful information intact. However, as far as we know, no attempt has been made to adjust for the variation due to DNA copy number changes in RNA-seq data normalization. In this article, we propose an integrated approach for RNA-seq data normalization. Comparisons show that the proposed normalization can improve power for downstream differentially expressed gene detection and generate more biologically meaningful results in gene profiling. In addition, our findings show that due to the effects of copy number changes, some housekeeping genes are not always suitable internal controls for studying gene expression. Using information from DNA copy number, integrated approach is successful in reducing noises due to both biological and nonbiological causes in RNA-seq data, thus increasing the accuracy of gene profiling.
SignalSpider: Probabilistic pattern discovery on multiple normalized ChIP-Seq signal profiles

KAUST Repository

Wong, Kachun

2014-09-05

Motivation: Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-Seq) measures the genome-wide occupancy of transcription factors in vivo. Different combinations of DNA-binding protein occupancies may result in a gene being expressed in different tissues or at different developmental stages. To fully understand the functions of genes, it is essential to develop probabilistic models on multiple ChIP-Seq profiles to decipher the combinatorial regulatory mechanisms by multiple transcription factors. Results: In this work, we describe a probabilistic model (SignalSpider) to decipher the combinatorial binding events of multiple transcription factors. Comparing with similar existing methods, we found SignalSpider performs better in clustering promoter and enhancer regions. Notably, SignalSpider can learn higher-order combinatorial patterns from multiple ChIP-Seq profiles. We have applied SignalSpider on the normalized ChIP-Seq profiles from the ENCODE consortium and learned model instances. We observed different higher-order enrichment and depletion patterns across sets of proteins. Those clustering patterns are supported by Gene Ontology (GO) enrichment, evolutionary conservation and chromatin interaction enrichment, offering biological insights for further focused studies. We also proposed a specific enrichment map visualization method to reveal the genome-wide transcription factor combinatorial patterns from the models built, which extend our existing fine-scale knowledge on gene regulation to a genome-wide level. Availability and implementation: The matrix-algebra-optimized executables and source codes are available at the authors\\' websites: http://www.cs.toronto.edu/∼wkc/SignalSpider. Contact: Supplementary information: Supplementary data are available at Bioinformatics online.
Probabilistic model for untargeted peak detection in LC-MS using Bayesian statistics

NARCIS (Netherlands)

Woldegebriel, M.; Vivó-Truyols, G.

2015-01-01

We introduce a novel Bayesian probabilistic peak detection algorithm for liquid chromatography mass spectroscopy (LC-MS). The final probabilistic result allows the user to make a final decision about which points in a 2 chromatogram are affected by a chromatographic peak and which ones are only
Probabilistic Model for Untargeted Peak Detection in LC-MS Using Bayesian Statistics.

Science.gov (United States)

Woldegebriel, Michael; Vivó-Truyols, Gabriel

2015-07-21

We introduce a novel Bayesian probabilistic peak detection algorithm for liquid chromatography-mass spectroscopy (LC-MS). The final probabilistic result allows the user to make a final decision about which points in a chromatogram are affected by a chromatographic peak and which ones are only affected by noise. The use of probabilities contrasts with the traditional method in which a binary answer is given, relying on a threshold. By contrast, with the Bayesian peak detection presented here, the values of probability can be further propagated into other preprocessing steps, which will increase (or decrease) the importance of chromatographic regions into the final results. The present work is based on the use of the statistical overlap theory of component overlap from Davis and Giddings (Davis, J. M.; Giddings, J. Anal. Chem. 1983, 55, 418-424) as prior probability in the Bayesian formulation. The algorithm was tested on LC-MS Orbitrap data and was able to successfully distinguish chemical noise from actual peaks without any data preprocessing.
Detection of Alicyclobacillus species in fruit juice using a random genomic DNA microarray chip.

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Jang, Jun Hyeong; Kim, Sun-Joong; Yoon, Bo Hyun; Ryu, Jee-Hoon; Gu, Man Bock; Chang, Hyo-Ihl

2011-06-01

This study describes a method using a DNA microarray chip to rapidly and simultaneously detect Alicyclobacillus species in orange juice based on the hybridization of genomic DNA with random probes. Three food spoilage bacteria were used in this study: Alicyclobacillus acidocaldarius, Alicyclobacillus acidoterrestris, and Alicyclobacillus cycloheptanicus. The three Alicyclobacillus species were adjusted to 2 × 10(3) CFU/ml and inoculated into pasteurized 100% pure orange juice. Cy5-dCTP labeling was used for reference signals, and Cy3-dCTP was labeled for target genomic DNA. The molar ratio of 1:1 of Cy3-dCTP and Cy5-dCTP was used. DNA microarray chips were fabricated using randomly fragmented DNA of Alicyclobacillus spp. and were hybridized with genomic DNA extracted from Bacillus spp. Genomic DNA extracted from Alicyclobacillus spp. showed a significantly higher hybridization rate compared with DNA of Bacillus spp., thereby distinguishing Alicyclobacillus spp. from Bacillus spp. The results showed that the microarray DNA chip containing randomly fragmented genomic DNA was specific and clearly identified specific food spoilage bacteria. This microarray system is a good tool for rapid and specific detection of thermophilic spoilage bacteria, mainly Alicyclobacillus spp., and is useful and applicable to the fruit juice industry.
Hydrocarbon isotope detection by elastic peak electron spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Kostanovskiy, I.A., E-mail: kostanovskiyia@gmail.com [National Research University MPEI, Krasnokazarmennaya 14, 111250 Moscow (Russian Federation); Afanas’ev, V.P. [National Research University MPEI, Krasnokazarmennaya 14, 111250 Moscow (Russian Federation); Naujoks, D. [Max-Planck-Institut für Plasmaphysik, Teilinstitut Greifswald, Wendelsteinstraße 1, D-17491 Greifswald (Germany); Mayer, M. [Max-Planck-Institut für Plasmaphysik, D-85748 Garching (Germany)

2015-07-15

Highlights: • PCVD hydrocarbon coatings containing protium or deuterium are analyzed via NRA, ERD, XPS and EPES. • EPES analysis with modern electron energy analyzer SPECS Phoibos 225 shows a clear signal from the hydrogen isotopes. • Different primary energies and scattering angles help to quantify isotope content from EPES spectra. - Abstract: Experimental results on the hydrocarbon isotope analysis by elastic peak electron spectroscopy are presented. Amorphous hydrocarbon samples (a-C:H, a-C:D) are prepared by PCVD and analyzed by nuclear reaction analysis (NRA), elastic recoil detection analysis (ERD), X-ray photoelectron spectroscopy (XPS) and elastic peak electron spectroscopy (EPES). Electron energy spectra show a clear signal from the hydrogen isotopes deuterium and protium. Different incident energies and scattering geometries help to resolve plasmon and elastic energy losses.
Hydrocarbon isotope detection by elastic peak electron spectroscopy

International Nuclear Information System (INIS)

Kostanovskiy, I.A.; Afanas’ev, V.P.; Naujoks, D.; Mayer, M.

2015-01-01

Highlights: • PCVD hydrocarbon coatings containing protium or deuterium are analyzed via NRA, ERD, XPS and EPES. • EPES analysis with modern electron energy analyzer SPECS Phoibos 225 shows a clear signal from the hydrogen isotopes. • Different primary energies and scattering angles help to quantify isotope content from EPES spectra. - Abstract: Experimental results on the hydrocarbon isotope analysis by elastic peak electron spectroscopy are presented. Amorphous hydrocarbon samples (a-C:H, a-C:D) are prepared by PCVD and analyzed by nuclear reaction analysis (NRA), elastic recoil detection analysis (ERD), X-ray photoelectron spectroscopy (XPS) and elastic peak electron spectroscopy (EPES). Electron energy spectra show a clear signal from the hydrogen isotopes deuterium and protium. Different incident energies and scattering geometries help to resolve plasmon and elastic energy losses
Evaluation of the peak MA-6600L microwave motion detection system

International Nuclear Information System (INIS)

1979-02-01

A series of tests was performed on the Peak MA-6600L motion detection system. The primary objectives of these tests were to determine sensor detection patterns and to quantitate the effects of intruder velocity. System susceptibility to fluorescent lights, oscillatory motion, and environmental factors was also examined
An R-peak detection method that uses an SVD filter and a search back system.

Science.gov (United States)

Jung, Woo-Hyuk; Lee, Sang-Goog

2012-12-01

In this paper, we present a method for detecting the R-peak of an ECG signal by using an singular value decomposition (SVD) filter and a search back system. The ECG signal was detected in two phases: the pre-processing phase and the decision phase. The pre-processing phase consisted of the stages for the SVD filter, Butterworth High Pass Filter (HPF), moving average (MA), and squaring, whereas the decision phase consisted of a single stage that detected the R-peak. In the pre-processing phase, the SVD filter removed noise while the Butterworth HPF eliminated baseline wander. The MA removed the remaining noise of the signal that had gone through the SVD filter to make the signal smooth, and squaring played a role in strengthening the signal. In the decision phase, the threshold was used to set the interval before detecting the R-peak. When the latest R-R interval (RRI), suggested by Hamilton et al., was greater than 150% of the previous RRI, the method of detecting the R-peak in such an interval was modified to be 150% or greater than the smallest interval of the two most latest RRIs. When the modified search back system was used, the error rate of the peak detection decreased to 0.29%, compared to 1.34% when the modified search back system was not used. Consequently, the sensitivity was 99.47%, the positive predictivity was 99.47%, and the detection error was 1.05%. Furthermore, the quality of the signal in data with a substantial amount of noise was improved, and thus, the R-peak was detected effectively. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.
Network analysis of ChIP-Seq data reveals key genes in prostate cancer.

Science.gov (United States)

Zhang, Yu; Huang, Zhen; Zhu, Zhiqiang; Liu, Jianwei; Zheng, Xin; Zhang, Yuhai

2014-09-03

Prostate cancer (PC) is the second most common cancer among men in the United States, and it imposes a considerable threat to human health. A deep understanding of its underlying molecular mechanisms is the premise for developing effective targeted therapies. Recently, deep transcriptional sequencing has been used as an effective genomic assay to obtain insights into diseases and may be helpful in the study of PC. In present study, ChIP-Seq data for PC and normal samples were compared, and differential peaks identified, based upon fold changes (with P-values calculated with t-tests). Annotations of these peaks were performed. Protein-protein interaction (PPI) network analysis was performed with BioGRID and constructed with Cytoscape, following which the highly connected genes were screened. We obtained a total of 5,570 differential peaks, including 3,726 differentially enriched peaks in tumor samples and 1,844 differentially enriched peaks in normal samples. There were eight significant regions of the peaks. The intergenic region possessed the highest score (51%), followed by intronic (31%) and exonic (11%) regions. The analysis revealed the top 35 highly connected genes, which comprised 33 differential genes (such as YWHAQ, tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein and θ polypeptide) from ChIP-Seq data and 2 differential genes retrieved from the PPI network: UBA52 (ubiquitin A-52 residue ribosomal protein fusion product (1) and SUMO2 (SMT3 suppressor of mif two 3 homolog (2) . Our findings regarding potential PC-related genes increase the understanding of PC and provides direction for future research.
A wavelet transform algorithm for peak detection and application to powder x-ray diffraction data.

Science.gov (United States)

Gregoire, John M; Dale, Darren; van Dover, R Bruce

2011-01-01

Peak detection is ubiquitous in the analysis of spectral data. While many noise-filtering algorithms and peak identification algorithms have been developed, recent work [P. Du, W. Kibbe, and S. Lin, Bioinformatics 22, 2059 (2006); A. Wee, D. Grayden, Y. Zhu, K. Petkovic-Duran, and D. Smith, Electrophoresis 29, 4215 (2008)] has demonstrated that both of these tasks are efficiently performed through analysis of the wavelet transform of the data. In this paper, we present a wavelet-based peak detection algorithm with user-defined parameters that can be readily applied to the application of any spectral data. Particular attention is given to the algorithm's resolution of overlapping peaks. The algorithm is implemented for the analysis of powder diffraction data, and successful detection of Bragg peaks is demonstrated for both low signal-to-noise data from theta-theta diffraction of nanoparticles and combinatorial x-ray diffraction data from a composition spread thin film. These datasets have different types of background signals which are effectively removed in the wavelet-based method, and the results demonstrate that the algorithm provides a robust method for automated peak detection.
GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases.

Science.gov (United States)

Zhu, Lihua Julie; Lawrence, Michael; Gupta, Ankit; Pagès, Hervé; Kucukural, Alper; Garber, Manuel; Wolfe, Scot A

2017-05-15

Genome editing technologies developed around the CRISPR-Cas9 nuclease system have facilitated the investigation of a broad range of biological questions. These nucleases also hold tremendous promise for treating a variety of genetic disorders. In the context of their therapeutic application, it is important to identify the spectrum of genomic sequences that are cleaved by a candidate nuclease when programmed with a particular guide RNA, as well as the cleavage efficiency of these sites. Powerful new experimental approaches, such as GUIDE-seq, facilitate the sensitive, unbiased genome-wide detection of nuclease cleavage sites within the genome. Flexible bioinformatics analysis tools for processing GUIDE-seq data are needed. Here, we describe an open source, open development software suite, GUIDEseq, for GUIDE-seq data analysis and annotation as a Bioconductor package in R. The GUIDEseq package provides a flexible platform with more than 60 adjustable parameters for the analysis of datasets associated with custom nuclease applications. These parameters allow data analysis to be tailored to different nuclease platforms with different length and complexity in their guide and PAM recognition sequences or their DNA cleavage position. They also enable users to customize sequence aggregation criteria, and vary peak calling thresholds that can influence the number of potential off-target sites recovered. GUIDEseq also annotates potential off-target sites that overlap with genes based on genome annotation information, as these may be the most important off-target sites for further characterization. In addition, GUIDEseq enables the comparison and visualization of off-target site overlap between different datasets for a rapid comparison of different nuclease configurations or experimental conditions. For each identified off-target, the GUIDEseq package outputs mapped GUIDE-Seq read count as well as cleavage score from a user specified off-target cleavage score prediction
Study of preamplifier, shaper and peak detector in readout ASIC for particle detector

International Nuclear Information System (INIS)

Wang Ke; Zhang Shengjun; Fan Lei; Li Xian

2014-01-01

Recently, kinds of particle detectors have used Application Specific Integrated Circuits (ASIC) in their electronics readout system and ASICs have been designed in China now. This project designed a multi-channel readout ASIC for general detector. The chip has Preamplifier, Shaper and Peak Detector embedded for easy readout. For each channel, signal which is preprocessed by a low-noise preamplifier is sent to the shaper to form a quasi-Gaussian pulse and keep its peak for readout. This chip and modules of individual Preamplifier, Shaper and Peak Detector have been manufactured, results will be reported in time. (authors)
Modeling ChIP sequencing in silico with applications.

Directory of Open Access Journals (Sweden)

Zhengdong D Zhang

2008-08-01

Full Text Available ChIP sequencing (ChIP-seq is a new method for genomewide mapping of protein binding sites on DNA. It has generated much excitement in functional genomics. To score data and determine adequate sequencing depth, both the genomic background and the binding sites must be properly modeled. To develop a computational foundation to tackle these issues, we first performed a study to characterize the observed statistical nature of this new type of high-throughput data. By linking sequence tags into clusters, we show that there are two components to the distribution of tag counts observed in a number of recent experiments: an initial power-law distribution and a subsequent long right tail. Then we develop in silico ChIP-seq, a computational method to simulate the experimental outcome by placing tags onto the genome according to particular assumed distributions for the actual binding sites and for the background genomic sequence. In contrast to current assumptions, our results show that both the background and the binding sites need to have a markedly nonuniform distribution in order to correctly model the observed ChIP-seq data, with, for instance, the background tag counts modeled by a gamma distribution. On the basis of these results, we extend an existing scoring approach by using a more realistic genomic-background model. This enables us to identify transcription-factor binding sites in ChIP-seq data in a statistically rigorous fashion.
Piezoresistive microcantilever based lab-on-a-chip system for detection of macronutrients in the soil

Science.gov (United States)

Patkar, Rajul S.; Ashwin, Mamta; Rao, V. Ramgopal

2017-12-01

Monitoring of soil nutrients is very important in precision agriculture. In this paper, we have demonstrated a micro electro mechanical system based lab-on-a-chip system for detection of various soil macronutrients which are available in ionic form K+, NO3-, and H2PO4-. These sensors are highly sensitive piezoresistive silicon microcantilevers coated with a polymer matrix containing methyltridodecylammonium nitrate ionophore/ nitrate ionophore VI for nitrate sensing, 18-crown-6 ether for potassium sensing and Tributyltin chloride for phosphate detection. A complete lab-on-a-chip system integrating a highly sensitive current excited Wheatstone's bridge based portable electronic setup along with arrays of microcantilever devices mounted on a printed circuit board with a liquid flow cell for on the site experimentation for soil test has been demonstrated.

Exploiting Speech Recognition Transcripts for Narrative Peak Detection in Short-Form Documentaries

NARCIS (Netherlands)

Larson, Martha; Jochems, Bart; Smits, Ewine; Ordelman, Roeland J.F.; Peters, Carol; Caputo, Barbara; Gonzalo, Julio

2010-01-01

Narrative peaks are points at which the viewer perceives a spike in the level of dramatic tension within the narrative ﬂow of a video. This paper reports on four approaches to narrative peak detection in television documentaries that were developed by a joint team consisting of members from Delft
Improved Peak Detection and Deconvolution of Native Electrospray Mass Spectra from Large Protein Complexes.

Science.gov (United States)

Lu, Jonathan; Trnka, Michael J; Roh, Soung-Hun; Robinson, Philip J J; Shiau, Carrie; Fujimori, Danica Galonic; Chiu, Wah; Burlingame, Alma L; Guan, Shenheng

2015-12-01

Native electrospray-ionization mass spectrometry (native MS) measures biomolecules under conditions that preserve most aspects of protein tertiary and quaternary structure, enabling direct characterization of large intact protein assemblies. However, native spectra derived from these assemblies are often partially obscured by low signal-to-noise as well as broad peak shapes because of residual solvation and adduction after the electrospray process. The wide peak widths together with the fact that sequential charge state series from highly charged ions are closely spaced means that native spectra containing multiple species often suffer from high degrees of peak overlap or else contain highly interleaved charge envelopes. This situation presents a challenge for peak detection, correct charge state and charge envelope assignment, and ultimately extraction of the relevant underlying mass values of the noncovalent assemblages being investigated. In this report, we describe a comprehensive algorithm developed for addressing peak detection, peak overlap, and charge state assignment in native mass spectra, called PeakSeeker. Overlapped peaks are detected by examination of the second derivative of the raw mass spectrum. Charge state distributions of the molecular species are determined by fitting linear combinations of charge envelopes to the overall experimental mass spectrum. This software is capable of deconvoluting heterogeneous, complex, and noisy native mass spectra of large protein assemblies as demonstrated by analysis of (1) synthetic mononucleosomes containing severely overlapping peaks, (2) an RNA polymerase II/α-amanitin complex with many closely interleaved ion signals, and (3) human TriC complex containing high levels of background noise. Graphical Abstract ᅟ.
Unveiling combinatorial regulation through the combination of ChIP information and in silico cis-regulatory module detection

Science.gov (United States)

Sun, Hong; Guns, Tias; Fierro, Ana Carolina; Thorrez, Lieven; Nijssen, Siegfried; Marchal, Kathleen

2012-01-01

Computationally retrieving biologically relevant cis-regulatory modules (CRMs) is not straightforward. Because of the large number of candidates and the imperfection of the screening methods, many spurious CRMs are detected that are as high scoring as the biologically true ones. Using ChIP-information allows not only to reduce the regions in which the binding sites of the assayed transcription factor (TF) should be located, but also allows restricting the valid CRMs to those that contain the assayed TF (here referred to as applying CRM detection in a query-based mode). In this study, we show that exploiting ChIP-information in a query-based way makes in silico CRM detection a much more feasible endeavor. To be able to handle the large datasets, the query-based setting and other specificities proper to CRM detection on ChIP-Seq based data, we developed a novel powerful CRM detection method ‘CPModule’. By applying it on a well-studied ChIP-Seq data set involved in self-renewal of mouse embryonic stem cells, we demonstrate how our tool can recover combinatorial regulation of five known TFs that are key in the self-renewal of mouse embryonic stem cells. Additionally, we make a number of new predictions on combinatorial regulation of these five key TFs with other TFs documented in TRANSFAC. PMID:22422841
A semi-automatic method for peak and valley detection in free-breathing respiratory waveforms

International Nuclear Information System (INIS)

Lu Wei; Nystrom, Michelle M.; Parikh, Parag J.; Fooshee, David R.; Hubenschmidt, James P.; Bradley, Jeffrey D.; Low, Daniel A.

2006-01-01

The existing commercial software often inadequately determines respiratory peaks for patients in respiration correlated computed tomography. A semi-automatic method was developed for peak and valley detection in free-breathing respiratory waveforms. First the waveform is separated into breath cycles by identifying intercepts of a moving average curve with the inspiration and expiration branches of the waveform. Peaks and valleys were then defined, respectively, as the maximum and minimum between pairs of alternating inspiration and expiration intercepts. Finally, automatic corrections and manual user interventions were employed. On average for each of the 20 patients, 99% of 307 peaks and valleys were automatically detected in 2.8 s. This method was robust for bellows waveforms with large variations
Systolic peak detection in acceleration photoplethysmograms measured from emergency responders in tropical conditions.

Science.gov (United States)

Elgendi, Mohamed; Norton, Ian; Brearley, Matt; Abbott, Derek; Schuurmans, Dale

2013-01-01

Photoplethysmogram (PPG) monitoring is not only essential for critically ill patients in hospitals or at home, but also for those undergoing exercise testing. However, processing PPG signals measured after exercise is challenging, especially if the environment is hot and humid. In this paper, we propose a novel algorithm that can detect systolic peaks under challenging conditions, as in the case of emergency responders in tropical conditions. Accurate systolic-peak detection is an important first step for the analysis of heart rate variability. Algorithms based on local maxima-minima, first-derivative, and slope sum are evaluated, and a new algorithm is introduced to improve the detection rate. With 40 healthy subjects, the new algorithm demonstrates the highest overall detection accuracy (99.84% sensitivity, 99.89% positive predictivity). Existing algorithms, such as Billauer's, Li's and Zong's, have comparable although lower accuracy. However, the proposed algorithm presents an advantage for real-time applications by avoiding human intervention in threshold determination. For best performance, we show that a combination of two event-related moving averages with an offset threshold has an advantage in detecting systolic peaks, even in heat-stressed PPG signals.
LipidSeq: a next-generation clinical resequencing panel for monogenic dyslipidemias[S

Science.gov (United States)

Johansen, Christopher T.; Dubé, Joseph B.; Loyzer, Melissa N.; MacDonald, Austin; Carter, David E.; McIntyre, Adam D.; Cao, Henian; Wang, Jian; Robinson, John F.; Hegele, Robert A.

2014-01-01

We report the design of a targeted resequencing panel for monogenic dyslipidemias, LipidSeq, for the purpose of replacing Sanger sequencing in the clinical detection of dyslipidemia-causing variants. We also evaluate the performance of the LipidSeq approach versus Sanger sequencing in 84 patients with a range of phenotypes including extreme blood lipid concentrations as well as additional dyslipidemias and related metabolic disorders. The panel performs well, with high concordance (95.2%) in samples with known mutations based on Sanger sequencing and a high detection rate (57.9%) of mutations likely to be causative for disease in samples not previously sequenced. Clinical implementation of LipidSeq has the potential to aid in the molecular diagnosis of patients with monogenic dyslipidemias with a high degree of speed and accuracy and at lower cost than either Sanger sequencing or whole exome sequencing. Furthermore, LipidSeq will help to provide a more focused picture of monogenic and polygenic contributors that underlie dyslipidemia while excluding the discovery of incidental pathogenic clinically actionable variants in nonmetabolism-related genes, such as oncogenes, that would otherwise be identified by a whole exome approach, thus minimizing potential ethical issues. PMID:24503134
Peaked signals from dark matter velocity structures in direct detection experiments

Science.gov (United States)

Lang, Rafael F.; Weiner, Neal

2010-06-01

In direct dark matter detection experiments, conventional elastic scattering of WIMPs results in exponentially falling recoil spectra. In contrast, theories of WIMPs with excited states can lead to nuclear recoil spectra that peak at finite recoil energies ER. The peaks of such signals are typically fairly broad, with ΔER/Epeak ~ 1. We show that in the presence of dark matter structures with low velocity dispersion, such as streams or clumps, peaks from up-scattering can become extremely narrow with FWHM of a few keV only. This differs dramatically from the conventionally expected WIMP spectrum and would, once detected, open the possibility to measure the dark matter velocity structure with high accuracy. As an intriguing example, we confront the observed cluster of 3 events near 42 keV from the CRESST commissioning run with this scenario. Inelastic dark matter particles with a wide range of parameters are capable of producing such a narrow peak. We calculate the possible signals at other experiments, and find that such particles could also give rise to the signal at DAMA, although not from the same stream. Over some range of parameters, a signal would be visible at xenon experiments. We show that such dark matter peaks are a very clear signal and can be easily disentangled from potential backgrounds, both terrestrial or due to WIMP down-scattering, by an enhanced annual modulation in both the amplitude of the signal and its spectral shape.
ChIPWig: a random access-enabling lossless and lossy compression method for ChIP-seq data.

Science.gov (United States)

Ravanmehr, Vida; Kim, Minji; Wang, Zhiying; Milenkovic, Olgica

2018-03-15

Chromatin immunoprecipitation sequencing (ChIP-seq) experiments are inexpensive and time-efficient, and result in massive datasets that introduce significant storage and maintenance challenges. To address the resulting Big Data problems, we propose a lossless and lossy compression framework specifically designed for ChIP-seq Wig data, termed ChIPWig. ChIPWig enables random access, summary statistics lookups and it is based on the asymptotic theory of optimal point density design for nonuniform quantizers. We tested the ChIPWig compressor on 10 ChIP-seq datasets generated by the ENCODE consortium. On average, lossless ChIPWig reduced the file sizes to merely 6% of the original, and offered 6-fold compression rate improvement compared to bigWig. The lossy feature further reduced file sizes 2-fold compared to the lossless mode, with little or no effects on peak calling and motif discovery using specialized NarrowPeaks methods. The compression and decompression speed rates are of the order of 0.2 sec/MB using general purpose computers. The source code and binaries are freely available for download at https://github.com/vidarmehr/ChIPWig-v2, implemented in C ++. milenkov@illinois.edu. Supplementary data are available at Bioinformatics online.
Cardinality enhancement utilizing Sequential Algorithm (SeQ code in OCDMA system

Directory of Open Access Journals (Sweden)

Fazlina C. A. S.

2017-01-01

Full Text Available Optical Code Division Multiple Access (OCDMA has been important with increasing demand for high capacity and speed for communication in optical networks because of OCDMA technique high efficiency that can be achieved, hence fibre bandwidth is fully used. In this paper we will focus on Sequential Algorithm (SeQ code with AND detection technique using Optisystem design tool. The result revealed SeQ code capable to eliminate Multiple Access Interference (MAI and improve Bit Error Rate (BER, Phase Induced Intensity Noise (PIIN and orthogonally between users in the system. From the results, SeQ shows good performance of BER and capable to accommodate 190 numbers of simultaneous users contrast with existing code. Thus, SeQ code have enhanced the system about 36% and 111% of FCC and DCS code. In addition, SeQ have good BER performance 10-25 at 155 Mbps in comparison with 622 Mbps, 1 Gbps and 2 Gbps bit rate. From the plot graph, 155 Mbps bit rate is suitable enough speed for FTTH and LAN networks. Resolution can be made based on the superior performance of SeQ code. Thus, these codes will give an opportunity in OCDMA system for better quality of service in an optical access network for future generation's usage
Cardinality enhancement utilizing Sequential Algorithm (SeQ) code in OCDMA system

Science.gov (United States)

Fazlina, C. A. S.; Rashidi, C. B. M.; Rahman, A. K.; Aljunid, S. A.

2017-11-01

Optical Code Division Multiple Access (OCDMA) has been important with increasing demand for high capacity and speed for communication in optical networks because of OCDMA technique high efficiency that can be achieved, hence fibre bandwidth is fully used. In this paper we will focus on Sequential Algorithm (SeQ) code with AND detection technique using Optisystem design tool. The result revealed SeQ code capable to eliminate Multiple Access Interference (MAI) and improve Bit Error Rate (BER), Phase Induced Intensity Noise (PIIN) and orthogonally between users in the system. From the results, SeQ shows good performance of BER and capable to accommodate 190 numbers of simultaneous users contrast with existing code. Thus, SeQ code have enhanced the system about 36% and 111% of FCC and DCS code. In addition, SeQ have good BER performance 10-25 at 155 Mbps in comparison with 622 Mbps, 1 Gbps and 2 Gbps bit rate. From the plot graph, 155 Mbps bit rate is suitable enough speed for FTTH and LAN networks. Resolution can be made based on the superior performance of SeQ code. Thus, these codes will give an opportunity in OCDMA system for better quality of service in an optical access network for future generation's usage
Experiment list: SRX186753 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available der=Lonza || datatype=ChipSeq || datatype description=Chromatin IP Sequencing || antibody antibodydescription=Rabbit polyclonal antib...on. Antibody Target: H3K79me2 || antibody targetdescription=H3K79me2 is a mark of the transcriptional transi...tion region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). || antibody... vendorname=Active Motif || antibody vendorid=39143 || controlid=wgEncodeEH0...00093 || replicate=1,2 || softwareversion=ScriptureVPaperR3 || cell sex=U || antibody=H3K79me2 || antibody antibody
Simultaneous detection of multiple HPV DNA via bottom-well microfluidic chip within an infra-red PCR platform.

Science.gov (United States)

Liu, Wenjia; Warden, Antony; Sun, Jiahui; Shen, Guangxia; Ding, Xianting

2018-03-01

Portable Polymerase Chain Reaction (PCR) devices combined with microfluidic chips or lateral flow stripes have shown great potential in the field of point-of-need testing (PoNT) as they only require a small volume of patient sample and are capable of presenting results in a short time. However, the detection for multiple targets in this field leaves much to be desired. Herein, we introduce a novel PCR platform by integrating a bottom-well microfluidic chip with an infra-red (IR) excited temperature control method and fluorescence co-detection of three PCR products. Microfluidic chips are utilized to partition different samples into individual bottom-wells. The oil phase in the main channel contains multi-walled carbon nanotubes which were used as a heat transfer medium that absorbs energy from the IR-light-emitting diode (LED) and transfers heat to the water phase below. Cyclical rapid heating and cooling necessary for PCR are achieved by alternative power switching of the IR-LED and Universal Serial Bus (USB) mini-fan with a pulse width modulation scheme. This design of the IR-LED PCR platform is economic, compact, and fully portable, making it a promising application in the field of PoNT. The bottom-well microfluidic chip and IR-LED PCR platform were combined to fulfill a three-stage thermal cycling PCR for 40 cycles within 90 min for Human Papilloma Virus (HPV) detection. The PCR fluorescent signal was successfully captured at the end of each cycle. The technique introduced here has broad applications in nucleic acid amplification and PoNT devices.
Detection of a putative virulence cadF gene of Campylobacter jejuni obtained from different sources using a microfabricated PCR chip

DEFF Research Database (Denmark)

Poulsen, Claus Riber; El-Ali, Jamil; Perch-Nielsen, Ivan R.

2005-01-01

A microfabricated polymerase chain reaction (PCR) chip made of epoxy-based photoresist (SU-8) was recently designed and developed. In this study, we tested whether the PCR chip could be used for rapid detection of a potential virulence determinant, the cadF gene of Campylobacter jejuni. PCR...... was performed using published PCR conditions and primers for the C. jejuni cadF gene. DNA isolated from a C. jejuni reference strain CCUG 11284, C. jejuni isolates obtained from different sources (chicken and human), and Campylobacter whole cells were used as templates in the PCR tests. Conventional PCR in tube...... was used as the control. After optimization of the PCR chip, PCR positives on the chip were obtained from 91.0% (10/11) of the tested chips. A fast transition time was achieved with the PCR chip, and therefore a faster cycling time and a shorter PCR program were obtained. Using the PCR chip, the cadF gene...
A novel peak detection approach with chemical noise removal using short-time FFT for prOTOF MS data.

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Zhang, Shuqin; Wang, Honghui; Zhou, Xiaobo; Hoehn, Gerard T; DeGraba, Thomas J; Gonzales, Denise A; Suffredini, Anthony F; Ching, Wai-Ki; Ng, Michael K; Wong, Stephen T C

2009-08-01

Peak detection is a pivotal first step in biomarker discovery from MS data and can significantly influence the results of downstream data analysis steps. We developed a novel automatic peak detection method for prOTOF MS data, which does not require a priori knowledge of protein masses. Random noise is removed by an undecimated wavelet transform and chemical noise is attenuated by an adaptive short-time discrete Fourier transform. Isotopic peaks corresponding to a single protein are combined by extracting an envelope over them. Depending on the S/N, the desired peaks in each individual spectrum are detected and those with the highest intensity among their peak clusters are recorded. The common peaks among all the spectra are identified by choosing an appropriate cut-off threshold in the complete linkage hierarchical clustering. To remove the 1 Da shifting of the peaks, the peak corresponding to the same protein is determined as the detected peak with the largest number among its neighborhood. We validated this method using a data set of serial peptide and protein calibration standards. Compared with MoverZ program, our new method detects more peaks and significantly enhances S/N of the peak after the chemical noise removal. We then successfully applied this method to a data set from prOTOF MS spectra of albumin and albumin-bound proteins from serum samples of 59 patients with carotid artery disease compared to vascular disease-free patients to detect peaks with S/N> or =2. Our method is easily implemented and is highly effective to define peaks that will be used for disease classification or to highlight potential biomarkers.
Rapid, Sensitive, and Reusable Detection of Glucose by a Robust Radiofrequency Integrated Passive Device Biosensor Chip

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Kim, Nam-Young; Adhikari, Kishor Kumar; Dhakal, Rajendra; Chuluunbaatar, Zorigt; Wang, Cong; Kim, Eun-Soo

2015-01-01

Tremendous demands for sensitive and reliable label-free biosensors have stimulated intensive research into developing miniaturized radiofrequency resonators for a wide range of biomedical applications. Here, we report the development of a robust, reusable radiofrequency resonator based integrated passive device biosensor chip fabricated on a gallium arsenide substrate for the detection of glucose in water-glucose solutions and sera. As a result of the highly concentrated electromagnetic energy between the two divisions of an intertwined spiral inductor coupled with an interdigital capacitor, the proposed glucose biosensor chip exhibits linear detection ranges with high sensitivity at center frequency. This biosensor, which has a sensitivity of up to 199 MHz/mgmL−1 and a short response time of less than 2 sec, exhibited an ultralow detection limit of 0.033 μM and a reproducibility of 0.61% relative standard deviation. In addition, the quantities derived from the measured S-parameters, such as the propagation constant (γ), impedance (Z), resistance (R), inductance (L), conductance (G) and capacitance (C), enabled the effective multi-dimensional detection of glucose. PMID:25588958
Peak detection method evaluation for ion mobility spectrometry by using machine learning approaches.

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Hauschild, Anne-Christin; Kopczynski, Dominik; D'Addario, Marianna; Baumbach, Jörg Ingo; Rahmann, Sven; Baumbach, Jan

2013-04-16

Ion mobility spectrometry with pre-separation by multi-capillary columns (MCC/IMS) has become an established inexpensive, non-invasive bioanalytics technology for detecting volatile organic compounds (VOCs) with various metabolomics applications in medical research. To pave the way for this technology towards daily usage in medical practice, different steps still have to be taken. With respect to modern biomarker research, one of the most important tasks is the automatic classification of patient-specific data sets into different groups, healthy or not, for instance. Although sophisticated machine learning methods exist, an inevitable preprocessing step is reliable and robust peak detection without manual intervention. In this work we evaluate four state-of-the-art approaches for automated IMS-based peak detection: local maxima search, watershed transformation with IPHEx, region-merging with VisualNow, and peak model estimation (PME).We manually generated Metabolites 2013, 3 278 a gold standard with the aid of a domain expert (manual) and compare the performance of the four peak calling methods with respect to two distinct criteria. We first utilize established machine learning methods and systematically study their classification performance based on the four peak detectors' results. Second, we investigate the classification variance and robustness regarding perturbation and overfitting. Our main finding is that the power of the classification accuracy is almost equally good for all methods, the manually created gold standard as well as the four automatic peak finding methods. In addition, we note that all tools, manual and automatic, are similarly robust against perturbations. However, the classification performance is more robust against overfitting when using the PME as peak calling preprocessor. In summary, we conclude that all methods, though small differences exist, are largely reliable and enable a wide spectrum of real-world biomedical applications.
Encapsulation of Fluidic Tubing and Microelectrodes in Microfluidic Devices: Integrating Off-Chip Process and Coupling Conventional Capillary Electrophoresis with Electrochemical Detection.

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Becirovic, Vedada; Doonan, Steven R; Martin, R Scott

2013-08-21

In this paper, an approach to fabricate epoxy or polystyrene microdevices with encapsulated tubing and electrodes is described. Key features of this approach include a fixed alignment between the fluidic tubing and electrodes, the ability to polish the device when desired, and the low dead volume nature of the fluidic interconnects. It is shown that a variety of tubing can be encapsulated with this approach, including fused silica capillary, polyetheretherketone (PEEK), and perfluoroalkoxy (PFA), with the resulting tubing/microchip interface not leading to significant band broadening or plug dilution. The applicability of the devices with embedded tubing is demonstrated by integrating several off-chip analytical methods to the microchip. This includes droplet transfer, droplet desegmentation, and microchip-based flow injection analysis. Off-chip generated droplets can be transferred to the microchip with minimal coalescence, while flow injection studies showed improved peak shape and sensitivity when compared to the use of fluidic interconnects with an appreciable dead volume. Importantly, it is shown that this low dead volume approach can be extended to also enable the integration of conventional capillary electrophoresis (CE) with electrochemical detection. This is accomplished by embedding fused silica capillary along with palladium (for grounding the electrophoresis voltage) and platinum (for detection) electrodes. With this approach, up to 128,000 theoretical plates for dopamine was possible. In all cases, the tubing and electrodes are housed in a rigid base; this results in extremely robust devices that will be of interest to researchers wanting to develop microchips for use by non-experts.
Automated Peak Detection and Matching Algorithm for Gas Chromatography–Differential Mobility Spectrometry

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Fong, Sim S.; Rearden, Preshious; Kanchagar, Chitra; Sassetti, Christopher; Trevejo, Jose; Brereton, Richard G.

2013-01-01

A gas chromatography–differential mobility spectrometer (GC-DMS) involves a portable and selective mass analyzer that may be applied to chemical detection in the field. Existing approaches examine whole profiles and do not attempt to resolve peaks. A new approach for peak detection in the 2D GC-DMS chromatograms is reported. This method is demonstrated on three case studies: a simulated case study; a case study of headspace gas analysis of Mycobacterium tuberculosis (MTb) cultures consisting of three matching GC-DMS and GC-MS chromatograms; a case study consisting of 41 GC-DMS chromatograms of headspace gas analysis of MTb culture and media. PMID:21204557
Optimal use of tandem biotin and V5 tags in ChIP assays

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Krpic Sanja

2009-02-01

Full Text Available Abstract Background Chromatin immunoprecipitation (ChIP assays coupled to genome arrays (Chip-on-chip or massive parallel sequencing (ChIP-seq lead to the genome wide identification of binding sites of chromatin associated proteins. However, the highly variable quality of antibodies and the availability of epitopes in crosslinked chromatin can compromise genomic ChIP outcomes. Epitope tags have often been used as more reliable alternatives. In addition, we have employed protein in vivo biotinylation tagging as a very high affinity alternative to antibodies. In this paper we describe the optimization of biotinylation tagging for ChIP and its coupling to a known epitope tag in providing a reliable and efficient alternative to antibodies. Results Using the biotin tagged erythroid transcription factor GATA-1 as example, we describe several optimization steps for the application of the high affinity biotin streptavidin system in ChIP. We find that the omission of SDS during sonication, the use of fish skin gelatin as blocking agent and choice of streptavidin beads can lead to significantly improved ChIP enrichments and lower background compared to antibodies. We also show that the V5 epitope tag performs equally well under the conditions worked out for streptavidin ChIP and that it may suffer less from the effects of formaldehyde crosslinking. Conclusion The combined use of the very high affinity biotin tag with the less sensitive to crosslinking V5 tag provides for a flexible ChIP platform with potential implications in ChIP sequencing outcomes.
Optimal use of tandem biotin and V5 tags in ChIP assays

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Kolodziej, Katarzyna E; Pourfarzad, Farzin; de Boer, Ernie; Krpic, Sanja; Grosveld, Frank; Strouboulis, John

2009-01-01

Background Chromatin immunoprecipitation (ChIP) assays coupled to genome arrays (Chip-on-chip) or massive parallel sequencing (ChIP-seq) lead to the genome wide identification of binding sites of chromatin associated proteins. However, the highly variable quality of antibodies and the availability of epitopes in crosslinked chromatin can compromise genomic ChIP outcomes. Epitope tags have often been used as more reliable alternatives. In addition, we have employed protein in vivo biotinylation tagging as a very high affinity alternative to antibodies. In this paper we describe the optimization of biotinylation tagging for ChIP and its coupling to a known epitope tag in providing a reliable and efficient alternative to antibodies. Results Using the biotin tagged erythroid transcription factor GATA-1 as example, we describe several optimization steps for the application of the high affinity biotin streptavidin system in ChIP. We find that the omission of SDS during sonication, the use of fish skin gelatin as blocking agent and choice of streptavidin beads can lead to significantly improved ChIP enrichments and lower background compared to antibodies. We also show that the V5 epitope tag performs equally well under the conditions worked out for streptavidin ChIP and that it may suffer less from the effects of formaldehyde crosslinking. Conclusion The combined use of the very high affinity biotin tag with the less sensitive to crosslinking V5 tag provides for a flexible ChIP platform with potential implications in ChIP sequencing outcomes. PMID:19196479

Lab-on-chip system combining a microfluidic-ELISA with an array of amorphous silicon photosensors for the detection of celiac disease epitopes

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Francesca Costantini

2015-12-01

Full Text Available This work presents a lab-on-chip system, which combines a glass-polydimethilsiloxane microfluidic network and an array of amorphous silicon photosensors for the diagnosis and follow-up of Celiac disease. The microfluidic chip implements an on-chip enzyme-linked immunosorbent assay (ELISA, relying on a sandwich immunoassay between antibodies against gliadin peptides (GPs and a secondary antibody marked with horseradish peroxidase (Ig-HRP. This enzyme catalyzes a chemiluminescent reaction, whose light intensity is detected by the amorphous silicon photosensors and transduced into an electrical signal that can be processed to recognize the presence of antibodies against GPs in the serum of people affected by Celiac syndrome.The correct operation of the developed lab-on-chip has been demonstrated using rabbit serum in the microfluidic ELISA. In particular, optimizing the dilution factors of both sera and Ig-HRP samples in the flowing solutions, the specific and non-specific antibodies against GPs can be successfully distinguished, showing the suitability of the presented device to effectively screen celiac disease epitopes. Keywords: Lab-on-chip, Celiac disease, Microfluidics, On-chip detection, ELISA, Amorphous silicon photosensors
Implementation of Microfluidic Chip Electrophoresis for the Detection of B-cell Clonality

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Vazan M

2016-04-01

Full Text Available Introduction: A clonal population of B-cells is defined as those cells arising from the mitotic division of a single somatic cell with the same rearrangement of immunoglobulin genes. This gives rise to DNA markers for each individual lymphoid cell and its progenies and enables us to study clonality in different B-cell malignancies using multiplex polymerase chain reaction - PCR. The BIOMED-2 protocol has been implemented for clonality detection in lymphoproliferative diseases and exploits multiplex PCR reaction, subsequently analyzed by heteroduplex analysis (HDA using polyacrylamide gel electrophoresis (PAGE. With the advent of miniaturization and automation of molecular biology methods, lab-on-chip technologies were developed and replace partially the conventional approaches. We tested device for microfluidic chip, which is used for B-cells clonality analysis, using a PCR reaction for three subregions called frameworks (FR of the immunoglobulin heavy locus (IGH gene.
Graphene Oxide-Poly(dimethylsiloxane)-Based Lab-on-a-Chip Platform for Heavy-Metals Preconcentration and Electrochemical Detection.

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Chałupniak, Andrzej; Merkoçi, Arben

2017-12-27

Herein, we present the application of a novel graphene oxide-poly(dimethylsiloxane) (GO-PDMS) composite in reversible adsorption/desorption, including detection of heavy metals. GO-PDMS was fabricated by simple blending of GO with silicon monomer in the presence of tetrahydrofuran, followed by polymerization initiated upon the addition of curing agent. We found GO concentration, curing agent concentration, pH, and contact time among the most important factors affecting the adsorption of Pb(II) used as a model heavy metal. The mechanism of adsorption is based on surface complexation, where oxygen active groups of negative charge can bind with bivalent metal ions Me(II). To demonstrate a practical application of this material, we fabricated microfluidic lab-on-a-chip platform for heavy-metals preconcentration and detection. This device consists of a screen-printed carbon electrode, a PDMS chip, and a GO-PDMS chip. The use of GO-PDMS preconcentration platform significantly improves the sensitivity of electrochemical detection of heavy metals (an increase of current up to 30× was observed), without the need of modifying electrodes or special reagents addition. Therefore, samples being so far below the limit of detection (0.5 ppb) were successfully detected. This approach is compatible also with real samples (seawater) as ionic strength was found as indifferent for the adsorption process. To the best of our knowledge, GO-PDMS was used for the first time in sensing application. Moreover, due to mechanical resistance and outstanding durability, it can be used multiple times unlike other GO-based platforms for heavy-metals adsorption.
A non-linear algorithm for current signal filtering and peak detection in SiPM

International Nuclear Information System (INIS)

Putignano, M; Intermite, A; Welsch, C P

2012-01-01

Read-out of Silicon Photomultipliers is commonly achieved by means of charge integration, a method particularly susceptible to after-pulsing noise and not efficient for low level light signals. Current signal monitoring, characterized by easier electronic implementation and intrinsically faster than charge integration, is also more suitable for low level light signals and can potentially result in much decreased after-pulsing noise effects. However, its use is to date limited by the need of developing a suitable read-out algorithm for signal analysis and filtering able to achieve current peak detection and measurement with the needed precision and accuracy. In this paper we present an original algorithm, based on a piecewise linear-fitting approach, to filter the noise of the current signal and hence efficiently identifying and measuring current peaks. The proposed algorithm is then compared with the optimal linear filtering algorithm for time-encoded peak detection, based on a moving average routine, and assessed in terms of accuracy, precision, and peak detection efficiency, demonstrating improvements of 1÷2 orders of magnitude in all these quality factors.
Neural Cell Chip Based Electrochemical Detection of Nanotoxicity.

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Kafi, Md Abdul; Cho, Hyeon-Yeol; Choi, Jeong Woo

2015-07-02

Development of a rapid, sensitive and cost-effective method for toxicity assessment of commonly used nanoparticles is urgently needed for the sustainable development of nanotechnology. A neural cell with high sensitivity and conductivity has become a potential candidate for a cell chip to investigate toxicity of environmental influences. A neural cell immobilized on a conductive surface has become a potential tool for the assessment of nanotoxicity based on electrochemical methods. The effective electrochemical monitoring largely depends on the adequate attachment of a neural cell on the chip surfaces. Recently, establishment of integrin receptor specific ligand molecules arginine-glycine-aspartic acid (RGD) or its several modifications RGD-Multi Armed Peptide terminated with cysteine (RGD-MAP-C), C(RGD)₄ ensure farm attachment of neural cell on the electrode surfaces either in their two dimensional (dot) or three dimensional (rod or pillar) like nano-scale arrangement. A three dimensional RGD modified electrode surface has been proven to be more suitable for cell adhesion, proliferation, differentiation as well as electrochemical measurement. This review discusses fabrication as well as electrochemical measurements of neural cell chip with particular emphasis on their use for nanotoxicity assessments sequentially since inception to date. Successful monitoring of quantum dot (QD), graphene oxide (GO) and cosmetic compound toxicity using the newly developed neural cell chip were discussed here as a case study. This review recommended that a neural cell chip established on a nanostructured ligand modified conductive surface can be a potential tool for the toxicity assessments of newly developed nanomaterials prior to their use on biology or biomedical technologies.
Neural Cell Chip Based Electrochemical Detection of Nanotoxicity

Directory of Open Access Journals (Sweden)

Md. Abdul Kafi

2015-07-01

Full Text Available Development of a rapid, sensitive and cost-effective method for toxicity assessment of commonly used nanoparticles is urgently needed for the sustainable development of nanotechnology. A neural cell with high sensitivity and conductivity has become a potential candidate for a cell chip to investigate toxicity of environmental influences. A neural cell immobilized on a conductive surface has become a potential tool for the assessment of nanotoxicity based on electrochemical methods. The effective electrochemical monitoring largely depends on the adequate attachment of a neural cell on the chip surfaces. Recently, establishment of integrin receptor specific ligand molecules arginine-glycine-aspartic acid (RGD or its several modifications RGD-Multi Armed Peptide terminated with cysteine (RGD-MAP-C, C(RGD4 ensure farm attachment of neural cell on the electrode surfaces either in their two dimensional (dot or three dimensional (rod or pillar like nano-scale arrangement. A three dimensional RGD modified electrode surface has been proven to be more suitable for cell adhesion, proliferation, differentiation as well as electrochemical measurement. This review discusses fabrication as well as electrochemical measurements of neural cell chip with particular emphasis on their use for nanotoxicity assessments sequentially since inception to date. Successful monitoring of quantum dot (QD, graphene oxide (GO and cosmetic compound toxicity using the newly developed neural cell chip were discussed here as a case study. This review recommended that a neural cell chip established on a nanostructured ligand modified conductive surface can be a potential tool for the toxicity assessments of newly developed nanomaterials prior to their use on biology or biomedical technologies.
Lab-on-chip components for molecular detection

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Adam, Tijjani; Dhahi, Th S.; Mohammed, Mohammed; Hashim, U.; Noriman, N. Z.; Dahham, Omar S.

2017-09-01

We successfully fabricated Lab on chip components and integrated for possible use in biomedical application. The sensor was fabricated by using conventional photolithography method integrated with PDMS micro channels for smooth delivery of sample to the sensing domain. The sensor was silanized and aminated with 3-Aminopropyl triethoxysilane (APTES) to functionalize the surface with biomolecules and create molecular binding chemistry. The resulting Si-O-Si- components were functionalized with oligonucleotides probe of HPV, which interacted with the single stranded HPV DNA target to create a field across on the device. The fabrication, immobilization and hybridization processes were characterized with current voltage (I-V) characterization (KEITHLEY, 6487). The sensor show selectivity for the HPV DNA target in a linear range from concentration 0.1 nM to 1 µM. This strategy presented a simple, rapid and sensitive platform for HPV detection and would become a powerful tool for pathogenic microorganisms screening in clinical diagnosis.
The Chip-Scale Atomic Clock - Prototype Evaluation

Science.gov (United States)

2007-11-01

39th Annual Precise Time and Time Interval (PTTI) Meeting THE CHIP-SCALE ATOMIC CLOCK – PROTOTYPE EVALUATION R. Lutwak *, A. Rashed...been supported by the Defense Advanced Research Projects Agency, Contract # NBCHC020050. REFERENCES [1] R. Lutwak , D. Emmons, W. Riley, and...D.C.), pp. 539-550. [2] R. Lutwak , D. Emmons, T. English, W. Riley, A. Duwel, M. Varghese, D. K. Serkland, and G. M. Peake, 2004, “The Chip-Scale
MetaRNA-Seq: An Interactive Tool to Browse and Annotate Metadata from RNA-Seq Studies

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Pankaj Kumar

2015-01-01

Full Text Available The number of RNA-Seq studies has grown in recent years. The design of RNA-Seq studies varies from very simple (e.g., two-condition case-control to very complicated (e.g., time series involving multiple samples at each time point with separate drug treatments. Most of these publically available RNA-Seq studies are deposited in NCBI databases, but their metadata are scattered throughout four different databases: Sequence Read Archive (SRA, Biosample, Bioprojects, and Gene Expression Omnibus (GEO. Although the NCBI web interface is able to provide all of the metadata information, it often requires significant effort to retrieve study- or project-level information by traversing through multiple hyperlinks and going to another page. Moreover, project- and study-level metadata lack manual or automatic curation by categories, such as disease type, time series, case-control, or replicate type, which are vital to comprehending any RNA-Seq study. Here we describe “MetaRNA-Seq,” a new tool for interactively browsing, searching, and annotating RNA-Seq metadata with the capability of semiautomatic curation at the study level.
In-situ volumetric topography of IC chips for defect detection using infrared confocal measurement with active structured light

International Nuclear Information System (INIS)

Chen, Liang-Chia; Le, Manh-Trung; Phuc, Dao Cong; Lin, Shyh-Tsong

2014-01-01

The article presents the development of in-situ integrated circuit (IC) chip defect detection techniques for automated clipping detection by proposing infrared imaging and full-field volumetric topography. IC chip inspection, especially held during or post IC packaging, has become an extremely critical procedure in IC fabrication to assure manufacturing quality and reduce production costs. To address this, in the article, microscopic infrared imaging using an electromagnetic light spectrum that ranges from 0.9 to 1.7 µm is developed to perform volumetric inspection of IC chips, in order to identify important defects such as silicon clipping, cracking or peeling. The main difficulty of infrared (IR) volumetric imaging lies in its poor image contrast, which makes it incapable of achieving reliable inspection, as infrared imaging is sensitive to temperature difference but insensitive to geometric variance of materials, resulting in difficulty detecting and quantifying defects precisely. To overcome this, 3D volumetric topography based on 3D infrared confocal measurement with active structured light, as well as light refractive matching principles, is developed to detect defects the size, shape and position of defects in ICs. The experimental results show that the algorithm is effective and suitable for in-situ defect detection of IC semiconductor packaging. The quality of defect detection, such as measurement repeatability and accuracy, is addressed. Confirmed by the experimental results, the depth measurement resolution can reach up to 0.3 µm, and the depth measurement uncertainty with one standard deviation was verified to be less than 1.0% of the full-scale depth-measuring range. (paper)
An integrated model of multiple-condition ChIP-Seq data reveals predeterminants of Cdx2 binding.

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Shaun Mahony

2014-03-01

Full Text Available Regulatory proteins can bind to different sets of genomic targets in various cell types or conditions. To reliably characterize such condition-specific regulatory binding we introduce MultiGPS, an integrated machine learning approach for the analysis of multiple related ChIP-seq experiments. MultiGPS is based on a generalized Expectation Maximization framework that shares information across multiple experiments for binding event discovery. We demonstrate that our framework enables the simultaneous modeling of sparse condition-specific binding changes, sequence dependence, and replicate-specific noise sources. MultiGPS encourages consistency in reported binding event locations across multiple-condition ChIP-seq datasets and provides accurate estimation of ChIP enrichment levels at each event. MultiGPS's multi-experiment modeling approach thus provides a reliable platform for detecting differential binding enrichment across experimental conditions. We demonstrate the advantages of MultiGPS with an analysis of Cdx2 binding in three distinct developmental contexts. By accurately characterizing condition-specific Cdx2 binding, MultiGPS enables novel insight into the mechanistic basis of Cdx2 site selectivity. Specifically, the condition-specific Cdx2 sites characterized by MultiGPS are highly associated with pre-existing genomic context, suggesting that such sites are pre-determined by cell-specific regulatory architecture. However, MultiGPS-defined condition-independent sites are not predicted by pre-existing regulatory signals, suggesting that Cdx2 can bind to a subset of locations regardless of genomic environment. A summary of this paper appears in the proceedings of the RECOMB 2014 conference, April 2-5.
Noise-tolerant instantaneous heart rate and R-peak detection using short-term autocorrelation for wearable healthcare systems.

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Fujii, Takahide; Nakano, Masanao; Yamashita, Ken; Konishi, Toshihiro; Izumi, Shintaro; Kawaguchi, Hiroshi; Yoshimoto, Masahiko

2013-01-01

This paper describes a robust method of Instantaneous Heart Rate (IHR) and R-peak detection from noisy electrocardiogram (ECG) signals. Generally, the IHR is calculated from the R-wave interval. Then, the R-waves are extracted from the ECG using a threshold. However, in wearable bio-signal monitoring systems, noise increases the incidence of misdetection and false detection of R-peaks. To prevent incorrect detection, we introduce a short-term autocorrelation (STAC) technique and a small-window autocorrelation (SWAC) technique, which leverages the similarity of QRS complex waveforms. Simulation results show that the proposed method improves the noise tolerance of R-peak detection.
Normal-Gamma-Bernoulli Peak Detection for Analysis of Comprehensive Two-Dimensional Gas Chromatography Mass Spectrometry Data.

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Kim, Seongho; Jang, Hyejeong; Koo, Imhoi; Lee, Joohyoung; Zhang, Xiang

2017-01-01

Compared to other analytical platforms, comprehensive two-dimensional gas chromatography coupled with mass spectrometry (GC×GC-MS) has much increased separation power for analysis of complex samples and thus is increasingly used in metabolomics for biomarker discovery. However, accurate peak detection remains a bottleneck for wide applications of GC×GC-MS. Therefore, the normal-exponential-Bernoulli (NEB) model is generalized by gamma distribution and a new peak detection algorithm using the normal-gamma-Bernoulli (NGB) model is developed. Unlike the NEB model, the NGB model has no closed-form analytical solution, hampering its practical use in peak detection. To circumvent this difficulty, three numerical approaches, which are fast Fourier transform (FFT), the first-order and the second-order delta methods (D1 and D2), are introduced. The applications to simulated data and two real GC×GC-MS data sets show that the NGB-D1 method performs the best in terms of both computational expense and peak detection performance.
Accurate LC peak boundary detection for ¹⁶O/¹⁸O labeled LC-MS data.

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Cui, Jian; Petritis, Konstantinos; Tegeler, Tony; Petritis, Brianne; Ma, Xuepo; Jin, Yufang; Gao, Shou-Jiang S J; Zhang, Jianqiu Michelle

2013-01-01

In liquid chromatography-mass spectrometry (LC-MS), parts of LC peaks are often corrupted by their co-eluting peptides, which results in increased quantification variance. In this paper, we propose to apply accurate LC peak boundary detection to remove the corrupted part of LC peaks. Accurate LC peak boundary detection is achieved by checking the consistency of intensity patterns within peptide elution time ranges. In addition, we remove peptides with erroneous mass assignment through model fitness check, which compares observed intensity patterns to theoretically constructed ones. The proposed algorithm can significantly improve the accuracy and precision of peptide ratio measurements.
Specific detection of oxytetracycline using DNA aptamer-immobilized interdigitated array electrode chip

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Kim, Yeon Seok; Niazi, Javed H [School of Life Sciences and Biotechnology, Korea University, Anam-dong, Seongbuk-gu, Seoul 136-701 (Korea, Republic of); Gu, Man Bock [School of Life Sciences and Biotechnology, Korea University, Anam-dong, Seongbuk-gu, Seoul 136-701 (Korea, Republic of)], E-mail: mbgu@korea.ac.kr

2009-02-23

An electrochemical sensing system for oxytetracycline (OTC) detection was developed using ssDNA aptamer immobilized on gold interdigitated array (IDA) electrode chip. A highly specific ssDNA aptamer that bind to OTC with high affinity was employed to discriminate other tetracyclines (TCs), such as doxycycline (DOX) and tetracycline (TET). The immobilized thiol-modified aptamer on gold electrode chip served as a biorecognition element for the target molecules and the electrochemical signals generated from interactions between the aptamers and the target molecules was evaluated by cyclic voltammetry (CV) and square wave voltammetry (SWV). The current decrease due to the interference of bound OTC, DOX or TET was analyzed with the electron flow produced by a redox reaction between ferro- and ferricyanide. The specificity of developed EC-biosensor for OTC was highly distinguishable from the structurally similar antibiotics (DOX and TET). The dynamic range was determined to be 1-100 nM of OTC concentration in semi-logarithmic coordinates.
Specific detection of oxytetracycline using DNA aptamer-immobilized interdigitated array electrode chip

International Nuclear Information System (INIS)

Kim, Yeon Seok; Niazi, Javed H.; Gu, Man Bock

2009-01-01

An electrochemical sensing system for oxytetracycline (OTC) detection was developed using ssDNA aptamer immobilized on gold interdigitated array (IDA) electrode chip. A highly specific ssDNA aptamer that bind to OTC with high affinity was employed to discriminate other tetracyclines (TCs), such as doxycycline (DOX) and tetracycline (TET). The immobilized thiol-modified aptamer on gold electrode chip served as a biorecognition element for the target molecules and the electrochemical signals generated from interactions between the aptamers and the target molecules was evaluated by cyclic voltammetry (CV) and square wave voltammetry (SWV). The current decrease due to the interference of bound OTC, DOX or TET was analyzed with the electron flow produced by a redox reaction between ferro- and ferricyanide. The specificity of developed EC-biosensor for OTC was highly distinguishable from the structurally similar antibiotics (DOX and TET). The dynamic range was determined to be 1-100 nM of OTC concentration in semi-logarithmic coordinates
Mapping RNA-seq Reads with STAR.

Science.gov (United States)

Dobin, Alexander; Gingeras, Thomas R

2015-09-03

Mapping of large sets of high-throughput sequencing reads to a reference genome is one of the foundational steps in RNA-seq data analysis. The STAR software package performs this task with high levels of accuracy and speed. In addition to detecting annotated and novel splice junctions, STAR is capable of discovering more complex RNA sequence arrangements, such as chimeric and circular RNA. STAR can align spliced sequences of any length with moderate error rates, providing scalability for emerging sequencing technologies. STAR generates output files that can be used for many downstream analyses such as transcript/gene expression quantification, differential gene expression, novel isoform reconstruction, and signal visualization. In this unit, we describe computational protocols that produce various output files, use different RNA-seq datatypes, and utilize different mapping strategies. STAR is open source software that can be run on Unix, Linux, or Mac OS X systems. Copyright © 2015 John Wiley & Sons, Inc.
Quantifying the impact of inter-site heterogeneity on the distribution of ChIP-seq data

Directory of Open Access Journals (Sweden)

Jonathan eCairns

2014-11-01

Full Text Available Chromatin Immunoprecipitation followed by sequencing (ChIP-seq is a valuable tool for epigenetic studies. Analysis of the data arising from ChIP-seq experiments often requires implicit or explicit statistical modelling of the read counts. The simple Poisson model is attractive, but does not provide a good fit to observed ChIP-seq data. Researchers therefore often either extend to a more general model (e.g. the Negative Binomial, and/or exclude regions of the genome that do not conform to the model. Since many modelling strategies employed for ChIP-seq data reduce to fitting a mixture of Poisson distributions, we explore the problem of inferring the optimal mixing distribution. We apply the Constrained Newton Method (CNM, which suggests the Negative Binomial - Negative Binomial (NB-NB mixture model as a candidate for modelling ChIP-seq data. We illustrate fitting the NB-NB model with an accelerated EM algorithm on four data sets from three species. Zero-inflated models have been suggested as an approach to improve model fit for ChIP-seq data. We show that the NB-NB mixture model requires no zero-inflation and suggest that in some cases the need for zero inflation is driven by the model's inability to cope with both artefactual large read counts and the frequently observed very low read counts.We see that the CNM-based approach is a useful diagnostic for the assessment of model fit and inference in ChIP-seq data and beyond. Use of the suggested NB-NB mixture model will be of value not only when calling peaks or otherwise modelling ChIP-seq data, but also when simulating data or constructing blacklists de novo.
Computational Methods for ChIP-seq Data Analysis and Applications

KAUST Repository

Ashoor, Haitham

2017-01-01

four main challenges. First, I address the problem of detecting histone modifications from ChIP-seq cancer samples. The presence of copy number variations (CNVs) in cancer samples results in statistical biases that lead to inaccurate predictions when
Computational Methods for ChIP-seq Data Analysis and Applications

KAUST Repository

Ashoor, Haitham

2017-04-25

The development of Chromatin immunoprecipitation followed by sequencing (ChIP-seq) technology has enabled the construction of genome-wide maps of protein-DNA interaction. Such maps provide information about transcriptional regulation at the epigenetic level (histone modifications and histone variants) and at the level of transcription factor (TF) activity. This dissertation presents novel computational methods for ChIP-seq data analysis and applications. The work of this dissertation addresses four main challenges. First, I address the problem of detecting histone modifications from ChIP-seq cancer samples. The presence of copy number variations (CNVs) in cancer samples results in statistical biases that lead to inaccurate predictions when standard methods are used. To overcome this issue I developed HMCan, a specially designed algorithm to handle ChIP-seq cancer data by accounting for the presence of CNVs. When using ChIP-seq data from cancer cells, HMCan demonstrates unbiased and accurate predictions compared to the standard state of the art methods. Second, I address the problem of identifying changes in histone modifications between two ChIP-seq samples with different genetic backgrounds (for example cancer vs. normal). In addition to CNVs, different antibody efficiency between samples and presence of samples replicates are challenges for this problem. To overcome these issues, I developed the HMCan-diff algorithm as an extension to HMCan. HMCan-diff implements robust normalization methods to address the challenges listed above. HMCan-diff significantly outperforms another state of the art methods on data containing cancer samples. Third, I investigate and analyze predictions of different methods for enhancer prediction based on ChIP-seq data. The analysis shows that predictions generated by different methods are poorly overlapping. To overcome this issue, I developed DENdb, a database that integrates enhancer predictions from different methods. DENdb also

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