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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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File list: Pol.Unc.50.RNA_polymerase_II.AllCell [Chip-atlas[Archive

Lifescience Database Archive (English)

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File list: Pol.Plc.10.RNA_polymerase_II.AllCell [Chip-atlas[Archive

Lifescience Database Archive (English)

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Lifescience Database Archive (English)

Full Text Available Pol.Plc.05.RNA_polymerase_II.AllCell hg19 RNA polymerase RNA polymerase II Placenta... http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Plc.05.RNA_polymerase_II.AllCell.bed ...

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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File list: Pol.Unc.05.RNA_polymerase_II.AllCell [Chip-atlas[Archive

Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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File list: Pol.Unc.05.RNA_Polymerase_II.AllCell [Chip-atlas[Archive

Lifescience Database Archive (English)

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File list: Pol.Unc.05.RNA_polymerase_II.AllCell [Chip-atlas[Archive

Lifescience Database Archive (English)

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File list: Pol.Unc.10.RNA_Polymerase_II.AllCell [Chip-atlas[Archive

Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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File list: Pol.Myo.10.RNA_polymerase_II.AllCell [Chip-atlas[Archive

Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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File list: Pol.Lng.50.RNA_polymerase_II.AllCell [Chip-atlas[Archive

Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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File list: Pol.Pan.05.RNA_polymerase_II.AllCell [Chip-atlas[Archive

Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

Full Text Available Pol.Unc.05.RNA_Polymerase_II.AllCell mm9 RNA polymerase RNA Polymerase II Unclassif...ied SRX254629 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Unc.05.RNA_Polymerase_II.AllCell.bed ...

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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File list: Pol.Epd.05.RNA_polymerase_II.AllCell [Chip-atlas[Archive

Lifescience Database Archive (English)

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File list: Pol.PSC.05.RNA_polymerase_II.AllCell [Chip-atlas[Archive

Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Lifescience Database Archive (English)

Full Text Available e3 (ab6002, abcam), Pol II (CTD4H8, Millipore) || chip antibody 1 manufacturer=ab...cam || chip antibody 2=Pol II (CTD4H8, Millipore) || chip antibody 2 manufacturer=Millipore http://dbarchive

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

Experiment list: SRX485220 [Chip-atlas[Archive

Lifescience Database Archive (English)

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Experiment list: SRX100488 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available romatin IP Sequencing || antibody antibodydescription=Mouse monoclonal to RNA pol...ymerase II CTD repeat YSPTSPS antibody (4H8) - ChIP Grade. Antibody Target: POL2 || antibody targetdescripti...essenger RNA in eukaryotes || antibody vendorname=abcam || antibody vendorid=ab54...08 || controlid=SL2455 || labexpid=SL2940,SL2939 || replicate=1,2 || softwareversion=MACS || antibody=Pol2-4H8 || antibody antibody...description=Mouse monoclonal to RNA polymerase II CTD repeat YSPTSPS antibody (4H8) - ChIP Grade || antibody

Experiment list: SRX485219 [Chip-atlas[Archive

Lifescience Database Archive (English)

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Experiment list: SRX190275 [Chip-atlas[Archive

Lifescience Database Archive (English)

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Experiment list: SRX100519 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available omatin IP Sequencing || antibody antibodydescription=Mouse monoclonal to RNA poly...merase II CTD repeat YSPTSPS antibody (4H8) - ChIP Grade. Antibody Target: POL2 || antibody targetdescriptio...ssenger RNA in eukaryotes || antibody vendorname=abcam || antibody vendorid=ab540...8 || controlid=SL3457 || labexpid=SL3830,SL3456 || replicate=1,2 || softwareversion=MACS || antibody=Pol2-4H8 || antibody antibody...description=Mouse monoclonal to RNA polymerase II CTD repeat YSPTSPS antibody (4H8) - ChIP Grade || antibody

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Lifescience Database Archive (English)

Full Text Available romatin IP Sequencing || antibody antibodydescription=Mouse monoclonal to RNA pol...ymerase II CTD repeat YSPTSPS antibody (4H8) - ChIP Grade. Antibody Target: POL2 || antibody targetdescripti...essenger RNA in eukaryotes || antibody vendorname=abcam || antibody vendorid=ab54...08 || controlid=SL1106 || labexpid=SL1104,SL2387 || softwareversion=MACS || cell sex=U || antibody=Pol2-4H8 || antibody antibody...description=Mouse monoclonal to RNA polymerase II CTD repeat YSPTSPS antibody (4H8) - Ch

Rapid Genome-wide Recruitment of RNA Polymerase II Drives Transcription, Splicing, and Translation Events during T Cell Responses

Directory of Open Access Journals (Sweden)

Kathrin Davari

2017-04-01

Full Text Available Summary: Activation of immune cells results in rapid functional changes, but how such fast changes are accomplished remains enigmatic. By combining time courses of 4sU-seq, RNA-seq, ribosome profiling (RP, and RNA polymerase II (RNA Pol II ChIP-seq during T cell activation, we illustrate genome-wide temporal dynamics for ∼10,000 genes. This approach reveals not only immediate-early and posttranscriptionally regulated genes but also coupled changes in transcription and translation for >90% of genes. Recruitment, rather than release of paused RNA Pol II, primarily mediates transcriptional changes. This coincides with a genome-wide temporary slowdown in cotranscriptional splicing, even for polyadenylated mRNAs that are localized at the chromatin. Subsequent splicing optimization correlates with increasing Ser-2 phosphorylation of the RNA Pol II carboxy-terminal domain (CTD and activation of the positive transcription elongation factor (pTEFb. Thus, rapid de novo recruitment of RNA Pol II dictates the course of events during T cell activation, particularly transcription, splicing, and consequently translation. : Davari et al. visualize global changes in RNA Pol II binding, transcription, splicing, and translation. T cells change their functional program by rapid de novo recruitment of RNA Pol II and coupled changes in transcription and translation. This coincides with fluctuations in RNA Pol II phosphorylation and a temporary reduction in cotranscriptional splicing. Keywords: RNA Pol II, cotranscriptional splicing, T cell activation, ribosome profiling, 4sU, H3K36, Ser-5 RNA Pol II, Ser-2 RNA Pol II, immune response, immediate-early genes

Enhancer SINEs Link Pol III to Pol II Transcription in Neurons

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Cristina Policarpi

2017-12-01

Full Text Available Summary: Spatiotemporal regulation of gene expression depends on the cooperation of multiple mechanisms, including the functional interaction of promoters with distally located enhancers. Here, we show that, in cortical neurons, a subset of short interspersed nuclear elements (SINEs located in the proximity of activity-regulated genes bears features of enhancers. Enhancer SINEs (eSINEs recruit the Pol III cofactor complex TFIIIC in a stimulus-dependent manner and are transcribed by Pol III in response to neuronal depolarization. Characterization of an eSINE located in proximity to the Fos gene (FosRSINE1 indicated that the FosRSINE1-encoded transcript interacts with Pol II at the Fos promoter and mediates Fos relocation to Pol II factories, providing an unprecedented molecular link between Pol III and Pol II transcription. Strikingly, knockdown of the FosRSINE1 transcript induces defects of both cortical radial migration in vivo and activity-dependent dendritogenesis in vitro, demonstrating that FosRSINE1 acts as a strong enhancer of Fos expression in diverse physiological contexts. : Spatiotemporal regulation of gene expression requires the interaction between promoters and distally located enhancers. Policarpi et al. identify a subset of SINEs that functions as enhancers for activity-dependent neuronal genes. The enhancer SINE FosRSINE1 regulates Fos transcription and is necessary for both activity-dependent dendritogenesis and proper brain development. Keywords: neuroscience, epigenetics, transcription, enhancers, SINEs, neuronal activity, neuronal development

iTAR: a web server for identifying target genes of transcription factors using ChIP-seq or ChIP-chip data.

Science.gov (United States)

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

Experiment list: SRX026424 [Chip-atlas[Archive

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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

Experiment list: SRX190249 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available datatype description=Chromatin IP Sequencing || antibody antibodydescription=Mous...e monoclonal to RNA polymerase II CTD repeat YSPTSPS antibody (4H8) - ChIP Grade. Antibody Target: POL2 || antibody...ible for synthesizing messenger RNA in eukaryotes || antibody vendorname=abcam || antibody... vendorid=ab5408 || controlid=SL1714 || labexpid=SL1963,SL5611 || softwareversion=MACS || cell sex=F || antibody...=Pol2-4H8 || antibody antibodydescription=Mouse monoclonal to RNA polymerase II CTD repeat YSPTSPS antibody

Experiment list: SRX190277 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available omatin IP Sequencing || antibody antibodydescription=Mouse monoclonal to RNA poly...merase II CTD repeat YSPTSPS antibody (4H8) - ChIP Grade. Antibody Target: POL2 || antibody targetdescriptio...ssenger RNA in eukaryotes || antibody vendorname=abcam || antibody vendorid=ab540...8 || controlid=SL1781 || labexpid=SL1363,SL5604 || softwareversion=MACS || cell sex=M || antibody=Pol2-4H8 || antibody antibody...description=Mouse monoclonal to RNA polymerase II CTD repeat YSPTSPS antibody (4H8) - ChI

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

Genome-wide analysis of KAP1, the 7SK snRNP complex, and RNA polymerase II

Directory of Open Access Journals (Sweden)

Ryan P. McNamara

2016-03-01

Full Text Available The transition of RNA polymerase II (Pol II from transcription initiation into productive elongation in eukaryotic cells is regulated by the P-TEFb kinase, which phosphorylates the C-terminal domain of paused Pol II at promoter-proximal regions. Our recent study found that P-TEFb (in an inhibited state bound to the 7SK snRNP complex interacts with the KAP1/TRIM28 transcriptional regulator, and that KAP1 and the 7SK snRNP co-occupy most gene promoters containing paused Pol II. Here we provide a detailed experimental description and analysis of the ChIP-seq datasets that have been deposited into Gene Expression Omnibus (GEO: GS72622, so that independent groups can replicate and expand upon these findings. We propose these datasets would provide valuable information for researchers studying mechanisms of transcriptional regulation including Pol II pausing and pause release. Keywords: P-TEFb/7SK snRNP, KAP1, RNA polymerase II, ChIP-seq, Transcription elongation

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

Science.gov (United States)

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.

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

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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

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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

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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

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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

Inference of RNA polymerase II transcription dynamics from chromatin immunoprecipitation time course data.

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Ciira wa Maina

2014-05-01

Full Text Available Gene transcription mediated by RNA polymerase II (pol-II is a key step in gene expression. The dynamics of pol-II moving along the transcribed region influence the rate and timing of gene expression. In this work, we present a probabilistic model of transcription dynamics which is fitted to pol-II occupancy time course data measured using ChIP-Seq. The model can be used to estimate transcription speed and to infer the temporal pol-II activity profile at the gene promoter. Model parameters are estimated using either maximum likelihood estimation or via Bayesian inference using Markov chain Monte Carlo sampling. The Bayesian approach provides confidence intervals for parameter estimates and allows the use of priors that capture domain knowledge, e.g. the expected range of transcription speeds, based on previous experiments. The model describes the movement of pol-II down the gene body and can be used to identify the time of induction for transcriptionally engaged genes. By clustering the inferred promoter activity time profiles, we are able to determine which genes respond quickly to stimuli and group genes that share activity profiles and may therefore be co-regulated. We apply our methodology to biological data obtained using ChIP-seq to measure pol-II occupancy genome-wide when MCF-7 human breast cancer cells are treated with estradiol (E2. The transcription speeds we obtain agree with those obtained previously for smaller numbers of genes with the advantage that our approach can be applied genome-wide. We validate the biological significance of the pol-II promoter activity clusters by investigating cluster-specific transcription factor binding patterns and determining canonical pathway enrichment. We find that rapidly induced genes are enriched for both estrogen receptor alpha (ERα and FOXA1 binding in their proximal promoter regions.

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.

Influenza Virus Mounts a Two-Pronged Attack on Host RNA Polymerase II Transcription.

Science.gov (United States)

Bauer, David L V; Tellier, Michael; Martínez-Alonso, Mónica; Nojima, Takayuki; Proudfoot, Nick J; Murphy, Shona; Fodor, Ervin

2018-05-15

Influenza virus intimately associates with host RNA polymerase II (Pol II) and mRNA processing machinery. Here, we use mammalian native elongating transcript sequencing (mNET-seq) to examine Pol II behavior during viral infection. We show that influenza virus executes a two-pronged attack on host transcription. First, viral infection causes decreased Pol II gene occupancy downstream of transcription start sites. Second, virus-induced cellular stress leads to a catastrophic failure of Pol II termination at poly(A) sites, with transcription often continuing for tens of kilobases. Defective Pol II termination occurs independently of the ability of the viral NS1 protein to interfere with host mRNA processing. Instead, this termination defect is a common effect of diverse cellular stresses and underlies the production of previously reported downstream-of-gene transcripts (DoGs). Our work has implications for understanding not only host-virus interactions but also fundamental aspects of mammalian transcription. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

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

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

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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: 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

Experiment list: SRX085450 [Chip-atlas[Archive

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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

Mitotic Transcriptional Activation: Clearance of Actively Engaged Pol II via Transcriptional Elongation Control in Mitosis.

Science.gov (United States)

Liang, Kaiwei; Woodfin, Ashley R; Slaughter, Brian D; Unruh, Jay R; Box, Andrew C; Rickels, Ryan A; Gao, Xin; Haug, Jeffrey S; Jaspersen, Sue L; Shilatifard, Ali

2015-11-05

Although it is established that some general transcription factors are inactivated at mitosis, many details of mitotic transcription inhibition (MTI) and its underlying mechanisms are largely unknown. We have identified mitotic transcriptional activation (MTA) as a key regulatory step to control transcription in mitosis for genes with transcriptionally engaged RNA polymerase II (Pol II) to activate and transcribe until the end of the gene to clear Pol II from mitotic chromatin, followed by global impairment of transcription reinitiation through MTI. Global nascent RNA sequencing and RNA fluorescence in situ hybridization demonstrate the existence of transcriptionally engaged Pol II in early mitosis. Both genetic and chemical inhibition of P-TEFb in mitosis lead to delays in the progression of cell division. Together, our study reveals a mechanism for MTA and MTI whereby transcriptionally engaged Pol II can progress into productive elongation and finish transcription to allow proper cellular division. Copyright © 2015 Elsevier Inc. All rights reserved.

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

Lifescience Database Archive (English)

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=

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

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

Lifescience Database Archive (English)

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

In Silico Pooling of ChIP-seq Control Experiments

Science.gov (United States)

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

Involvement of specialized DNA polymerases Pol II, Pol IV and DnaE2 in DNA replication in the absence of Pol I in Pseudomonas putida

International Nuclear Information System (INIS)

Sidorenko, Julia; Jatsenko, Tatjana; Saumaa, Signe; Teras, Riho; Tark-Dame, Mariliis; Horak, Rita; Kivisaar, Maia

2011-01-01

The majority of bacteria possess a different set of specialized DNA polymerases than those identified in the most common model organism Escherichia coli. Here, we have studied the ability of specialized DNA polymerases to substitute Pol I in DNA replication in Pseudomonas putida. Our results revealed that P. putida Pol I-deficient cells have severe growth defects in LB medium, which is accompanied by filamentous cell morphology. However, growth of Pol I-deficient bacteria on solid rich medium can be restored by reduction of reactive oxygen species in cells. Also, mutants with improved growth emerge rapidly. Similarly to the initial Pol I-deficient P. putida, its adapted derivatives express a moderate mutator phenotype, which indicates that DNA replication carried out in the absence of Pol I is erroneous both in the original Pol I-deficient bacteria and the adapted derivatives. Analysis of the spectra of spontaneous Rif r mutations in P. putida strains lacking different DNA polymerases revealed that the presence of specialized DNA polymerases Pol II and Pol IV influences the frequency of certain base substitutions in Pol I-proficient and Pol I-deficient backgrounds in opposite ways. Involvement of another specialized DNA polymerase DnaE2 in DNA replication in Pol I-deficient bacteria is stimulated by UV irradiation of bacteria, implying that DnaE2-provided translesion synthesis partially substitutes the absence of Pol I in cells containing heavily damaged DNA.

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

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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

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

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

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

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

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/

CMT: a constrained multi-level thresholding approach for ChIP-Seq data analysis.

Directory of Open Access Journals (Sweden)

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.

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

Predicting stimulation-dependent enhancer-promoter interactions from ChIP-Seq time course data

Directory of Open Access Journals (Sweden)

Tomasz Dzida

2017-09-01

Full Text Available We have developed a machine learning approach to predict stimulation-dependent enhancer-promoter interactions using evidence from changes in genomic protein occupancy over time. The occupancy of estrogen receptor alpha (ERα, RNA polymerase (Pol II and histone marks H2AZ and H3K4me3 were measured over time using ChIP-Seq experiments in MCF7 cells stimulated with estrogen. A Bayesian classifier was developed which uses the correlation of temporal binding patterns at enhancers and promoters and genomic proximity as features to predict interactions. This method was trained using experimentally determined interactions from the same system and was shown to achieve much higher precision than predictions based on the genomic proximity of nearest ERα binding. We use the method to identify a genome-wide confident set of ERα target genes and their regulatory enhancers genome-wide. Validation with publicly available GRO-Seq data demonstrates that our predicted targets are much more likely to show early nascent transcription than predictions based on genomic ERα binding proximity alone.

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.

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

Observatorio de Política Internacional II. AMERICAS - Ecuador. Política y fútbol

OpenAIRE

Neira Fernández, Enrique

2007-01-01

Observatorio de Política Internacional II. AMÉRICAS (Neira Fernández, Enrique) RECIENTES Año 2008 Nicaragua. Un remedo revolucionario Bolivia. ¿Una o dislocada? Paraguay. El ex obispo presidente Perú. El rojo sangre de sendero luminoso Estados Unidos. Panorama tras las elecciones primarias RECIENTES Año 2007 Argentina. Contundente triunfo de Cristina Fernández Bolivia. Nuevos rumbos ¡no más embrollo! Ecuador. Nueva constitución, nuevo rumbo Guatemala....

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.

Replication restart in UV-irradiated Escherichia coli involving pols II, III, V, PriA, RecA and RecFOR proteins.

Science.gov (United States)

Rangarajan, Savithri; Woodgate, Roger; Goodman, Myron F

2002-02-01

In Escherichia coli, UV-irradiated cells resume DNA synthesis after a transient inhibition by a process called replication restart. To elucidate the role of several key proteins involved in this process, we have analysed the time dependence of replication restart in strains carrying a combination of mutations in lexA, recA, polB (pol II), umuDC (pol V), priA, dnaC, recF, recO or recR. We find that both pol II and the origin-independent primosome-assembling function of PriA are essential for the immediate recovery of DNA synthesis after UV irradiation. In their absence, translesion replication or 'replication readthrough' occurs approximately 50 min after UV and is pol V-dependent. In a wild-type, lexA+ background, mutations in recF, recO or recR block both pathways. Similar results were obtained with a lexA(Def) recF strain. However, lexA(Def) recO or lexA(Def) recR strains, although unable to facilitate PriA-pol II-dependent restart, were able to perform pol V-dependent readthrough. The defects in restart attributed to mutations in recF, recO or recR were suppressed in a recA730 lexA(Def) strain expressing constitutively activated RecA (RecA*). Our data suggest that in a wild-type background, RecF, O and R are important for the induction of the SOS response and the formation of RecA*-dependent recombination intermediates necessary for PriA/Pol II-dependent replication restart. In con-trast, only RecF is required for the activation of RecA that leads to the formation of pol V (UmuD'2C) and facilitates replication readthrough.

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

Evidence that Mediator is essential for Pol II transcription, but is not a required component of the preinitiation complex in vivo.

Science.gov (United States)

Petrenko, Natalia; Jin, Yi; Wong, Koon Ho; Struhl, Kevin

2017-07-12

The Mediator complex has been described as a general transcription factor, but it is unclear if it is essential for Pol II transcription and/or is a required component of the preinitiation complex (PIC) in vivo. Here, we show that depletion of individual subunits, even those essential for cell growth, causes a general but only modest decrease in transcription. In contrast, simultaneous depletion of all Mediator modules causes a drastic decrease in transcription. Depletion of head or middle subunits, but not tail subunits, causes a downstream shift in the Pol II occupancy profile, suggesting that Mediator at the core promoter inhibits promoter escape. Interestingly, a functional PIC and Pol II transcription can occur when Mediator is not detected at core promoters. These results provide strong evidence that Mediator is essential for Pol II transcription and stimulates PIC formation, but it is not a required component of the PIC in vivo.

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

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.

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

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: 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

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

Syndromes associated with Homo sapiens pol II regulatory genes.

Science.gov (United States)

Bina, M; Demmon, S; Pares-Matos, E I

2000-01-01

The molecular basis of human characteristics is an intriguing but an unresolved problem. Human characteristics cover a broad spectrum, from the obvious to the abstract. Obvious characteristics may include morphological features such as height, shape, and facial form. Abstract characteristics may be hidden in processes that are controlled by hormones and the human brain. In this review we examine exaggerated characteristics presented as syndromes. Specifically, we focus on human genes that encode transcription factors to examine morphological, immunological, and hormonal anomalies that result from deletion, insertion, or mutation of genes that regulate transcription by RNA polymerase II (the Pol II genes). A close analysis of abnormal phenotypes can give clues into how sequence variations in regulatory genes and changes in transcriptional control may give rise to characteristics defined as complex traits.

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: SRX150451 [Chip-atlas[Archive

Lifescience Database Archive (English)

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

Experiment list: SRX150472 [Chip-atlas[Archive

Lifescience Database Archive (English)

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

Experiment list: SRX191067 [Chip-atlas[Archive

Lifescience Database Archive (English)

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

Experiment list: SRX1121725 [Chip-atlas[Archive

Lifescience Database Archive (English)

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: SRX150623 [Chip-atlas[Archive

Lifescience Database Archive (English)

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

Lifescience Database Archive (English)

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

Lifescience Database Archive (English)

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

Lifescience Database Archive (English)

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

Lifescience Database Archive (English)

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

Lifescience Database Archive (English)

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

Lifescience Database Archive (English)

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

Lifescience Database Archive (English)

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

Lifescience Database Archive (English)

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

Lifescience Database Archive (English)

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

Lifescience Database Archive (English)

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

Experiment list: SRX150674 [Chip-atlas[Archive

Lifescience Database Archive (English)

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

Lifescience Database Archive (English)

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

Lifescience Database Archive (English)

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

Lifescience Database Archive (English)

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

Lifescience Database Archive (English)

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

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: SRX810433 [Chip-atlas[Archive

Lifescience Database Archive (English)

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

Lifescience Database Archive (English)

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

Lifescience Database Archive (English)

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

Lifescience Database Archive (English)

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

Experiment list: SRX150720 [Chip-atlas[Archive

Lifescience Database Archive (English)

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

Lifescience Database Archive (English)

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

Lifescience Database Archive (English)

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

Lifescience Database Archive (English)

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

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

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://

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.

File list: Pol.CDV.05.AllAg.Cardiomyocytes [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.CDV.05.AllAg.Cardiomyocytes mm9 RNA polymerase Cardiovascular Cardiomyocytes ht...tp://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.CDV.05.AllAg.Cardiomyocytes.bed ...

File list: Pol.CDV.20.AllAg.Cardiomyocytes [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.CDV.20.AllAg.Cardiomyocytes mm9 RNA polymerase Cardiovascular Cardiomyocytes ht...tp://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.CDV.20.AllAg.Cardiomyocytes.bed ...

File list: Pol.CDV.10.AllAg.Cardiomyocytes [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.CDV.10.AllAg.Cardiomyocytes mm9 RNA polymerase Cardiovascular Cardiomyocytes ht...tp://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.CDV.10.AllAg.Cardiomyocytes.bed ...

File list: Pol.CDV.50.AllAg.Cardiomyocytes [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.CDV.50.AllAg.Cardiomyocytes mm9 RNA polymerase Cardiovascular Cardiomyocytes ht...tp://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.CDV.50.AllAg.Cardiomyocytes.bed ...

Construction and test of the first Belle II SVD ladder implementing the origami chip-on-sensor design

International Nuclear Information System (INIS)

Irmler, C.; Bauer, A.; Bergauer, T.; Adamczyk, K.; Bacher, S.; Aihara, H.; Angelini, C.; Batignani, G.; Bettarini, S.; Bosi, F.; Aziz, T.; Babu, V.; Bahinipati, S.; Barberio, E.; Baroncelli, Ti.; Baroncelli, To.; Basith, A.K.; Behera, P.K.; Bhuyan, B.; Bilka, T.

2016-01-01

The Belle II Silicon Vertex Detector comprises four layers of double-sided silicon strip detectors (DSSDs), consisting of ladders with two to five sensors each. All sensors are individually read out by APV25 chips with the Origami chip-on-sensor concept for the central DSSDs of the ladders. The chips sit on flexible circuits that are glued on the top of the sensors. This concept allows a low material budget and an efficient cooling of the chips by a single pipe per ladder. We present the construction of the first SVD ladders and results from precision measurements and electrical tests

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-

File list: Pol.Dig.10.AllAg.Intestines [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Dig.10.AllAg.Intestines mm9 RNA polymerase Digestive tract Intestines SRX112957...,SRX143802 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Dig.10.AllAg.Intestines.bed ...

File list: Pol.Dig.20.AllAg.Intestines [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Dig.20.AllAg.Intestines mm9 RNA polymerase Digestive tract Intestines SRX112957...,SRX143802 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Dig.20.AllAg.Intestines.bed ...

File list: Pol.Dig.05.AllAg.Intestines [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Dig.05.AllAg.Intestines mm9 RNA polymerase Digestive tract Intestines SRX112957...,SRX143802 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Dig.05.AllAg.Intestines.bed ...

File list: Pol.Dig.50.AllAg.Intestines [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Dig.50.AllAg.Intestines mm9 RNA polymerase Digestive tract Intestines SRX112957...,SRX143802 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Dig.50.AllAg.Intestines.bed ...

File list: Pol.Liv.20.AllAg.Hepatocytes [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Liv.20.AllAg.Hepatocytes mm9 RNA polymerase Liver Hepatocytes ERX204069,ERX2040...60,ERX204064 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Liv.20.AllAg.Hepatocytes.bed ...

File list: Pol.Liv.05.AllAg.Hepatocytes [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Liv.05.AllAg.Hepatocytes mm9 RNA polymerase Liver Hepatocytes ERX204060,ERX2040...69,ERX204064 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Liv.05.AllAg.Hepatocytes.bed ...

File list: Pol.Liv.10.AllAg.Hepatocytes [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Liv.10.AllAg.Hepatocytes mm9 RNA polymerase Liver Hepatocytes ERX204060,ERX2040...69,ERX204064 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Liv.10.AllAg.Hepatocytes.bed ...

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.

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

Segurança pública e seqüestros no Rio de Janeiro 1995-1996 Public security and kidnappings in Rio de Janeiro (1995-1996

Directory of Open Access Journals (Sweden)

Cesar Caldeira

1997-05-01

Full Text Available O crime de extorsão mediante seqüestro, em regra praticado por quadrilhas, tornou-se um problema e desafio para a política de segurança pública e a ação policial. A alta incidência de seqüestros, os efeitos sociais dramáticos que gera e sua repercussão sobre a opinião pública e a imagem da cidade, fizeram dessa prática delituosa um ponto de referência significativo no debate social e político sobre crime organizado. Seqüestros motivaram protestos sociais, inclusive, o movimento Reage Rio (Caminhada pela Paz. Este trabalho tenta contextualizar o problema dos seqüestros. Discute a política de segurança pública do Estado do Rio de Janeiro tendo em vista o projeto de uma cidade voltada aos negócios, uma cidade internacional, que é desejada pelas elites empresariais e políticas dominantes no Rio neste período. Focaliza o ascenso do movimento de "lei e ordem" e as ações anti-seqüestro das polícias. Por fim, apresenta dados coletados, num projeto de pesquisa em andamento, que procura estudar o chamado "crime organizado" e a política de segurança pública, a partir de delitos comumente associados à quadrilhas como seqüestros extorsivos, narcotráfico, assaltos a bancos e outros.Abduction and detention of a person for ransom (kidnapping, a crime committed generally by gangs, has become a serious problem and challenge to public safety and police action.The high incidence of kidnappings, their dramatic ocurrence and their repercussions on public opinion and image of the city of Rio, have made this offense an outstanding point of reference for social and political debate on organized crime. Kidnappings have motivated public protests, including in part, the huge demonstration Reage Rio (a peace march. This paper strives to be contextual. It discusses the public safety policy of the State of Rio de Janeiro in view of the project of a business-oriented, international city, desired by the entrepreneurial and political elite. It

File list: Pol.Neu.05.AllAg.Brain [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Neu.05.AllAg.Brain mm9 RNA polymerase Neural Brain SRX236085,ERX132833,SRX01708...2,SRX680480,SRX020249 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Neu.05.AllAg.Brain.bed ...

File list: Pol.Neu.50.AllAg.Brain [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Neu.50.AllAg.Brain mm9 RNA polymerase Neural Brain SRX236085,ERX132833,SRX01708...2,SRX680480,SRX020249 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Neu.50.AllAg.Brain.bed ...

File list: Pol.Neu.10.AllAg.Brain [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Neu.10.AllAg.Brain mm9 RNA polymerase Neural Brain SRX236085,ERX132833,SRX01708...2,SRX680480,SRX020249 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Neu.10.AllAg.Brain.bed ...

File list: Pol.Neu.20.AllAg.Brain [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Neu.20.AllAg.Brain mm9 RNA polymerase Neural Brain SRX236085,ERX132833,SRX01708...2,SRX680480,SRX020249 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Neu.20.AllAg.Brain.bed ...

Biotechnological applications of mobile group II introns and their reverse transcriptases: gene targeting, RNA-seq, and non-coding RNA analysis.

Science.gov (United States)

Enyeart, Peter J; Mohr, Georg; Ellington, Andrew D; Lambowitz, Alan M

2014-01-13

Mobile group II introns are bacterial retrotransposons that combine the activities of an autocatalytic intron RNA (a ribozyme) and an intron-encoded reverse transcriptase to insert site-specifically into DNA. They recognize DNA target sites largely by base pairing of sequences within the intron RNA and achieve high DNA target specificity by using the ribozyme active site to couple correct base pairing to RNA-catalyzed intron integration. Algorithms have been developed to program the DNA target site specificity of several mobile group II introns, allowing them to be made into 'targetrons.' Targetrons function for gene targeting in a wide variety of bacteria and typically integrate at efficiencies high enough to be screened easily by colony PCR, without the need for selectable markers. Targetrons have found wide application in microbiological research, enabling gene targeting and genetic engineering of bacteria that had been intractable to other methods. Recently, a thermostable targetron has been developed for use in bacterial thermophiles, and new methods have been developed for using targetrons to position recombinase recognition sites, enabling large-scale genome-editing operations, such as deletions, inversions, insertions, and 'cut-and-pastes' (that is, translocation of large DNA segments), in a wide range of bacteria at high efficiency. Using targetrons in eukaryotes presents challenges due to the difficulties of nuclear localization and sub-optimal magnesium concentrations, although supplementation with magnesium can increase integration efficiency, and directed evolution is being employed to overcome these barriers. Finally, spurred by new methods for expressing group II intron reverse transcriptases that yield large amounts of highly active protein, thermostable group II intron reverse transcriptases from bacterial thermophiles are being used as research tools for a variety of applications, including qRT-PCR and next-generation RNA sequencing (RNA-seq). The

File list: Pol.Gon.10.AllAg.Testis [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Gon.10.AllAg.Testis mm9 RNA polymerase Gonad Testis SRX349391,SRX112975,SRX1437...96,SRX237511,SRX237510,SRX244355 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Gon.10.AllAg.Testis.bed ...

File list: Pol.Gon.05.AllAg.Testis [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Gon.05.AllAg.Testis mm9 RNA polymerase Gonad Testis SRX349391,SRX112975,SRX1437...96,SRX237511,SRX244355,SRX237510 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Gon.05.AllAg.Testis.bed ...

File list: Pol.Gon.20.AllAg.Testis [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Gon.20.AllAg.Testis mm9 RNA polymerase Gonad Testis SRX349391,SRX112975,SRX1437...96,SRX237511,SRX237510,SRX244355 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Gon.20.AllAg.Testis.bed ...

File list: Pol.Neu.10.AllAg.Cerebellum [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Neu.10.AllAg.Cerebellum mm9 RNA polymerase Neural Cerebellum SRX062952,SRX14381...7,SRX026426,SRX026423,SRX026425,SRX026424 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Neu.10.AllAg.Cerebellum.bed ...

File list: Pol.Neu.50.AllAg.Cerebellum [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Neu.50.AllAg.Cerebellum mm9 RNA polymerase Neural Cerebellum SRX062952,SRX14381...7,SRX026426,SRX026425,SRX026424,SRX026423 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Neu.50.AllAg.Cerebellum.bed ...

File list: Pol.Neu.05.AllAg.Cerebellum [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Neu.05.AllAg.Cerebellum mm9 RNA polymerase Neural Cerebellum SRX062952,SRX14381...7,SRX026424,SRX026426,SRX026423,SRX026425 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Neu.05.AllAg.Cerebellum.bed ...

File list: Pol.Neu.20.AllAg.Cerebellum [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Neu.20.AllAg.Cerebellum mm9 RNA polymerase Neural Cerebellum SRX062952,SRX14381...7,SRX026426,SRX026423,SRX026425,SRX026424 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Neu.20.AllAg.Cerebellum.bed ...

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

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: 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

Promoter2.0: for the recognition of PolII promoter sequences

DEFF Research Database (Denmark)

Knudsen, Steen; Knudsen, Steen

1999-01-01

Motivation : A new approach to the prediction of eukaryotic PolII promoters from DNA sequence takesadvantage of a combination of elements similar to neural networks and genetic algorithms to recognize a set ofdiscrete subpatterns with variable separation as one pattern: a promoter. The neural...... of optimization, the algorithm was able todiscriminate between vertebrate promoter and non-promoter sequences in a test set with a correlationcoefficient of 0.63. In addition, all five known transcription start sites on the plus strand of the completeadenovirus genome were within 161 bp of 35 predicted...

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

File list: Pol.Emb.05.AllAg.Embryonic_palates [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Emb.05.AllAg.Embryonic_palates mm9 RNA polymerase Embryo Embryonic palates http...://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Emb.05.AllAg.Embryonic_palates.bed ...

File list: Pol.Emb.20.AllAg.Embryonic_palates [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Emb.20.AllAg.Embryonic_palates mm9 RNA polymerase Embryo Embryonic palates http...://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Emb.20.AllAg.Embryonic_palates.bed ...

File list: Pol.Bld.20.AllAg.Polymorphonuclear_leukocytes [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Bld.20.AllAg.Polymorphonuclear_leukocytes hg19 RNA polymerase Blood Polymorphonuclear... leukocytes http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Bld.20.AllAg.Polymorphonuclear_leukocytes.bed ...

File list: Pol.Bld.50.AllAg.Polymorphonuclear_leukocytes [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Bld.50.AllAg.Polymorphonuclear_leukocytes hg19 RNA polymerase Blood Polymorphonuclear... leukocytes http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Bld.50.AllAg.Polymorphonuclear_leukocytes.bed ...

File list: Pol.Bld.05.AllAg.Polymorphonuclear_leukocytes [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Bld.05.AllAg.Polymorphonuclear_leukocytes hg19 RNA polymerase Blood Polymorphonuclear... leukocytes http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Bld.05.AllAg.Polymorphonuclear_leukocytes.bed ...

File list: Pol.Adl.05.AllAg.Octopaminergic_neurons [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Adl.05.AllAg.Octopaminergic_neurons dm3 RNA polymerase Adult Octopaminergic neurons... http://dbarchive.biosciencedbc.jp/kyushu-u/dm3/assembled/Pol.Adl.05.AllAg.Octopaminergic_neurons.bed ...

File list: Pol.Adl.20.AllAg.Octopaminergic_neurons [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Adl.20.AllAg.Octopaminergic_neurons dm3 RNA polymerase Adult Octopaminergic neurons... http://dbarchive.biosciencedbc.jp/kyushu-u/dm3/assembled/Pol.Adl.20.AllAg.Octopaminergic_neurons.bed ...

File list: Pol.Adl.50.AllAg.Octopaminergic_neurons [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Adl.50.AllAg.Octopaminergic_neurons dm3 RNA polymerase Adult Octopaminergic neurons... http://dbarchive.biosciencedbc.jp/kyushu-u/dm3/assembled/Pol.Adl.50.AllAg.Octopaminergic_neurons.bed ...

File list: Pol.Adl.10.AllAg.Octopaminergic_neurons [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Adl.10.AllAg.Octopaminergic_neurons dm3 RNA polymerase Adult Octopaminergic neurons... http://dbarchive.biosciencedbc.jp/kyushu-u/dm3/assembled/Pol.Adl.10.AllAg.Octopaminergic_neurons.bed ...

File list: Pol.CDV.10.AllAg.Atrioventicular_canals [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.CDV.10.AllAg.Atrioventicular_canals mm9 RNA polymerase Cardiovascular Atrioventicular canals... http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.CDV.10.AllAg.Atrioventicular_canals.bed ...

File list: Pol.CDV.05.AllAg.Atrioventicular_canals [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.CDV.05.AllAg.Atrioventicular_canals mm9 RNA polymerase Cardiovascular Atrioventicular canals... http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.CDV.05.AllAg.Atrioventicular_canals.bed ...

File list: Pol.CDV.50.AllAg.Atrioventicular_canals [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.CDV.50.AllAg.Atrioventicular_canals mm9 RNA polymerase Cardiovascular Atrioventicular canals... http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.CDV.50.AllAg.Atrioventicular_canals.bed ...

File list: Pol.CDV.20.AllAg.Atrioventicular_canals [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.CDV.20.AllAg.Atrioventicular_canals mm9 RNA polymerase Cardiovascular Atrioventicular canals... http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.CDV.20.AllAg.Atrioventicular_canals.bed ...

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.

File list: Pol.CDV.05.AllAg.Endocardial_cells [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.CDV.05.AllAg.Endocardial_cells hg19 RNA polymerase Cardiovascular Endocardial c...ells http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.CDV.05.AllAg.Endocardial_cells.bed ...

File list: Pol.CDV.50.AllAg.Endocardial_cells [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.CDV.50.AllAg.Endocardial_cells hg19 RNA polymerase Cardiovascular Endocardial c...ells http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.CDV.50.AllAg.Endocardial_cells.bed ...

File list: Pol.CDV.20.AllAg.Endocardial_cells [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.CDV.20.AllAg.Endocardial_cells hg19 RNA polymerase Cardiovascular Endocardial c...ells http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.CDV.20.AllAg.Endocardial_cells.bed ...

File list: Pol.CDV.10.AllAg.Endocardial_cells [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.CDV.10.AllAg.Endocardial_cells hg19 RNA polymerase Cardiovascular Endocardial c...ells http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.CDV.10.AllAg.Endocardial_cells.bed ...

File list: Pol.Kid.20.AllAg.Nephrectomy_sample [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Kid.20.AllAg.Nephrectomy_sample hg19 RNA polymerase Kidney Nephrectomy sample h...ttp://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Kid.20.AllAg.Nephrectomy_sample.bed ...

File list: Pol.Kid.10.AllAg.Nephrectomy_sample [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Kid.10.AllAg.Nephrectomy_sample hg19 RNA polymerase Kidney Nephrectomy sample h...ttp://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Kid.10.AllAg.Nephrectomy_sample.bed ...

File list: Pol.Kid.05.AllAg.Nephrectomy_sample [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Kid.05.AllAg.Nephrectomy_sample hg19 RNA polymerase Kidney Nephrectomy sample h...ttp://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Kid.05.AllAg.Nephrectomy_sample.bed ...

File list: Pol.Liv.50.AllAg.Carcinoma,_Hepatocellular [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Liv.50.AllAg.Carcinoma,_Hepatocellular mm9 RNA polymerase Liver Carcinoma, Hepa...tocellular http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Liv.50.AllAg.Carcinoma,_Hepatocellular.bed ...

File list: Pol.Liv.10.AllAg.Carcinoma,_Hepatocellular [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Liv.10.AllAg.Carcinoma,_Hepatocellular mm9 RNA polymerase Liver Carcinoma, Hepa...tocellular http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Liv.10.AllAg.Carcinoma,_Hepatocellular.bed ...

File list: Pol.Lng.10.AllAg.Lung_adenocarcinoma [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Lng.10.AllAg.Lung_adenocarcinoma mm9 RNA polymerase Lung Lung adenocarcinoma ht...tp://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Lng.10.AllAg.Lung_adenocarcinoma.bed ...

File list: Pol.CDV.10.AllAg.Carotid_Arteries [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.CDV.10.AllAg.Carotid_Arteries hg19 RNA polymerase Cardiovascular Carotid Arteri...es http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.CDV.10.AllAg.Carotid_Arteries.bed ...

File list: Pol.CDV.05.AllAg.Carotid_Arteries [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.CDV.05.AllAg.Carotid_Arteries hg19 RNA polymerase Cardiovascular Carotid Arteri...es http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.CDV.05.AllAg.Carotid_Arteries.bed ...

File list: Pol.CDV.50.AllAg.Carotid_Arteries [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.CDV.50.AllAg.Carotid_Arteries hg19 RNA polymerase Cardiovascular Carotid Arteri...es http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.CDV.50.AllAg.Carotid_Arteries.bed ...

File list: Pol.Emb.20.AllAg.Embryonic_pancreas [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Emb.20.AllAg.Embryonic_pancreas mm9 RNA polymerase Embryo Embryonic pancreas ht...tp://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Emb.20.AllAg.Embryonic_pancreas.bed ...

File list: Pol.Emb.10.AllAg.Embryonic_pancreas [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Emb.10.AllAg.Embryonic_pancreas mm9 RNA polymerase Embryo Embryonic pancreas ht...tp://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Emb.10.AllAg.Embryonic_pancreas.bed ...

File list: Pol.Emb.05.AllAg.Embryonic_pancreas [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Emb.05.AllAg.Embryonic_pancreas mm9 RNA polymerase Embryo Embryonic pancreas ht...tp://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Emb.05.AllAg.Embryonic_pancreas.bed ...

File list: Pol.Emb.20.AllAg.Neuronal_cells [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Emb.20.AllAg.Neuronal_cells dm3 RNA polymerase Embryo Neuronal cells SRX110756 ...http://dbarchive.biosciencedbc.jp/kyushu-u/dm3/assembled/Pol.Emb.20.AllAg.Neuronal_cells.bed ...

File list: Pol.Emb.50.AllAg.Neuronal_cells [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Emb.50.AllAg.Neuronal_cells dm3 RNA polymerase Embryo Neuronal cells SRX110756 ...http://dbarchive.biosciencedbc.jp/kyushu-u/dm3/assembled/Pol.Emb.50.AllAg.Neuronal_cells.bed ...

File list: Pol.Emb.05.AllAg.Neuronal_cells [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Emb.05.AllAg.Neuronal_cells dm3 RNA polymerase Embryo Neuronal cells SRX110756 ...http://dbarchive.biosciencedbc.jp/kyushu-u/dm3/assembled/Pol.Emb.05.AllAg.Neuronal_cells.bed ...

File list: Pol.Emb.10.AllAg.Neuronal_cells [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Emb.10.AllAg.Neuronal_cells dm3 RNA polymerase Embryo Neuronal cells SRX110756 ...http://dbarchive.biosciencedbc.jp/kyushu-u/dm3/assembled/Pol.Emb.10.AllAg.Neuronal_cells.bed ...

File list: Pol.Dig.50.AllAg.Intestinal_villus [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Dig.50.AllAg.Intestinal_villus mm9 RNA polymerase Digestive tract Intestinal vi...llus http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Dig.50.AllAg.Intestinal_villus.bed ...

File list: Pol.Dig.50.AllAg.Intestine,_Small [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Dig.50.AllAg.Intestine,_Small hg19 RNA polymerase Digestive tract Intestine, Sm...all http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Dig.50.AllAg.Intestine,_Small.bed ...

File list: Pol.Dig.10.AllAg.Intestine,_Small [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Dig.10.AllAg.Intestine,_Small hg19 RNA polymerase Digestive tract Intestine, Sm...all http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Dig.10.AllAg.Intestine,_Small.bed ...

File list: Pol.Dig.10.AllAg.Intestinal_crypt [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Dig.10.AllAg.Intestinal_crypt mm9 RNA polymerase Digestive tract Intestinal cry...pt http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Dig.10.AllAg.Intestinal_crypt.bed ...

File list: Pol.Dig.20.AllAg.Intestine,_Small [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Dig.20.AllAg.Intestine,_Small hg19 RNA polymerase Digestive tract Intestine, Sm...all http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Dig.20.AllAg.Intestine,_Small.bed ...

File list: Pol.Dig.50.AllAg.Intestinal_adenoma [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Dig.50.AllAg.Intestinal_adenoma mm9 RNA polymerase Digestive tract Intestinal a...denoma http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Dig.50.AllAg.Intestinal_adenoma.bed ...

File list: Pol.PSC.20.AllAg.Embryoid_Bodies [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.PSC.20.AllAg.Embryoid_Bodies mm9 RNA polymerase Pluripotent stem cell Embryoid Bodie...s http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.PSC.20.AllAg.Embryoid_Bodies.bed ...

File list: Pol.PSC.50.AllAg.Embryoid_Bodies [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.PSC.50.AllAg.Embryoid_Bodies mm9 RNA polymerase Pluripotent stem cell Embryoid Bodie...s http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.PSC.50.AllAg.Embryoid_Bodies.bed ...

File list: Pol.PSC.05.AllAg.Embryoid_Bodies [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.PSC.05.AllAg.Embryoid_Bodies mm9 RNA polymerase Pluripotent stem cell Embryoid Bodie...s http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.PSC.05.AllAg.Embryoid_Bodies.bed ...

File list: Pol.PSC.10.AllAg.Embryoid_Bodies [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.PSC.10.AllAg.Embryoid_Bodies mm9 RNA polymerase Pluripotent stem cell Embryoid Bodie...s http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.PSC.10.AllAg.Embryoid_Bodies.bed ...

File list: Pol.Emb.20.AllAg.Embryonic_heart [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Emb.20.AllAg.Embryonic_heart mm9 RNA polymerase Embryo Embryonic heart SRX11293...9 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Emb.20.AllAg.Embryonic_heart.bed ...

File list: Pol.Emb.10.AllAg.Embryonic_heart [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Emb.10.AllAg.Embryonic_heart mm9 RNA polymerase Embryo Embryonic heart SRX11293...9 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Emb.10.AllAg.Embryonic_heart.bed ...

File list: Pol.Emb.05.AllAg.Embryonic_heart [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Emb.05.AllAg.Embryonic_heart mm9 RNA polymerase Embryo Embryonic heart SRX11293...9 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Emb.05.AllAg.Embryonic_heart.bed ...

File list: Pol.Emb.10.AllAg.Embryobic_liver [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Emb.10.AllAg.Embryobic_liver mm9 RNA polymerase Embryo Embryobic liver SRX11295...1 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Emb.10.AllAg.Embryobic_liver.bed ...

File list: Pol.Emb.05.AllAg.Embryobic_liver [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Emb.05.AllAg.Embryobic_liver mm9 RNA polymerase Embryo Embryobic liver SRX11295...1 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Emb.05.AllAg.Embryobic_liver.bed ...

File list: Pol.Emb.50.AllAg.Embryobic_liver [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Emb.50.AllAg.Embryobic_liver mm9 RNA polymerase Embryo Embryobic liver SRX11295...1 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Emb.50.AllAg.Embryobic_liver.bed ...

File list: Pol.Emb.20.AllAg.Embryobic_liver [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Emb.20.AllAg.Embryobic_liver mm9 RNA polymerase Embryo Embryobic liver SRX11295...1 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Emb.20.AllAg.Embryobic_liver.bed ...

File list: Pol.Emb.50.AllAg.Embryonic_heart [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Emb.50.AllAg.Embryonic_heart mm9 RNA polymerase Embryo Embryonic heart SRX11293...9 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Emb.50.AllAg.Embryonic_heart.bed ...

File list: Pol.Oth.20.AllAg.Olfactory_epithelium [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Oth.20.AllAg.Olfactory_epithelium mm9 RNA polymerase Others Olfactory epithelium... SRX112963,SRX143827 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Oth.20.AllAg.Olfactory_epithelium.bed ...

File list: Pol.Oth.50.AllAg.Olfactory_epithelium [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Oth.50.AllAg.Olfactory_epithelium mm9 RNA polymerase Others Olfactory epithelium... SRX112963,SRX143827 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Oth.50.AllAg.Olfactory_epithelium.bed ...

File list: Pol.Oth.10.AllAg.Olfactory_epithelium [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Oth.10.AllAg.Olfactory_epithelium mm9 RNA polymerase Others Olfactory epithelium... SRX112963,SRX143827 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Oth.10.AllAg.Olfactory_epithelium.bed ...

File list: Pol.Oth.05.AllAg.Olfactory_epithelium [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Oth.05.AllAg.Olfactory_epithelium mm9 RNA polymerase Others Olfactory epithelium... SRX143827,SRX112963 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Oth.05.AllAg.Olfactory_epithelium.bed ...

File list: Pol.Adl.05.AllAg.Young_adult [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Adl.05.AllAg.Young_adult ce10 RNA polymerase Adult Young adult SRX395531,SRX331...RX043965 http://dbarchive.biosciencedbc.jp/kyushu-u/ce10/assembled/Pol.Adl.05.AllAg.Young_adult.bed ...

File list: Pol.Adl.10.AllAg.Young_adult [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Adl.10.AllAg.Young_adult ce10 RNA polymerase Adult Young adult SRX395531,SRX331...RX043965 http://dbarchive.biosciencedbc.jp/kyushu-u/ce10/assembled/Pol.Adl.10.AllAg.Young_adult.bed ...

File list: Pol.Adl.20.AllAg.Young_adult [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Adl.20.AllAg.Young_adult ce10 RNA polymerase Adult Young adult SRX331268,SRX331...RX043964 http://dbarchive.biosciencedbc.jp/kyushu-u/ce10/assembled/Pol.Adl.20.AllAg.Young_adult.bed ...

File list: Pol.Brs.20.AllAg.Mammary_cells [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Brs.20.AllAg.Mammary_cells mm9 RNA polymerase Breast Mammary cells SRX852566,SR...X852567,SRX187510,SRX187515 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Brs.20.AllAg.Mammary_cells.bed ...

File list: Pol.Brs.05.AllAg.Mammary_cells [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Brs.05.AllAg.Mammary_cells mm9 RNA polymerase Breast Mammary cells SRX187510,SR...X187515,SRX852567,SRX852566 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Brs.05.AllAg.Mammary_cells.bed ...

File list: Pol.Emb.10.AllAg.Mixed_embryo [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Emb.10.AllAg.Mixed_embryo ce10 RNA polymerase Embryo Mixed embryo SRX208771,SRX...208773,SRX208772,SRX208774 http://dbarchive.biosciencedbc.jp/kyushu-u/ce10/assembled/Pol.Emb.10.AllAg.Mixed_embryo.bed ...

File list: Pol.Emb.50.AllAg.Mixed_embryo [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Emb.50.AllAg.Mixed_embryo ce10 RNA polymerase Embryo Mixed embryo SRX208772,SRX...208773,SRX208774,SRX208771 http://dbarchive.biosciencedbc.jp/kyushu-u/ce10/assembled/Pol.Emb.50.AllAg.Mixed_embryo.bed ...

File list: Pol.Emb.10.AllAg.Early_embryo [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Emb.10.AllAg.Early_embryo ce10 RNA polymerase Embryo Early embryo SRX495119,SRX...495120,SRX043866,SRX043864,SRX043865,SRX043863 http://dbarchive.biosciencedbc.jp/kyushu-u/ce10/assembled/Pol.Emb.10.AllAg.Early_embryo.bed ...

File list: Pol.Neu.10.AllAg.Cortical_neuron [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Neu.10.AllAg.Cortical_neuron mm9 RNA polymerase Neural Cortical neuron SRX21773...5,SRX759296,SRX217736,SRX759295,SRX759293,SRX759294 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Neu.10.AllAg.Cortical_neuron.bed ...

File list: Pol.Neu.20.AllAg.Cortical_neuron [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Neu.20.AllAg.Cortical_neuron mm9 RNA polymerase Neural Cortical neuron SRX75929...5,SRX759296,SRX217735,SRX759294,SRX759293,SRX217736 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Neu.20.AllAg.Cortical_neuron.bed ...

File list: Pol.Neu.05.AllAg.Cortical_neuron [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Neu.05.AllAg.Cortical_neuron mm9 RNA polymerase Neural Cortical neuron SRX21773...5,SRX217736,SRX759296,SRX759293,SRX759294,SRX759295 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Neu.05.AllAg.Cortical_neuron.bed ...

File list: Pol.Neu.50.AllAg.Cortical_neuron [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Neu.50.AllAg.Cortical_neuron mm9 RNA polymerase Neural Cortical neuron SRX75929...5,SRX759296,SRX759293,SRX759294,SRX217735,SRX217736 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Neu.50.AllAg.Cortical_neuron.bed ...

File list: Pol.Emb.20.AllAg.Muscle_cells [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Emb.20.AllAg.Muscle_cells dm3 RNA polymerase Embryo Muscle cells SRX110760,SRX1...X110758,SRX110765,SRX110766,SRX110769 http://dbarchive.biosciencedbc.jp/kyushu-u/dm3/assembled/Pol.Emb.20.AllAg.Muscle_cells.bed ...

File list: Pol.Emb.05.AllAg.Muscle_cells [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Emb.05.AllAg.Muscle_cells dm3 RNA polymerase Embryo Muscle cells SRX110762,SRX1...X110759,SRX110770,SRX110768,SRX110763 http://dbarchive.biosciencedbc.jp/kyushu-u/dm3/assembled/Pol.Emb.05.AllAg.Muscle_cells.bed ...

File list: Pol.Emb.50.AllAg.Muscle_cells [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Emb.50.AllAg.Muscle_cells dm3 RNA polymerase Embryo Muscle cells SRX110760,SRX1...X110765,SRX110769,SRX110766,SRX110758 http://dbarchive.biosciencedbc.jp/kyushu-u/dm3/assembled/Pol.Emb.50.AllAg.Muscle_cells.bed ...

File list: Pol.Emb.20.AllAg.Early_embryo [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Emb.20.AllAg.Early_embryo ce10 RNA polymerase Embryo Early embryo SRX495120,SRX...495119,SRX043864,SRX043866,SRX043863,SRX043865 http://dbarchive.biosciencedbc.jp/kyushu-u/ce10/assembled/Pol.Emb.20.AllAg.Early_embryo.bed ...

Observatorio de Política Internacional II. AMERICAS - Elecciones en U.S.A.

OpenAIRE

Neira Fernández, Enrique

2007-01-01

Observatorio de Política Internacional II. AMÉRICAS (Neira Fernández, Enrique) RECIENTES Año 2008 Nicaragua. Un remedo revolucionario Bolivia. ¿Una o dislocada? Paraguay. El ex obispo presidente Perú. El rojo sangre de sendero luminoso Estados Unidos. Panorama tras las elecciones primarias RECIENTES Año 2007 Argentina. Contundente triunfo de Cristina Fernández Bolivia. Nuevos rumbos ¡no más embrollo! Ecuador. Nueva constitución, nuevo rumbo Guatemala....

Comparative transcript profiling of the fertile and sterile flower buds of pol CMS in B. napus.

Science.gov (United States)

An, Hong; Yang, Zonghui; Yi, Bin; Wen, Jing; Shen, Jinxiong; Tu, Jinxing; Ma, Chaozhi; Fu, Tingdong

2014-04-03

The Polima (pol) system of cytoplasmic male sterility (CMS) and its fertility restoration gene Rfp have been used in hybrid breeding in Brassica napus, which has greatly improved the yield of rapeseed. However, the mechanism of the male sterility transition in pol CMS remains to be determined. To investigate the transcriptome during the male sterility transition in pol CMS, a near-isogenic line (NIL) of pol CMS was constructed. The phenotypic features and sterility stage were confirmed by anatomical analysis. Subsequently, we compared the genomic expression profiles of fertile and sterile young flower buds by RNA-Seq. A total of 105,481,136 sequences were successfully obtained. These reads were assembled into 112,770 unigenes, which composed the transcriptome of the bud. Among these unigenes, 72,408 (64.21%) were annotated using public protein databases and classified into functional clusters. In addition, we investigated the changes in expression of the fertile and sterile buds; the RNA-seq data showed 1,148 unigenes had significantly different expression and they were mainly distributed in metabolic and protein synthesis pathways. Additionally, some unigenes controlling anther development were dramatically down-regulated in sterile buds. These results suggested that an energy deficiency caused by orf224/atp6 may inhibit a series of genes that regulate pollen development through nuclear-mitochondrial interaction. This results in the sterility of pol CMS by leading to the failure of sporogenous cell differentiation. This study may provide assistance for detailed molecular analysis and a better understanding of pol CMS in B. napus.

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.

File list: Pol.Neu.50.RNA_Polymerase_III.AllCell [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Neu.50.RNA_Polymerase_III.AllCell mm9 RNA polymerase RNA Polymerase III Neural ...http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Neu.50.RNA_Polymerase_III.AllCell.bed ...

File list: Pol.Myo.10.RNA_Polymerase_III.AllCell [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Myo.10.RNA_Polymerase_III.AllCell mm9 RNA polymerase RNA Polymerase III Muscle ...http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Myo.10.RNA_Polymerase_III.AllCell.bed ...

File list: Pol.Lar.50.RNA_polymerase_III.AllCell [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Lar.50.RNA_polymerase_III.AllCell ce10 RNA polymerase RNA polymerase III Larvae... http://dbarchive.biosciencedbc.jp/kyushu-u/ce10/assembled/Pol.Lar.50.RNA_polymerase_III.AllCell.bed ...

File list: Pol.Oth.20.RNA_Polymerase_III.AllCell [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Oth.20.RNA_Polymerase_III.AllCell mm9 RNA polymerase RNA Polymerase III Others ...http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Oth.20.RNA_Polymerase_III.AllCell.bed ...

File list: Pol.Oth.05.RNA_Polymerase_III.AllCell [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Oth.05.RNA_Polymerase_III.AllCell mm9 RNA polymerase RNA Polymerase III Others ...http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Oth.05.RNA_Polymerase_III.AllCell.bed ...

File list: Pol.Myo.05.RNA_Polymerase_III.AllCell [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Myo.05.RNA_Polymerase_III.AllCell mm9 RNA polymerase RNA Polymerase III Muscle ...http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Myo.05.RNA_Polymerase_III.AllCell.bed ...

File list: Pol.Brs.50.RNA_Polymerase_III.AllCell [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Brs.50.RNA_Polymerase_III.AllCell mm9 RNA polymerase RNA Polymerase III Breast ...http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Brs.50.RNA_Polymerase_III.AllCell.bed ...

File list: Pol.Lar.20.RNA_polymerase_III.AllCell [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Lar.20.RNA_polymerase_III.AllCell ce10 RNA polymerase RNA polymerase III Larvae... http://dbarchive.biosciencedbc.jp/kyushu-u/ce10/assembled/Pol.Lar.20.RNA_polymerase_III.AllCell.bed ...

File list: Pol.Emb.05.RNA_Polymerase_III.AllCell [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Emb.05.RNA_Polymerase_III.AllCell mm9 RNA polymerase RNA Polymerase III Embryo ...http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Emb.05.RNA_Polymerase_III.AllCell.bed ...

File list: Pol.Emb.10.RNA_polymerase_III.AllCell [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Emb.10.RNA_polymerase_III.AllCell ce10 RNA polymerase RNA polymerase III Embryo... http://dbarchive.biosciencedbc.jp/kyushu-u/ce10/assembled/Pol.Emb.10.RNA_polymerase_III.AllCell.bed ...

File list: Pol.Spl.10.RNA_Polymerase_III.AllCell [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Pol.Spl.10.RNA_Polymerase_III.AllCell mm9 RNA polymerase RNA Polymerase III Spleen ...http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Spl.10.RNA_Polymerase_III.AllCell.bed ...