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ChIP-Seq of Histone Methylation and RNAP2 in Human Jurkat cells.

ABSTRACT: Three transcriptional states can be defined by histone modifications and RNA polymerase II enriched at promoters and across the body of genes. To gain insight into the active, poised and silent genes in human T-ALL cells, two antibodies against RNAP2, and antibodies against H3K4me3, H3K79me2, and H3K27me3 were used for chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq).

ORGANISM(S): Homo sapiens

PROVIDER: GSE23080 | GEO | 2010/07/24

SECONDARY ACCESSION(S): PRJNA131693

REPOSITORIES: GEO

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ChIP-Seq of Histone Methylation and RNAP2 in Human Jurkat cells.

Project description:Three transcriptional states can be defined by histone modifications and RNA polymerase II enriched at promoters and across the body of genes. To gain insight into the active, poised and silent genes in human T-ALL cells, two antibodies against RNAP2, and antibodies against H3K4me3, H3K79me2, and H3K27me3 were used for chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq). Genomic DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. ChIP was performed using an antibody against RNAP2, H3K4me3, H3K79me2, and H3K27me3 using whole cell extract (WCE) as a background control. ChIP was performed using a two antibody against hypophosphorylated forms of RNAP2 in two biological replicates. All other ChIPs were done in biological replicates with a single lane of sequencing.

2010-07-24 | E-GEOD-23080 | biostudies-arrayexpress

ChIP-Seq of H3K79me2 in Mouse Embryonic Fibroblasts

Project description:H3K79 dimethylation is a mark of transcriptional elongation. To gain insight into the set of genes actively transcribed in MEFs, chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) was performed to determine the presence of H3K79me2 across the genome. DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. ChIP was performed using an antibody against H3K79me2.

2010-06-15 | E-GEOD-22268 | biostudies-arrayexpress

The Polycomb group mutant esc leads to augmented the levels of paused Pol II in the Drosophila embryo.

Project description:The role of Polycomb group (PcG) was studied on RNA Polymerase II (Pol II) pausing phenomenon. Wild type and Polycomb mutant (esc) embryos were used for ChIP-Seq experiments using Pol II and histone methylation antibodies. Enhanced Pol II occupancy was observed for thousands of genes in esc mutant embryos, including genes not known to be bound by PRC2 or having H3K27me3 associated. Most of these genes exhibit a concomitant reduction in H3K27me3 and increase in H3K4me3 at promoter-proximal regions. Silent genes lacking promoter-associated paused Pol II in wild-type embryos are converted into âpoisedâ genes with paused Pol II in esc mutants. We suggest that this conversion of silent genes into poised genes might render differentiated cell types susceptible to switches in identity in PcG mutants. ChIP-Seq data was generated for antibodies against Pol-II, H3K4me3, H3K27me3 in both wild type and esc mutant Drosophila embryos (0-2hr, 8-12hr, and 18-24hr embryos). In addition GRO-Seq data was generated for 18-24hr esc mutant embryos.

2011-06-14 | E-GEOD-28833 | biostudies-arrayexpress

Mapping of cohesin, CTCF and a collection of tissue-specific and ubiquitous transcriptional regulators using ChIP-seq in primary wild type and Rad21-cohesin haploinsufficient mouse liver

Project description:Mapping of cohesin, CTCF and a collection of tissue-specific and ubiquitous transcriptional regulators using ChIP-seq in primary mouse liver. The following antibodies were used: CTCF (upstate, 07729), STAG1 (abcam, ab4457), STAG2 (abcam, 4464), RAD21 (abcam, ab992), CEBPA (santa cruz, sc9314), HNF4A (aviva systems biology, ARP31946), FOXA1 (abcam, ab5089), FOXA2 (santa cruz, sc6554), HNF6 (santa cruz, sc13050), HNF1A (santa cruz, sc6547), PREP1 (santa cruz, sc6245), NRSF/REST (santa cruz, sc25398), GABPA (santa cruz, sc22810), E2F4 (santa cruz, sc1082), p300 (santa cruz, sc585), CBP (santa cruz, sc369), RNAP2 (abcam, ab5408), H3K4me1 (abcam, ab8895), H3K4me3 (abcam, ab8580), H3K36me3 (abcam, ab9050), H3K79me2 (abcam, ab3594), H2AK5ac (abcam, 1764)

2012-06-22 | E-MTAB-941 | biostudies-arrayexpress

H3K27me3, H3K79me2, and Suz12 ChIP-Seq in Human Embryonic Stem Cells (BG03).

Project description:H3K27me3 is a chromatin modification depositied by Suz12, a component of the Polycomb Group 2 complex, and is associated with transcriptional repression. In contrast, H3K79me2 is a chromatin modification associated with active gene transcription. It is deposited by the histone methyltransferase Dot1L and generally is localized just downstream of the transcriptional start site and extends down the body of the gene. To gain insight into the transcriptional state of genes in hES cells, chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) was performed to determine the genome-wide occupancy of the H3K27me3 and H3K79me2 chromatin modifications and genome-wide occupancy of the Suz12. DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing A sample of whole cell extract was sequenced and used as the background to determine enrichment. ChIP was performed using an antibody against H3K27me3, H3K79me2, and Suz12 (Abcam).

2010-10-01 | E-GEOD-24463 | biostudies-arrayexpress

ChIP-Seq of H3K79me2 in Mouse Embryonic Fibroblasts

2010-06-15 | GSE22268 | GEO

ChIP-seq for H3K4me3, H3K27me3, H3K79me2 in MCF10A cells

Project description:We performed ChIP-Seq against histones H3K4me3, H3K27me3, and H3K79me2 in MCF10A cells to identify transcription factors with bivalent and pseudo-bivalent epigenetic modifications.

2018-02-01 | GSE109721 | GEO

The Polycomb group mutant esc leads to augmented the levels of paused Pol II in the Drosophila embryo.

2011-06-15 | GSE28833 | GEO

Antibody performance in ChIP-sequencing assays: From quality scores of public datasets to quantitative certification

Project description:We have established a certification system for antibodies to be used in chromatin immunoprecipitation assays coupled to massive parallel sequencing (ChIP-seq). This certification comprises a standardized ChIP procedure and the attribution of a numerical quality control indicator (QCi) to biological replicate experiments. The QCi computation is based on a universally applicable quality assessment that quantitates the global deviation of randomly sampled subsets of ChIP-seq dataset with the original genome-aligned sequence reads. Comparison with a QCi database for >28,000 ChIP-seq assays were used to attribute quality grades (ranging from ‘AAA’ to ‘DDD’) to a given dataset. In the present report we used the numerical QC system to assess the factors influencing the quality of ChIP-seq assays, including the nature of the target, the sequencing depth and the commercial source of the antibody. We have used this approach specifically to certify mono and polyclonal antibodies obtained from Active Motif directed against the histone modification marks H3K4me3, H3K27ac and H3K9ac for ChIP-seq. The antibodies received the grades AAA to BBA (www.ngs-qc.org). We propose to attribute such quantitative grading of all antibodies attributed with the label “ChIP-seq grade”.

2016-01-07 | GSE76618 | GEO

ChIP-Seq of chromatin marks at distal enhancers in Mouse Embryonic Stem Cells and adult tissues.

Project description:Enhancers are enriched by histone H3 lysine 4 mono methylation (H3K4me1). To gain insight into the relation between enhancers and developmental state, chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) was performed in several cell types to determine the genome-wide binding targets of H3K4me1 and several other possible enhancer associated modifications. DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. A chromatin IP against histone H3 or whole cell extract was sequenced and used as the background to determine enrichment. ChIP was performed mainly using antibodies against the chromatin marks H3K4me1 and H3K27ac.

2010-10-31 | E-GEOD-24164 | biostudies-arrayexpress

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