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EpiChip: Gene-by-gene quantification of epigenetic modification levels

ABSTRACT: Using datasets for the H3KAc histone modification in Th2 cells and an accompanying IgG control, we present an analysis strategy termed 'EpiChip' that alternates between single gene and global data distribution levels and allows a clear distinction between experimental background and signal. Examination of H3KAc histone modifications in one cell type plus an IgG control.

ORGANISM(S): Mus musculus

SUBMITTER: Daniel Hebenstreit

PROVIDER: E-GEOD-23092 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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EpiChIP: gene-by-gene quantification of epigenetic modification levels.

Hebenstreit Daniel D Gu Muxin M Haider Syed S Turner Daniel J DJ Liò Pietro P Teichmann Sarah A SA

Nucleic acids research 20101203 5

The combination of chromatin immunoprecipitation with next-generation sequencing technology (ChIP-seq) is a powerful and increasingly popular method for mapping protein-DNA interactions in a genome-wide fashion. The conventional way of analyzing this data is to identify sequencing peaks along the chromosomes that are significantly higher than the read background. For histone modifications and other epigenetic marks, it is often preferable to find a characteristic region of enrichment in sequenci ...[more]

PMID: 21131282

Similar Datasets

EpiChip: Gene-by-gene quantification of epigenetic modification levels

Project description:Using datasets for the H3KAc histone modification in Th2 cells and an accompanying IgG control, we present an analysis strategy termed 'EpiChip' that alternates between single gene and global data distribution levels and allows a clear distinction between experimental background and signal.

2010-12-07 | GSE23092 | GEO

Histone architecture of stem-cell memory T cells reveals progressive remodeling of epigenetic landscape in antigen-experienced CD8 T cells

Project description:We investigated the genomic landscape of histone modifications in antigen-experienced CD8+ T cells. Using a ChIP-Seq approach coupled with global gene expression profiling [GSE67825], we generated genome-wide histone H3 lysine 4 (H3K4me3) and H3 lysine 27 (H3K27me3) trimethylation maps in distinct subsets of CD8+ T cells - naïve, stem cell memory, central memory, and effector memory. To gain insight into how histone architecture is remodeled during the differentiation of activated T cells

2015-04-15 | E-GEOD-67881 | biostudies-arrayexpress

GlobaGlobal involvement of lysine crotonylation in protein modification and transcription regulation in ricel involvement of lysine crotonylation in protein modification and transcription regulation in rice

Project description:Lysine crotonylation (Kcr) is a newly discovered post-translational modification (PTM) existing in mammalian. Here, we performed a global crotonylome analysis of rice (Oryza sativa L. japonica) using high accuracy nano-LC-MS/MS in combination with crotonylated peptide enrichment. A total of 1,265 lysine crotonylation sites were identified on 690 proteins in rice seedlings. Subcellular localization analysis revealed that 51% of the crotonylated proteins identified were predicted to be associated with chloroplasts. The photosynthesis-associated proteins were also mostly enriched in total crotonylated proteins. Furthermore, to assess the relevance between histone Kcr and the genome, we performed a genomic localization analysis of histone Kcr by ChIP-seq analysis. Of the 10,923 identified peak regions, the majority (86.7%) of the enriched peaks were located in genes, especially exons. Furthermore, the degree of histone Kcr modification was positively correlated with gene expression in genic regions. Compared with other published histone modification data, the Kcr was co-located with the active histone modifications. Interestingly, histone Kcr facilitated expression of genes with existing active histone modifications. In addition, 77% of histone Kcr modifications overlapped with DNase hypersensitive sites (DHSs) in intergenic regions of the rice genome, and might mark other cis-regulatory DNA elements which are different from IPA1, a transcription activator in rice seedling. Overall, our results provide a comprehensive understanding of the biological functions of the crotonylome and new active histone modification in transcriptional regulation in plants.

2018-07-23 | PXD008716 | Pride

An mRNA-sequencing atlas of mouse CD4+ T cell transcriptomes

Project description:PolyA+ mRNA-seq was performed on naive, Th1, Th2, Th17, splenic Treg, and in vitro-induced Treg (iTreg) cells.

2015-05-14 | E-MTAB-2582 | biostudies-arrayexpress

ZMYM2-WT, ZMYM2-SIM2mut, and FOXO3 ChIP-seq in a U2OS stable cell line

Project description:Chromatin immuno-precipitation using anti-Flag (Sigma) or control IgG (Millipore) antibodies in a U2OS stable cell line. ZMYM2 has the synonym ZNF198. Note: paired-end sequencing libraires were created in this experiment but only the forward (R1) reads are available in this submission. The 'LIBRARY_LAYOUT' attribute is therefore set to be 'SINGLE' ather than 'PAIRED'.

2015-06-23 | E-MTAB-2701 | biostudies-arrayexpress

Transcription profiling of mouse wild type or Batf deficient T cells cultured under various combinations of IL-6 orTGF-beta

Project description:Wild type and Batf deficient T cells were stimulated under various combinations of IL-6 or TGF-beta.

2009-06-01 | E-MEXP-2152 | biostudies-arrayexpress

Natural variation of histone modification and its impact on gene expression in rat

Project description:Histone modifications are epigenetic marks that play fundamental roles in many biological processes including the control of chromatin-mediated regulation of gene expression. To begin to understand the impact of natural variation on histone methylation levels we generated and quantified large-scale genome-wide ChIP-seq data in a panel of rat recombinant inbred strains and their parental progenitors. Linkage analysis identified hundreds of cis- and trans-acting loci responsible for quantitative differences in histone trimethyl-lysine levels in left ventricular heart and liver tissues. We assessed the association of histone methylation and gene expression levels by generating deep RNA-seq profiles across the segregating population. Among the main findings, causal modelling of DNA variation together with histone methylation and gene expression levels enhanced the prediction of gene expression traits (eQTLs) by ~20%. Moreover, allele specific differences of histone trimethyl-lysine levels at alternative promoters were associated with differential usage of transcriptional start sites. Our data suggest that genetic variation has widespread impact on histone modifications. The highly adapted interplay between DNA variation and chromatin structure has consequences on gene and isoform expression as direct functional outcome and demonstrated new avenues to find novel genotype Ð phenotype relationships. NOTE: Additional processed data files were added to this experiment on the 24th April 2014. They are in the zip archive E-MTAB-1102.additional.1.zip which is available under the 'Click to browse all available files' link.

2012-05-30 | E-MTAB-1102 | biostudies-arrayexpress

ATM-deficient B cell lymphomas

Project description:Ataxia-telangiectasia mutated (ATM) kinase plays a central role in maintaining genomic integrity. In both humans and mice, ATM deficiency is associated with an increased incidence of lymphoid cancers that are primarily T cell in origin. We demonstrate here that when T cells are removed as targets for lymphomagenesis and as mediators of immune surveillance, ATM-deficient mice exclusively develop early onset IgM+ B cell lymphomas that by histology and gene expression profiling resemble the activated B cell-like (ABC) subset of human diffuse large B cell lymphomas (DLBCL). These ATM-deficient B cell tumors show considerable chromosomal instability and a recurrent genomic amplification of a 4.48 Mb region on chromosome 18 that contains Malt1 and is orthologous to a region similarly amplified in human ABC-DLBCL. Further, the amplification of Malt1 in these lymphomas correlates with their dependence on NF-kB, MALT1, and BCR signaling for survival, paralleling human ABC-DLBCL. This study reveals that ATM protects against development of B cell lymphomas that model human ABC-DLBCL and identifies a role for T cells in preventing the emergence of these tumors. We performed gene expression profiling on nine ATMKO.CD3epsilonKO lymphoma cell lines (n=12, 3 technical repeats). We analyzed gene expression of anti-IgM stimulated primary B cells from both ATMKO.CD3epsilonKO (n=7, 5 technical repeats) and ATMWT.CD3epsilonKO mice (n=2), and GC B cells isolated from SRBC-immunized ATMWT mice (n=3, 1 biological repeat and 2 technical repeats). We analyzed gene expression following treatment of two ATMKO.CD3epsilonKO lymphoma cell lines with the BTK inhibitor, PCI-32765, at time points (1, 3, 6, and 24 hours) as compared to time points with vehicle (DMSO) (n=8).

2015-12-09 | E-GEOD-68505 | biostudies-arrayexpress

A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways [T-cells]

Project description:To characterize the largely unknown functions of oxidised methylcytosines (oxi-mC; 5hmC/5fC/5caC) in DNA, several sequencing protocols have been recently developed. Quantitative analysis is complicated because DNA methylation modifications need to be deconvoluted from the data which is affected by several experimental parameters, including e.g. imperfect bisulphite conversion, oxidation efficiencies, various chemical labeling and protection steps, and sequencing errors. Here, we present a hierarchical generative model, Lux, for integrative analysis of any combination of BS-seq and âoxi-mCâ-seq (BS-seq/oxBS-seq/TAB-seq/fCAB-seq/CAB-seq/redBS-seq/MAB-seq) data. We show that Lux improves quantification and comparison of methylation levels over existing methods and that Lux can easily process any oxi-mC-seq data sets to quantify all cytosine modifications simultaneously together with their experimental parameters. Application of Lux to targeted data from Tet2 knockdown ESCs and T cells during development demonstrates DNA modification quantification at unprecedented detail, quantifies active demethylation pathway and reveals 5hmC localization in putative regulatory regions. Examine the distribution of C, 5mC, and 5hmC in DP, CD4 SP, and naÃ¯ve CD4 T cells within selected loci. Half of the samples are measured using the traditional bisulphite-seq protocol but the other half is measured using the oxidative bisulphite-seq protocol (oxBS-seq).

2016-07-03 | E-GEOD-68575 | biostudies-arrayexpress

Histone protein and peptide reactivity within patients with systemic lupus erythematosus (SLE) from the ABCoN cohort

Project description:The aim of the study was to test the hypothesis that IFN high SLE patient sera is more reactive to whole histone proteins and post-translationally modified histone peptides than IFN low patient sera. We diluted patient sera 1:250 and incubated dilutions on a nitrocellulose-platform array printed with whole protein and peptide histone antigens. In this study, serum from 30 patients subsetted into high and low interferon signature categories were profiled for IgG autoantibody reactivity to whole histone proteins, unmodified and post-translationally modified histone peptides. IFN high patient sera was found using the significance analysis of microarrays (SAM) algorithm to be significantly more reactive with whole histone and modified histone peptide antigens.

2011-12-02 | E-GEOD-34070 | biostudies-arrayexpress

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