BLUEPRINT DNase accessibility (NCMLS)
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ABSTRACT:
PROVIDER: EGAS00001000351 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:We futher characterized genome-wide chromatin accessibility of WT and SRC-2-/- mouse liver at CT10 through DNase-Seq. In addition,chromatin accessibility was significantly reduced in SRC-2-/- mouse liver compared to WT mice at CT10. DNase-Seq was carried out in WT and SRC-2-/- mice in liver at CT10 using two doses of DNaseI.
2015-12-07 | E-GEOD-67859 | biostudies-arrayexpress
Project description:Mitosis entails global alterations to chromosome structure and nuclear architecture, concomitant with transient silencing of transcription. How cells transmit transcriptional states through mitosis remains incompletely understood. While many nuclear factors dissociate from mitotic chromosomes, the observation that certain nuclear factors and chromatin features remain associated with individual loci during mitosis originated the hypothesis that they could provide transcriptional memory through mitosis. To obtain the first genome-wide view of the dynamics of chromatin structure during mitosis, we compared the DNase sensitivity of interphase and mitotic chromatin at two stages of cellular maturation in a rapidly dividingmurine erythroblastmodel. Despite global chromosome condensation visible during mitosis at the microscopic level, the chromatin accessibility landscape is largely unaltered. However, mitotic chromatin accessibility is locally dynamic, with individual loci maintaining none, some, or all of their interphase accessibility. Mitotic reduction in accessibility occurs primarily within narrow, highly hypersensitive sites that frequently coincide with transcription factor binding sites, whereas broader domains of moderate accessibility tend to be more stable. In mitosis, proximal promoters generally maintain their accessibility, whereas distal regulatory elements preferentially lose accessibility. Promoters with the highest degree of accessibility preservation in mitosis tend to also be accessible across many murine tissues in interphase. Transcription factor GATA1 exerts site-specific changes in interphase accessibility that are most pronounced at distal regulatory elements, but does not visibly influence mitotic accessibility. We conclude that features of open chromatin are remarkably stable through mitosis and are modulated at the level of individual genes and regulatory elements. Dnase-Seq data is integrated with Chip-seq [GSE36589, GSE30142] and RNA-seq to examine epigentic changes in mitosis. We performed DNase-seq on two cell lines, G1E and G1E-ER4, both on an asynchronus population, and on a sample of cells in mitosis; each of the 4 experiments in triplicate.
2014-10-01 | E-GEOD-61885 | biostudies-arrayexpress
Project description:DNase-seq and ChIP-seq determine that C/EBP maintains chromatin accessibility in liver and facilitates glucocorticoid receptor recruitment to steroid response elements DNase-seq and ChIP-seq (GR, C/EBPb and RNAPII) in intact liver from adrenalectomized mice injected with dex (1h)
2013-04-17 | E-GEOD-46047 | biostudies-arrayexpress
Project description:Using DNase-seq, mRNA-seq and publicly available ChIP-seq data sets, we examined the role of chromatin accessibility (DNase-seq) in androgen receptor binding to the genome (ChIP-seq) and AR-mediated transcriptional changes (mRNA-seq). Our data reveals genome-wide changes in chromatin structure that correspond to AR binding and differential gene expression. A focused examination of DNase-seq data around androgen receptor motifs within androgen receptor ChIP-seq peaks reveals distinct patterns of protection from DNaseI cleavage. Examination of chromatin accessibility (DNase-seq), AR binding (AR ChIP-seq), and transcription (mRNA-seq) in LNCaP cells before and after 12 hours of 1 nM R1881 treatment This Series represents the RNA-Seq data only. Exon microarray data generated under the same conditions is available through GSE15805. The DNase-seq data is publicly available through GSE32970 as well as the UCSC genome browser (genome.ucsc.edu) under Regulation::ENCODE DNase/FAIRE::Duke DNaseI HS:LNCaP and LNCaP + Andro. The accession numbers for the ChIP-seq experiments used are GSE14097 and GSE28126.
2012-08-14 | E-GEOD-34780 | biostudies-arrayexpress
Project description:While it is well established that variation in gene expression levels can be influenced by single nucleotide polymorphisms (SNPs), little is known about the regulatory mechanisms by which this occurs. To address this gap, we used DNaseI sequencing to measure genome-wide chromatin accessibility in 70 Yoruba lymphoblastoid cell lines (LCLs), for which genome-wide genotypes and estimates of gene expression levels based on RNA-sequencing are also available. We obtained a total of 2.8 billion uniquely mapped DNase-seq reads, which allowed us to produce genome-wide maps of chromatin accessibility for each individual. We identified 7,759 locations at which DNase-seq read depth correlates significantly with variation at a nearby SNP or indel (FDR=10%). We call such variants 'chromatin accessibility Quantitative Trait Loci' (or caQTLs). Most caQTLs lie within or very near the target DNaseI hypersensitive sites, and they are strongly enriched within inferred transcription factor binding sites. We find that a substantial fraction (14%) of caQTLs are also significantly associated with variation in the expression levels of nearby genes (namely, these loci are also classified as eQTLs), suggesting that changes in chromatin accessibility or transcription factor binding frequently lead to gene expression changes. Conversely, 12% of eQTL SNPs are also classified as caQTLs and, accounting for incomplete power, we estimate that the true fraction may be as high as 41%. Our observations indicate that caQTLs are abundant in the human genome, and are likely to be significant contributors to phenotypic variation. DNaseI-Seq on 70 YRI Hapmap cell lines. Each individual sequenced on several lanes of a flow cell on the Illumina Genome Analyzer II
2012-01-26 | E-GEOD-31388 | biostudies-arrayexpress
Project description:We futher characterized genome-wide chromatin accessibility of WT and SRC-2-/- mouse liver at CT10 through DNase-Seq. In addition,chromatin accessibility was significantly reduced in SRC-2-/- mouse liver compared to WT mice at CT10.
2015-12-07 | GSE67859 | GEO
Project description:Synergistic model of chromatin predicts Dnase-I accessibility
| PRJNA318029 | ENA
Project description:Chronic lymphocytic leukemia (CLL) is characterized by substantial clinical heterogeneity, despite relatively few genetic alterations. To provide a basis for studying epigenome deregulation in CLL, we established genome-wide chromatin accessibility maps for 88 CLL samples from 55 patients using the ATAC-seq assay, and we also performed ChIPmentation and RNA-seq profiling for ten representative samples. Based on the resulting dataset, we devised and applied a bioinformatic method that links chromatin profiles to clinical annotations. Our analysis identified sample-specific variation on top of a shared core of CLL regulatory regions. IGHV mutation status â which distinguishes the two major subtypes of CLL â was accurately predicted by the chromatin profiles, and gene regulatory networks inferred for IGHV-mutated vs. IGHV-unmutated samples identified characteristic differences between these two disease subtypes. In summary, we found widespread heterogeneity in the CLL chromatin landscape, established a community resource for studying epigenome deregulation in leukemia, and demonstrated the feasibility of chromatin accessibility mapping in cancer cohorts and clinical research. Genome-wide profiling of chromatin states and gene expression levels in 88 CLL samples from 55 individuals gave rise to 88 ATAC-seq profiles, 40 ChIPmentation profiles (10 samples, each with 3 different antibodies and matched immunoglobulin control), and 10 RNA-seq profiles. Raw sequence data has been deposited at the EBI's European Genome-phenome Archive (EGA) under the accession number EGAS00001001821 (controlled access to protect patient privacy).
2016-06-26 | E-GEOD-81274 | biostudies-arrayexpress
Project description:This experiment contains a subset of data from the BLUEPRINT Epigenome project ( http://www.blueprint-epigenome.eu ), which aims at producing a reference haemopoetic epigenomes for the research community. 4 samples of primary cells from tonsil with cell surface markes CD20med/CD38high in young individuals (3 to 10 years old) are included in this experiment. This ArrayExpress record contains only meta-data. Raw data files have been archived at the European Genome-Phenome Archive (EGA, www.ebi.ac.uk/ega) by the consortium, with restricted access to protect sample donors' identity. The relevant accessions of EGA data sets is EGAD00001001523. Details on how to apply for data access via the BLUEPRINT data access committee are on the EGA data set pages. The mapping of samples to these EGA accessions can be found in the 'Sample Data Relationship Format' file of this ArrayExpress record. Information on individual samples and sequencing libraries can also be found on the BLUEPRINT data coordination centre (DCC) website: http://dcc.blueprint-epigenome.eu
2016-05-12 | E-MTAB-4754 | biostudies-arrayexpress
Project description:To identify chromatin mechanisms of neuronal differentiation, we characterized the relationship between chromatin accessibility and gene expression in cerebellar granule neurons (CGNs) of the developing mouse. We used DNase-seq to globally map accessibility of cis-regulatory elements and RNA-seq to profile transcript abundance at key points in postnatal neuronal differentiation in vivo and in culture. We observed thousands of chromatin accessibility changes as CGNs differentiated and determined that many of these regions function as stage-specific neuronal enhancers. Motif discovery within differentially accessible chromatin regions suggested a novel role for the Zic family of transcription factors in CGN maturation, and we confirmed the association of Zic with these elements by ChIP-seq. Knockdown of Zic1 and Zic2 indicated Zic transcription factors are required to coordinate mature neuronal gene expression patterns. These data reveal chromatin dynamics at thousands of gene regulatory elements that facilitate gene expression patterns necessary for neuronal differentiation and function. Biological triplicate DNase-seq and RNA-seq samples from 3 in vivo cerebellum developmental stages (P7, P14, P60) and 3 cultured CGN stages (isolated granule neuron precursors, +3DIV, and +7DIV) obtained. Zic1 and Zic2 were separately knocked down by lentiviral shRNA in cultured CGNs followed by RNA-seq (2 biological replicates per KD and 2 controls). Zic1/2 ChIP-seq was performed with in vivo cerebellum at two developmental stages (P7 and P60) in duplicate with matching input and IgG controls.
2015-02-27 | E-GEOD-60731 | biostudies-arrayexpress