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Series GSE75426 Query DataSets for GSE75426
Status Public on Nov 30, 2015
Title Local compartment changes and regulatory landscape alterations in histone H1-depleted cells
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Linker histone H1 is a core chromatin component that binds to nucleosome core particles and the linker DNA between nucleosomes. It has been implicated in chromatin compaction and gene regulation and is anticipated to play a role in higher-order genome structure. We find that depletion of histone H1 changes the epigenetic signature of thousands of potential regulatory sites across the genome. Many of them show cooperative loss or gain of multiple chromatin marks. Epigenetic alterations cluster to gene-dense topologically associated domains (TADs) that already showed a high density of corresponding chromatin features. Genome organization at the three-dimensional level is largely intact, but we find changes in the structural segmentation of chromosomes specifically for the epigenetically most modified TADs.
Overall design We have used a combination of genome-wide approaches including DNA methylation, histone modification and DNaseI hypersensitivity profiling as well as Hi-C to investigate the impact of reduced cellular levels of histone H1 in embryonic stem cells on chromatin folding and function.
Contributor(s) Geeven G, Skoultchi AI, de Laat W
Citation(s) 26700097
Submission date Nov 25, 2015
Last update date May 15, 2019
Contact name Geert Geeven
Organization name Hubrecht Institute
Department Biomedical Genomics
Lab Wouter de Laat
Street address Uppsalalaan 8
City Utrecht
State/province Utrecht
ZIP/Postal code 3584 CT
Country Netherlands
Platforms (4)
GPL9185 Illumina Genome Analyzer (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (41)
GSM1954922 WT ESC Hi-C NlaIII
GSM1954923 WT ESC Hi-C DpnII
GSM1954924 H1 TKO ESC Hi-C NlaIII
BioProject PRJNA304179
SRA SRP066683

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE75426_H1_TKO_ESC_H3K27me3_peaks.bed.gz 449.5 Kb (ftp)(http) BED
GSE75426_H1_TKO_ESC_H3K4me1_R1_peaks.bed.gz 955.8 Kb (ftp)(http) BED
GSE75426_H1_TKO_ESC_H3K4me1_R2_peaks.bed.gz 963.2 Kb (ftp)(http) BED
GSE75426_H1_TKO_ESC_H3K4me3_R1_peaks.bed.gz 526.5 Kb (ftp)(http) BED
GSE75426_H1_TKO_ESC_H3K4me3_R2_peaks.bed.gz 534.4 Kb (ftp)(http) BED
GSE75426_H1_TKO_ESC_H3K9me3_peaks.bed.gz 627.6 Kb (ftp)(http) BED
GSE75426_H3K4me1_WT_vs_TKO_diffReps_output.txt.gz 584.8 Kb (ftp)(http) TXT
GSE75426_H3K4me3_WT_vs_TKO_diffReps_output.txt.gz 121.7 Kb (ftp)(http) TXT
GSE75426_RAW.tar 1.4 Gb (http)(custom) TAR (of BED, TXT)
GSE75426_WT_ESC_H3K27me3_peaks.bed.gz 286.6 Kb (ftp)(http) BED
GSE75426_WT_ESC_H3K4me1_R1_peaks.bed.gz 974.6 Kb (ftp)(http) BED
GSE75426_WT_ESC_H3K4me1_R2_peaks.bed.gz 832.6 Kb (ftp)(http) BED
GSE75426_WT_ESC_H3K4me3_R1_peaks.bed.gz 483.0 Kb (ftp)(http) BED
GSE75426_WT_ESC_H3K4me3_R2_peaks.bed.gz 573.5 Kb (ftp)(http) BED
GSE75426_WT_ESC_H3K9me3_peaks.bed.gz 565.3 Kb (ftp)(http) BED
GSE75426_WT_ESC_vs_H1_TKO_ESC_DNA_methylation_assay_HELP.txt.gz 33.6 Mb (ftp)(http) TXT
GSE75426_WT_ESC_vs_H1_TKO_ESC_RNA-Seq_cuffDiff.txt.gz 16.9 Kb (ftp)(http) TXT
GSE75426_WT_H1_TKO_ESC_RNA-Seq_FPKM.txt.gz 372.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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