|
| 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.
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| |
|
| 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 |
| E-mail(s) |
geertgeeven@yahoo.com
|
| 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) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
|
| Samples (41)
|
|
| Relations |
| BioProject |
PRJNA304179 |
| SRA |
SRP066683 |
| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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