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Series GSE38442 Query DataSets for GSE38442
Status Public on Jul 09, 2012
Title Independence of Repressive Histone Marks and Chromatin Compaction during Senescent Heterochromatic Layer Formation (ChIP-Seq)
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The expansion of repressive epigenetic marks has been implicated in heterochromatin formation during embryonic development, but the general applicability of this mechanism is unclear. Here we show that nuclear rearrangement of repressive histone marks H3K9me3 and H3K27me3 into non-overlapping structural layers characterizes senescence-associated heterochromatic foci (SAHF) formation in human fibroblasts. However, the global landscape of these repressive marks remains unchanged upon SAHF formation, suggesting that in somatic cells heterochromatin can be formed through the spatial repositioning of pre-existing repressively marked histones. This model is reinforced by the correlation of pre-senescent replication timing with both the subsequent layered structure of SAHFs and the global landscape of the repressive marks, allowing us to integrate microscopic and genomic information. Furthermore, modulation of SAHF structure does not affect the occupancy of these repressive marks nor vice versa. These experiments reveal that high-order heterochromatin formation and epigenetic remodeling of the genome can be discrete events.
 
Overall design ChIP-seq for different histone marks in both growing and Ras-induced senescent fibroblasts, in the presence or absence of certain sh-RNAs
K9me3Grow2.bed (growing) Chip Seq Analysis of H3K9me3 in ER:Ras expressing IMR90 human diploid fibroblasts d6 4OHT
K9me3Sen2.bed (senescent) Chip Seq Analysis of H3K9me3 in ER:Ras expressing IMR90 human diploid fibroblasts with no treatment
K9me2Grow3.bed (growing) Chip Seq Analysis of H3K9me2 in ER:Ras expressing IMR90 human diploid fibroblasts with no treatment
K9me2Sen3.bed (senescent) Chip Seq Analysis of H3K9me2 in ER:Ras expressing IMR90 human diploid fibroblasts d6 4OHT
K27me3Sen3.bed (senescent) Chip Seq Analysis of H3K27me3 in ER:Ras expressing IMR90 human diploid fibroblasts d6 4OHT
K27me3Grow2.bed (growing) Chip Seq Analysis of H3K27me3 in ER:Ras expressing IMR90 human diploid fibroblasts with no treatment
K36me3Grow2.bed (growing) Chip Seq Analysis of H3K36me3 in ER:Ras expressing IMR90 human diploid fibroblasts with no treatment
K36me3Sen2.bed (senescent) Chip Seq Analysis of H3K36me3 in ER:Ras expressing IMR90 human diploid fibroblasts d6 4OHT
K4me3Grow2.bed (growing) Chip Seq Analysis of H3K4me3 in ER:Ras expressing IMR90 human diploid fibroblasts with no treatment
K4me3Sen3.bed (senescent) Chip Seq Analysis of H3K4me3 in ER:Ras expressing IMR90 human diploid fibroblasts d6 4OHT
 
Contributor(s) Narita M, Salama R
Citation(s) 22795131
Submission date Jun 04, 2012
Last update date May 15, 2019
Contact name Rafik Salama
E-mail(s) rafik.salama@ndm.ox.ac.uk
Organization name Cancer Research UK
Street address Li Ka Shing Centre, Robinson Way
City Cambridge
ZIP/Postal code CB2 0RE
Country United Kingdom
 
Platforms (3)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (52)
GSM942071 Chip Seq H3K9me3 in ER:Ras expressing IMR90 d6 4OHT with sh-HMGA1/MSCV SLX3599
GSM942072 Chip Seq H3K9me3 in ER:Ras expressing IMR90 d6 4OHT with sh-Rb SLX3607
GSM942073 Chip Seq H3K9me3 in ER:Ras-induced senescent IMR90 with Lenti-sh-HMGA1 SLX3611
This SubSeries is part of SuperSeries:
GSE38448 Independence of Repressive Histone Marks and Chromatin Compaction during Senescent Heterochromatic Layer Formation
Relations
BioProject PRJNA167970
SRA SRP013501

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Supplementary file Size Download File type/resource
GSE38442_K27me3Grow2.bed.gz 130.8 Kb (ftp)(http) BED
GSE38442_K27me3Sen3.bed.gz 145.6 Kb (ftp)(http) BED
GSE38442_K36me3Grow2.bed.gz 82.4 Kb (ftp)(http) BED
GSE38442_K36me3Sen2.bed.gz 84.3 Kb (ftp)(http) BED
GSE38442_K4me3Grow2.bed.gz 489.1 Kb (ftp)(http) BED
GSE38442_K4me3Sen3.bed.gz 469.5 Kb (ftp)(http) BED
GSE38442_K9me2Grow3.bed.gz 60.0 Kb (ftp)(http) BED
GSE38442_K9me2Sen3.bed.gz 64.2 Kb (ftp)(http) BED
GSE38442_K9me3Grow2.bed.gz 103.9 Kb (ftp)(http) BED
GSE38442_K9me3Sen2.bed.gz 211.3 Kb (ftp)(http) BED
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