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Series GSE135088 Query DataSets for GSE135088
Status Public on Oct 05, 2020
Title Transcription-driven cohesin accumulation is associated with secretory phenotype of senescence [ChIP-Seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Senescence is a stable form of cell cycle arrest that is triggered in response to various pathophysiological stimuli. The three-dimensional structure of senescent cells has been previously characterised, mostly in terms of macro-domains or changes between large heterochromatic regions. In the present body of work, using a combination of HiC and targetted Capture Hi-C, we aimed to investigate the association between gene expression and local chromatin structure in senescence, particularly focusing on enhancer-promoter (EP) interactions. We show that many EP contacts are rewired in RAS-induced Senescence compared to ‘normal’, growing cells and that these are associated with cohesin binding changes and possible loop re-organisation. The genes affected by altered chromatin interactions correspond to the two main axes of senescence gene regulation: cell cycle and inflammation. Our findings are potentially relevant during ageing and in cancers with cohesin mutations, where cell cycle and inflammation are also deregulated.
Overall design ChIP-seq of CTCF and cohesin components RAD21 and SMC3 in growing and (RAS-induced) senescent IMR90 fibroblasts
Contributor(s) Olan I, Parry A
Citation(s) 33247104
Submission date Jul 30, 2019
Last update date Jan 04, 2021
Contact name Ioana Olan
Organization name University of Cambridge
Department Cancer Research UK Cambridge Institute
Lab Narita Lab
Street address Robinson Way
City Cambridge
State/province Cambridgeshire
ZIP/Postal code CB2 0RE
Country United Kingdom
Platforms (3)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (65)
GSM3985193 CTCF_Growing_1
GSM3985194 CTCF_RIS_1
GSM3985195 Growing_Input_1
This SubSeries is part of SuperSeries:
GSE135093 Transcription-driven cohesin accumulation is associated with secretory phenotype of senescence
BioProject PRJNA557423
SRA SRP216830

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
GSE135088_RAW.tar 8.0 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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