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Series GSE40740 Query DataSets for GSE40740
Status Public on Dec 19, 2013
Title Genome wide co-localization of Polycomb orthologs and their effects on gene expression in human fibroblasts
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary We have identfied antibodies that support chromatin immunoprecipitation (ChIP) of 11 components of Polycomb repressive complex 1 (PRC1) and shown that multiple variants of PRC1 associate with the same DNA. By performing ChIP-seq with antibodies against CBX6, CBX7, CBX8, RING1 and RING2, in two strains of human fibroblasts, we find that all five proteins co-localize at multiple sites in the genome. The binding profiles have inherent architecture that is conserved between the two strains, but there are also a substantial number of differences between the strains, possibly reflecting their anatomical position. The presence of PcG proteins does not equate with gene silencing and their genomic position does not change at senescence.
 
Overall design Chromatin immunoprecipitation and sequencing (ChIP-seq) in two strains of human fibroblasts using antibodies against three Pc orthologs (CBX6, CBX7 and CBX8) and both Psc orthologs (RING1 and 2). Validation by ChIP-PCR and re-ChIP. Strand specific RNA-seq and validation by qRT-PCR.
 
Contributor(s) Pemberton H, Anderton E, Patel H, Brookes S, Palermo R, Stock J, Rodriguez-Niedenführ M, Racek T, de Breed L, Stewart A, Matthews N, Peters G
Citation(s) 24485159
Submission date Sep 10, 2012
Last update date May 15, 2019
Contact name Gordon Peters
E-mail(s) gordon.peters@cancer.org.uk
Phone +44 207 269 3049
Organization name CRUK London Research Institute
Lab Molecular Oncology
Street address 44 Lincolns Inn Fields
City London
ZIP/Postal code WC2A 3LY
Country United Kingdom
 
Platforms (1)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
Samples (27)
GSM1295076 CBX6 BF ChipSeq (biological replicate 1 and 2)
GSM1295077 CBX7 BF ChipSeq (biological replicate 1 and 2)
GSM1295078 CBX8 BF ChipSeq (biological replicate 1 and 2)
Relations
BioProject PRJNA174794
SRA SRP015678

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
GSE40740_BF_vs_HS_RNASeq_RefSeq.tsv.gz 243.8 Kb (ftp)(http) TSV
GSE40740_RAW.tar 13.2 Gb (http)(custom) TAR (of BED, WIG)
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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