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Series GSE101966 Query DataSets for GSE101966
Status Public on Sep 29, 2017
Title ARID1A and ARID1B loss in HCT116 cells
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
Summary ARID1A, a subunit of the SWI/SNF chromatin remodeling complex, is frequently mutated in cancer. Deficiency in its homolog ARID1B is synthetically lethal with ARID1A mutation. However, the functional relationship between these homologs has not been explored. Here we use ATAC-seq, genome-wide histone modification mapping, and expression analysis to examine colorectal cancer cells lacking one or both ARID proteins. We find that ARID1A has a dominant role in maintaining chromatin accessibility at enhancers, while the contribution of ARID1B is evident only in the context of ARID1A mutation. Changes in accessibility are predictive of changes in expression and correlate with loss of H3K4me and H3K27ac marks, nucleosome spacing, and transcription factor binding, particularly at growth pathway genes including MET. We find that ARID1B knockdown in ARID1A mutant ovarian cancer cells causes similar loss of enhancer architecture, suggesting that this is a conserved function underlying the synthetic lethality between ARID1A and ARID1B.
 
Overall design ATAC-seq, histone modification ChIP-seq, RNA-seq in WT and homozygous ARID1A knockout HCT116 colorectal cancer cells expressing shRNA targeting ARID1B or scrambled control.
 
Contributor(s) Kelso TW, Porter D, Hargreaves DC
Citation(s) 28967863
Submission date Jul 27, 2017
Last update date Nov 17, 2022
Contact name Diana C. Hargreaves
E-mail(s) dhargreaves@salk.edu
Organization name The Salk Institute for Biological Studies
Street address 10010 North Torrey Pines Road
City San Diego
State/province CA
ZIP/Postal code 92037
Country USA
 
Platforms (2)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (52)
GSM2719724 HCT116 ATAC-seq-WT-Rep1
GSM2719725 HCT116 ATAC-seq-WT-Rep2
GSM2719726 HCT116 ATAC-seq-ARID1BKD-Rep1
This SubSeries is part of SuperSeries:
GSE101975 ARID1A and ARID1B loss in HCT116 and TOV21G cells
Relations
BioProject PRJNA396039
SRA SRP113704

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

Supplementary file Size Download File type/resource
GSE101966_HCT116_FPKM.txt.gz 1.4 Mb (ftp)(http) TXT
GSE101966_RAW.tar 23.1 Mb (http)(custom) TAR (of TXT)
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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