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Series GSE69566 Query DataSets for GSE69566
Status Public on Nov 30, 2015
Title Combinatorial Regulation Mediated by Biochemically Distinct Forms of SWI/SNF [ChIP-Seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The precise makeup of chromatin remodeling complexes is important for determining cell type and cell function. The SWI/SNF chromatin remodeling complex is made up of multiple subunits that can be filled by mutually exclusive proteins. Inclusion or exclusion of these proteins has profound functional consequences, yet we currently understand little about the direct functional relationship between these biochemically distinct forms of remodeling complexes. Here we combine chromatin immunoprecipitation, transcriptome analysis, and transcription factor binding information from the ENCODE project to determine the functional relationship between three biochemically distinct forms of SWI/SNF. We find widespread overlap in transcriptional regulation and the genomic binding of the three ARID (AT-Rich Interacting Domain) subunits of SWI/SNF. Despite the numerous similarities in their transcriptional regulation and the co-factors bound with each ARID we identify several novel interaction modalities. Previous work has found examples of competition or subunit switching at individual loci, and we find this functional relationship is widespread, and in these cases gene expression changes following loss of one ARID depend on the function of another ARID. We also identify a previously unknown cooperative interaction between ARID1B and ARID2 in the repression of a large number of genes. Together these data help untangle the complicated combinatorial relationships between a highly heterogenous chromatin remodeling family.
 
Overall design We performed ChIP for 4 subunits of SWI/SNF (Arid1a, Arid1b, Arid2, Snf5) and 2 replicates of each, as well as Input. HepG2 cells were fixed in 0.3% formaldehyde for 30 minutes at 4 degrees C, then washed and cell pellets were stored at -80 until immunoprecipitation. Nuclei were released using Dounce homogenizer and layered over a sucrose cushion. Chromatin was then prepared by digesting with micrococcal nuclease for 15 minutes at 37 degrees. Chromatin equivalent to 2x10^7 cells was used in each IP with the antibodies listed.

All scripts used in the data analysis are available at: http://github.com/jraab/raab_swisnf_2015/
 
Contributor(s) Raab JR, Magnuson T
Citation(s) 26716708
Submission date Jun 04, 2015
Last update date May 15, 2019
Contact name Jesse Raab
E-mail(s) jesse.r.raab@gmail.com
Organization name University of North Carolina Chapel Hill
Department Genetics
Street address 120 Mason Farm Rd
City Chapel Hill
ZIP/Postal code 27599
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (9)
GSM1704011 Arid1a ChIP Replicate1
GSM1704012 Arid1a ChIP Replicate 2
GSM1704013 Arid1b ChIP Replicate 1
This SubSeries is part of SuperSeries:
GSE69568 Genome-Wide Transcriptional Regulation Mediated By Biochemically Distinct Forms of SWI/SNF
Relations
BioProject PRJNA285873
SRA SRP059067

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
GSE69566_arid1a.bw 271.4 Mb (ftp)(http) BW
GSE69566_arid1a_annotated.csv.gz 258.8 Kb (ftp)(http) CSV
GSE69566_arid1b.bw 162.3 Mb (ftp)(http) BW
GSE69566_arid1b_annotated.csv.gz 182.6 Kb (ftp)(http) CSV
GSE69566_arid2.bw 283.7 Mb (ftp)(http) BW
GSE69566_arid2_annotated.csv.gz 258.8 Kb (ftp)(http) CSV
GSE69566_input.bw 461.8 Mb (ftp)(http) BW
GSE69566_snf5.bw 212.4 Mb (ftp)(http) BW
GSE69566_snf5_peaks_cf.bed.gz 249.8 Kb (ftp)(http) BED
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Raw data are available in SRA
Processed data are available on Series record

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