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Series GSE118514 Query DataSets for GSE118514
Status Public on Aug 15, 2018
Title CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Background: Recent genome-wide association studies (GWAS) have identified more than 100 loci associated with increased risk of prostate cancer, most of which are in non-coding regions of the genome. Understanding the function of these non-coding risk loci is critical to elucidate the genetic susceptibility to prostate cancer. Results: We generated genome-wide regulatory element maps and performed genome-wide chromosome confirmation capture assays (in situ Hi-C) in normal and tumorigenic prostate cells. Using this information, we annotated the regulatory potential of 2,181 fine-mapped PCa risk-associated SNPs and predicted a set of target genes that are regulated by PCa risk-related H3K27Ac-mediated loops. We next identified PCa risk-associated CTCF sites involved in long-range chromatin loops. We used CRISPR-mediated deletion to remove PCa risk-associated CTCF anchor regions and the CTCF anchor regions looped to the PCa risk-associated CTCF sites; we observed up to 100 fold increases in expression of genes within the loops when the PCa risk-associated CTCF anchor regions were deleted. Conclusions: We have identified GWAS risk loci involved in long-range loops that function to repress gene expression within chromatin loops. Our studies provide new insights into the genetic susceptibility to prostate cancer.
Overall design ChIP-seq, RNA-seq, Hi-C in prostate cells.
Contributor(s) Guo Y, Perez A, Lay F, Rhie SK, Farnham PJ
Citation(s) 30296942
Submission date Aug 14, 2018
Last update date Mar 27, 2019
Contact name Yu (Phoebe) Guo
Organization name Univ. of Southern California
Street address 1450 Biggy Street, NRT 6514
City Los Angeles
State/province California
ZIP/Postal code 90089
Country USA
Platforms (3)
GPL9052 Illumina Genome Analyzer (Homo sapiens)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (32)
GSM3331351 22Rv1_delSite3_Clone5/6-B8
GSM3356400 22Rv1_delSite3_Clone5/6-F3
GSM3356401 22Rv1_delSite3_Clone5/6-H3
BioProject PRJNA485892
SRA SRP157894

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
GSE118514_22Rv1_HiC_10k.raw.matrix.txt.gz 654.6 Mb (ftp)(http) TXT
GSE118514_22Rv1_HiC_40k.raw.matrix.txt.gz 370.9 Mb (ftp)(http) TXT
GSE118514_ENCODE_accession_numbers_used_in_this_study_.xls.gz 15.9 Kb (ftp)(http) XLS
GSE118514_RAW.tar 12.0 Mb (http)(custom) TAR (of GFF, NARROWPEAK, TAB)
GSE118514_RWPE1_comb_HiC_40k.raw.matrix.txt.gz 82.6 Mb (ftp)(http) TXT
GSE118514_RWPE1_comb_HiC_5k.raw.matrix.txt.gz 11.2 Mb (ftp)(http) TXT
GSE118514_hg19_10k.bed.gz 1.7 Mb (ftp)(http) BED
GSE118514_hg19_40k.bed.gz 464.7 Kb (ftp)(http) BED
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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