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Series GSE118629 Query DataSets for GSE118629
Status Public on Sep 13, 2019
Title A prostate cancer chromatin interaction map
Organism Homo sapiens
Experiment type Other
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome

Prostate cancer (PCa) is the leading cancer among men in the United States. To understand gene regulation in 3D, chromatin interactions in prostate cancer cell is measured using in situ Hi-C.
To better understand the impact of chromatin structure on regulation of the prostate cancer transcriptome, we developed high-resolution chromatin interaction maps in normal and prostate cancer cells using in situ Hi-C. By combining the in situ Hi-C data with active and repressive histone marks, CTCF binding sites, nucleosome-depleted regions, and transcriptome profiling, we identified topologically associating domains that changed in size and epigenetic states between normal and prostate cancer cells. Moreover, we identified normal and prostate cancer-specific enhancer-promoter loops and involved transcription factors. This creation of 3D epigenomic maps will enable a better understanding of prostate cancer biology and mechanisms of gene regulation.
Overall design Examination of prostate cancer epithelial cell 22Rv1 chromatin interactions using Hi-C
In situ Hi-C, ChIP-seq using active and repressive histone marks and CTCF binding sites, NOMe-seq for nucleosome-depleted regions, and RNA-seq for transcriptome profiling in prostate epithelial cells to characterize prostate cancer epigenomic transcriptome.

Please note that processed data was generated from all replicates and is linked to the corresponding rep1 sample records (or to Series records).
Contributor(s) Rhie SK, Perez AA, Lay FD, Schreiner S, Luo Z, Farnham PJ
Citation(s) 31515496
Submission date Aug 16, 2018
Last update date Sep 23, 2019
Contact name Suhn K Rhie
Organization name University of Southern California
Street address 1450 Biggy Street
City Los Angeles
State/province CA
ZIP/Postal code 90089
Country USA
Platforms (3)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (35)
GSM3335732 in situ Hi-C in 22Rv1 rep1
GSM3335733 in situ Hi-C in 22Rv1 rep2
GSM3564252 in situ Hi-C in RWPE1 rep1
BioProject PRJNA486278
SRA SRP158113

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
GSE118629_22Rv1_HiC_10k.normalized.matrix.txt.gz 1.5 Gb (ftp)(http) TXT
GSE118629_22Rv1_HiC_10k.raw.matrix.txt.gz 654.6 Mb (ftp)(http) TXT
GSE118629_22Rv1_HiC_40k.normalized.matrix.txt.gz 923.5 Mb (ftp)(http) TXT
GSE118629_22Rv1_HiC_40k.raw.matrix.txt.gz 370.9 Mb (ftp)(http) TXT
GSE118629_RAW.tar 6.5 Gb (http)(custom) TAR (of BROADPEAK, TXT)
GSE118629_RNASeq.processed.quantification.genes.txt.gz 1.8 Mb (ftp)(http) TXT
GSE118629_hg19_10k.bed.gz 1.7 Mb (ftp)(http) BED
GSE118629_hg19_40k.bed.gz 464.7 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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