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Series GSE98898 Query DataSets for GSE98898
Status Public on Nov 01, 2017
Title A prostate cancer risk element functions as a repressive loop that regulates HOXA13
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Prostate cancer (PCa) is the leading cancer among men in the United States, with genetic factors contributing to ~42% of the susceptibility to PCa. To understand the causal genetic factors associated with PCa, we have focused on a PCa risk region located at 7p15.2. We performed Hi-C analysis and demonstrated that this region has long range interactions with the HOXA locus, located ~873 kb away. Using the CRISPR/Cas9 system, we deleted a 4 kb region encompassing several prostate cancer risk-associated SNPs and performed RNA-seq to investigate transcriptomic changes in RWPE1 prostate cells lacking the regulatory element. Our results suggest that the risk element affects the expression of HOXA13 and HOTTIP, but not other genes in the HOXA locus, via a repressive loop. Forced expression of HOXA13 was also performed to gain insight into the mechanisms by which this risk element affects prostate cancer risk.
Overall design Examination of normal prostate epithelial cell RWPE-1 genomic interactions by Hi-C. A prostate cancer risk region at 7p15.2 was deleted and HOXA13 gene was forced expressed in RWPE-1 cells, the transcriptomic changes were investigated by RNA-seq.
Contributor(s) Luo Z, Lay FD, Rhie SK, Farnham PJ
Citation(s) 29117547
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 CA136924 Prostate Cancer Risk Enhancers UNIVERSITY OF SOUTHERN CALIFORNIA PEGGY J Farnham
Submission date May 15, 2017
Last update date May 15, 2019
Contact name Zhifei Luo
Organization name University of Southern California
Street address 1450 Biggy Street, NRT 6514
City Los Angeles
State/province CA
ZIP/Postal code 90089-9601
Country USA
Platforms (3)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (38)
GSM2627201 Deletion RNA-seq rep1
GSM2627202 Deletion RNA-seq rep2
GSM2627203 Deletion RNA-seq rep3
BioProject PRJNA386902
SRA SRP107176

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Supplementary file Size Download File type/resource
GSE98898_Deletion_vs_Control_DESeq2.txt.gz 1.1 Mb (ftp)(http) TXT
GSE98898_Deletion_vs_Control_DESeq2_C42B.txt.gz 1.1 Mb (ftp)(http) TXT
GSE98898_Overexpression_DESeq2.txt.gz 1.0 Mb (ftp)(http) TXT
GSE98898_RWPE1_comb_HiC_40k.raw.matrix.txt.gz 82.6 Mb (ftp)(http) TXT
GSE98898_RWPE1_comb_HiC_5k.raw.matrix.txt.gz 11.2 Mb (ftp)(http) TXT
GSE98898_TPM.txt.gz 1.1 Mb (ftp)(http) TXT
GSE98898_TPM_C42B.txt.gz 1.1 Mb (ftp)(http) TXT
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