Data access committee for genomic and clinical data produced by the Institute for Biomedical Technology.

This DAC controls 6 datasets

Dataset ID	Description	Samples
EGAD00001000600	NOTE TO CURATOR: Please include all runs associated with study EGAS00001000526. The Webin run browser only shows the first 90 runs, so we do not know all the necessary run identifiers.We report the integrative sequencing of genomic, transcriptomic and DNA methylation changes in 28 untreated (PC) and 13 castration resistant prostate cancers (CRPC). AR, TGF-β and WNT signaling pathways were altered in CRPCs. We identified two new fusion genes, TMPRSS2-SKIL and DOT1L-HES6. Fusion analysis in an independent cohort validated SKIL as a recurrent 3’ fusion partner and oncogene in prostate cancer. The HES6 fusion was found in an AR-negative CRPC, and HES6 overexpression in vitro led to androgen independent growth. A distinct DNA methylation signature was found for CRPC. Transcriptome assembly uncovered 128 previously unannotated prostate cancer associated transcripts, including the ERG regulated transcript TPCAT-10-36067 whose knockdown had a dramatic effect on the growth, invasiveness, and rate of apoptosis of prostate cancer cells.	-
EGAD00001000609	Whole transcriptome sequencing of 28 untreated prostate cancers, 13 castration resistant prostate cancers, and 12 benign prostatic hyperplasias.	53
EGAD00001000610	Methylated DNA immunoprecipitation sequencing of 28 untreated prostate cancers, 11 castration resistant prostate cancers, and 12 benign prostatic hyperplasias.	51
EGAD00001000611	Small RNA sequencing of 28 untreated prostate cancers, 12 castration resistant prostate cancers, and 3 benign prostatic hyperplasias.	43
EGAD00001000612	Low coverage whole genome sequencing of 27 untreated prostate cancers, 9 castration resistant prostate cancers, and 4 benign prostatic hyperplasias.	40
EGAD00001007921	Two sections of cryopreserved prostate cancer tissue from one untreated prostate cancer patient were profiled for spatial transcriptomics using the Visium Spatial library preparation protocol from 10x Genomics. The GRCh38 aligned sequencing reads from the two prostate cancer tissue sections are provided as BAM files.	2