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Series GSE157272 Query DataSets for GSE157272
Status Public on Sep 01, 2021
Title DNA methylation profiling across six histological states of prostate cancer
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary In spite of its prevalence as one of the world’s leading malignancies, prostate cancer (PCa) continues to evade molecular taxonomic sub-classification. However, gross clinical differences are observed within the umbrella term ‘prostate adenocarcinoma’; the majority of tumors appear indolent in nature, whilst a subset manifest aggressively. Contributing factors towards this resistance to molecular classification are an atypically low mutation frequency and a poorly delineated pathobiology. Conversely, epigenetic changes are evidenced to be amongst the earliest and most-widespread aberrations in PCa . We thus hypothesized that delineating epigenomic alterations during the stepwise progression of PCa would improve our understanding of the disease pathobiology and the molecular underpinning of indolent and aggressive tumors. Herein, we report the first epigenomic roadmap of prostate tumorigenesis, in which we dissected DNA methylation and microRNA expression in enriched epithelial cells across the entire trajectory of PCa, through tumor initiation, primary disease and metastatic dissemination. Infinium Human Methylation450K Beachip (Illumina) technology was employed to assess the methylation status of >485,000 CpG sites throughout the genome across six histological stages of prostate cancer (PCa) tumorigenesis: benign (n=10), proliferative inflammatory atrophy (PIA; n=7), high grade prostatic intra-epithelial neoplasia (HGPIN; n=6), indolent PCa (PCI, n=7), agressive PCa (PCA; n=8) and lethal metastatic PCa (PCM; n=6). Three peripheral blood lymphocytes (PBL) samples were also included for control purposes.
 
Overall design Bisulfite converted DNA for 47 samples was profiled by the Illumina Infinium Human Methylation450K array
 
Contributor(s) Silva R, O'Rourke CJ, Perry AS
Citation(s) 34454584
Submission date Sep 01, 2020
Last update date Sep 01, 2021
Contact name Antoinette Perry
E-mail(s) antoinette.perry@ucd.ie
Organization name University College Dublin
Street address Science West, University College Dublin, Belfield, Dublin, Ireland
City Dublin
ZIP/Postal code D4
Country Ireland
 
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (48)
GSM4760498 B01_benign prostate tissue
GSM4760499 B02_benign prostate tissue
GSM4760500 B03_benign prostate tissue
Relations
BioProject PRJNA660747

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
GSE157272_IDAT_file_annotation.csv.gz 811 b (ftp)(http) CSV
GSE157272_Matrix_processed.txt.gz 132.8 Mb (ftp)(http) TXT
GSE157272_Matrix_signal_intensities.txt.gz 115.4 Mb (ftp)(http) TXT
GSE157272_RAW.tar 566.7 Mb (http)(custom) TAR (of IDAT)
Processed data included within Sample table
Processed data are available on Series record
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