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Series GSE47915 Query DataSets for GSE47915
Status Public on Dec 23, 2014
Title Human Prostate Cancer Illumina Infinium Human Methylation450 (HM450K bead array) BeadChip samples (benign vs tumor)
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary In order to examine the impact our probe filtering efforts might have on the analysis of real-world primary data, we analyzed clinical prostate cancer specimens. This included profiling of four prostate tumour tissue samples and four benign prostate tissues using the Illumina Infinium Human Methylation450 (HM450K bead array) BeadChip. These samples were used to explore the effects on analysis with and without a probe filtering.
Overall design Four tumour samples containing Gleason 6 cancer and four benign samples from other prostate glands containing Gleason 6 cancer were selected for study. Tissue samples were cryosectioned for histopathological assessment. Genomic DNA was extracted from the homogenized samples using the Allprep Micro Kit (Qiagen, CA, USA) following manufacturer’s instructions and bisulfite converted using the Zymo EZ DNA Methylation kit (Zymo Research Corporation, CA, USA). The resulting libraries were hybridized onto the Illumina HumanMethylation450 (HM450K bead array) BeadChip. Raw intensity data was generated using an iScan microarray reader (Illumina).
Contributor(s) Hovens CM, Hong MK, Pedersen JS
Citation(s) 24447442
Submission date Jun 13, 2013
Last update date Mar 22, 2019
Contact name Haroon Naeem
Organization name Monash University
Department Monash Bioinformatics Platform
Street address 15 Innovation Walk (Room G98), Wellington Road
City Melbourne
State/province Clayton, VIC
ZIP/Postal code 3800
Country Australia
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (8)
GSM1162363 6264509108_Benign_prostate_cancer_HM450K
GSM1162364 6264509130_1_Tumor_prostate_cancer_Gleason6_HM450K
GSM1162365 6264509130_2_Tumor_prostate_cancer_Gleason6_HM450K
BioProject PRJNA208302

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
GSE47915_RAW.tar 247.9 Mb (http)(custom) TAR (of IDAT)
GSE47915_signal_intensities.txt.gz 23.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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