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Sample GSM1162382 Query DataSets for GSM1162382
Status Public on Dec 23, 2014
Title 6285650050_Benign_prostate_cancer_HM450K
Sample type genomic
 
Source name Prostate 8
Organism Homo sapiens
Characteristics gender: male
disease state: Gleason 6 prostate cancer
tissue: benign prostate tissues
Growth protocol Patients undergoing radical prostatectomy for prostate cancer had fresh frozen samples of cancer as well as adjacent benign prostate tissue prospectively stored in a cancer biorepository program (http://www.ncbi.nlm.nih.gov/pubmed/22406482)
Extracted molecule genomic DNA
Extraction protocol 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 BeadChip.
Label Cy5 and Cy3
Label protocol Standard Illumina Protocol
 
Hybridization protocol bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 (HM450K bead array) Beadchip using standard Illumina protocol
Scan protocol Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
Description benign samples from other prostate glands containing Gleason 6 cance
Data processing Raw intensity data was generated using an iScan microarray reader (Illumina).
 
Submission date Jun 13, 2013
Last update date Dec 23, 2014
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
 
Platform ID GPL13534
Series (1)
GSE47915 Human Prostate Cancer Illumina Infinium Human Methylation450 (HM450K bead array) BeadChip samples (benign vs tumor)

Data table header descriptions
ID_REF
VALUE normalized (using Bioconductor minfi package with SWAN normalization) Average Beta

Data table
ID_REF VALUE
cg00050873 0.826266904
cg00212031 0.079592671
cg00213748 0.873175966
cg00214611 0.079286551
cg00455876 0.791349661
cg01707559 0.099991605
cg02004872 0.032411821
cg02011394 0.95879197
cg02050847 0.97235837
cg02233190 0.060826257
cg02494853 0.028921113
cg02839557 0.049123551
cg02842889 0.046416462
cg03052502 0.986958744
cg03155755 0.892824043
cg03244189 0.110717734
cg03443143 0.907857573
cg03683899 0.040006131
cg03695421 0.640517688
cg03706273 0.041329739

Total number of rows: 485512

Table truncated, full table size 10859 Kbytes.




Supplementary file Size Download File type/resource
GSM1162382_6285650050_R01C01_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1162382_6285650050_R01C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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