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Sample GSM1162363 Query DataSets for GSM1162363
Status Public on Dec 23, 2014
Title 6264509108_Benign_prostate_cancer_HM450K
Sample type genomic
 
Source name Prostate 1
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 0.892654286
cg00212031 0.051574213
cg00213748 0.84796807
cg00214611 0.052034884
cg00455876 0.822937626
cg01707559 0.090982941
cg02004872 0.03465982
cg02011394 0.952243544
cg02050847 0.900315187
cg02233190 0.02795006
cg02494853 0.041851991
cg02839557 0.040586923
cg02842889 0.031192449
cg03052502 0.980999715
cg03155755 0.925002018
cg03244189 0.084854465
cg03443143 0.934087728
cg03683899 0.045019544
cg03695421 0.578054179
cg03706273 0.045113624

Total number of rows: 485512

Table truncated, full table size 10860 Kbytes.




Supplementary file Size Download File type/resource
GSM1162363_6264509108_R01C02_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1162363_6264509108_R01C02_Red.idat.gz 4.0 Mb (ftp)(http) IDAT
Processed data included within Sample table

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