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Sample GSM1162364 Query DataSets for GSM1162364
Status Public on Dec 23, 2014
Title 6264509130_1_Tumor_prostate_cancer_Gleason6_HM450K
Sample type genomic
 
Source name Prostate 2
Organism Homo sapiens
Characteristics gender: male
disease state: Gleason 6 prostate cancer
tissue: prostate cancer tumor
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 Gleason 6 cancer
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 0.597186282
cg00212031 0.040195496
cg00213748 0.763471731
cg00214611 0.040870843
cg00455876 0.757360698
cg01707559 0.094250189
cg02004872 0.032537159
cg02011394 0.867815806
cg02050847 0.978115009
cg02233190 0.058738353
cg02494853 0.059304781
cg02839557 0.015076661
cg02842889 0.041513094
cg03052502 0.866094919
cg03155755 0.882570971
cg03244189 0.062134503
cg03443143 0.680485629
cg03683899 0.030594832
cg03695421 0.402339701
cg03706273 0.288387492

Total number of rows: 485512

Table truncated, full table size 10860 Kbytes.




Supplementary file Size Download File type/resource
GSM1162364_6264509130_R04C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1162364_6264509130_R04C02_Red.idat.gz 4.0 Mb (ftp)(http) IDAT
Processed data included within Sample table

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