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Sample GSM1606959 Query DataSets for GSM1606959
Status Public on May 19, 2015
Title AOCS_166_ICGC_DBDE_20130904_020
Sample type genomic
Source name Primarytumour
Organism Homo sapiens
Characteristics gender: Female
tissue: Primarytumour
cell type: high grade serous ovarian cancer
Treatment protocol NA
Growth protocol NA
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from fresh frozen tissues using AllPrep DNA/RNA Mini Kit (Qiagen). Genomic DNA (500ng) was bisulfite converted using EZ DNA methylation Kit (Zimo Research) following the manufacturer’s protocol with modification for Illumina Infinium Methyaltion arrays
Label cy3/cy5
Label protocol Bisulfite converted genomic DNAwas whole genome amplified and labeled using Illumina protocol
Hybridization protocol Samples were hybridized to Infinium Human Methylation 450K BeadChips (Illumina) according to the manufacturer’s protocol.
Scan protocol Arrays were scanned on Iscan (Illumina)
Description Raw data for arrays used for methylation analysis
Data processing Data was background corrected, normalized to internal controls and QC was performed at the probe and sample level. COMBAT was used to remove batch effects (Johnson et al., 2007)
Submission date Feb 10, 2015
Last update date May 19, 2015
Contact name Ann-Marie Patch
Organization name QIMR Berghofer Medical Research Institute
Street address 300 Herston Road
City Herston
State/province QLD
ZIP/Postal code 4006
Country Australia
Platform ID GPL13534
Series (2)
GSE65820 Whole genome characterisation of chemoresistant ovarian cancer [Illumina_450K_Methylation]
GSE65821 Whole genome characterisation of chemoresistant ovarian cancer

Data table header descriptions
VALUE Average Beta

Data table
cg00000029 0.219567641
cg00000108 0.93122543
cg00000109 0.834011141
cg00000165 0.752482673
cg00000236 0.877124591
cg00000289 0.576468151
cg00000292 0.628709774
cg00000321 0.584530849
cg00000363 0.105267429
cg00000622 0.033711233
cg00000658 0.786853915
cg00000714 0.065349143
cg00000721 0.934814624
cg00000734 0.064450379
cg00000769 0.038639814
cg00000807 0.827020166
cg00000884 0.789845705
cg00000905 0.098308644
cg00000924 0.591817236
cg00000948 0.877561684

Total number of rows: 485005

Table truncated, full table size 10851 Kbytes.

Supplementary file Size Download File type/resource
GSM1606959_9445229158_R03C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1606959_9445229158_R03C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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