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Sample GSM1606931 Query DataSets for GSM1606931
Status Public on May 19, 2015
Title AOCS_139_ICGC_DBPC_20130205_150
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 Nov 09, 2022
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
Reanalyzed by GSM6483121
Reanalyzed by GSE217673

Data table header descriptions
VALUE Average Beta

Data table
cg00000029 0.220353699
cg00000108 0.922241479
cg00000109 0.839950491
cg00000165 0.396125179
cg00000236 0.807183593
cg00000289 0.543034586
cg00000292 0.746426718
cg00000321 0.378453241
cg00000363 0.183073545
cg00000622 0.02295556
cg00000658 0.816693486
cg00000714 0.106001644
cg00000721 0.909765297
cg00000734 0.073287998
cg00000769 0.059614281
cg00000807 0.81880806
cg00000884 0.819836341
cg00000905 0.099635786
cg00000924 0.36602904
cg00000948 0.770872054

Total number of rows: 485005

Table truncated, full table size 10847 Kbytes.

Supplementary file Size Download File type/resource
GSM1606931_9445229078_R04C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1606931_9445229078_R04C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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