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Sample GSM1606890 Query DataSets for GSM1606890
Status Public on May 19, 2015
Title AOCS_092_ICGC_DBPC_20130205_061
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 GSM6483094
Reanalyzed by GSE217673

Data table header descriptions
VALUE Average Beta

Data table
cg00000029 0.131102043
cg00000108 0.933085475
cg00000109 0.824273185
cg00000165 0.235259099
cg00000236 0.826811597
cg00000289 0.534005057
cg00000292 0.704429307
cg00000321 0.308329425
cg00000363 0.28392579
cg00000622 0.018536196
cg00000658 0.83057906
cg00000714 0.08972293
cg00000721 0.921646853
cg00000734 0.067426059
cg00000769 0.04394325
cg00000807 0.816930556
cg00000884 0.828471525
cg00000905 0.101588134
cg00000924 0.566797256
cg00000948 0.840109511

Total number of rows: 485005

Table truncated, full table size 10851 Kbytes.

Supplementary file Size Download File type/resource
GSM1606890_9298768178_R01C01_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1606890_9298768178_R01C01_Red.idat.gz 4.0 Mb (ftp)(http) IDAT
Processed data included within Sample table

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