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Sample GSM1606870 Query DataSets for GSM1606870
Status Public on May 19, 2015
Title AOCS_065_ICGC_DBPC_20130205_031
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 GSM6483081
Reanalyzed by GSE217673

Data table header descriptions
VALUE Average Beta

Data table
cg00000029 0.230052807
cg00000108 0.901860569
cg00000109 0.841023919
cg00000165 0.154481824
cg00000236 0.818793772
cg00000289 0.620863891
cg00000292 0.848188352
cg00000321 0.590656149
cg00000363 0.130141293
cg00000622 0.025932452
cg00000658 0.804775357
cg00000714 0.107279084
cg00000721 0.900044386
cg00000734 0.085270363
cg00000769 0.060199713
cg00000807 0.857047642
cg00000884 0.824022617
cg00000905 0.110399769
cg00000924 0.711556597
cg00000948 0.83665468

Total number of rows: 485005

Table truncated, full table size 10850 Kbytes.

Supplementary file Size Download File type/resource
GSM1606870_9341679080_R04C01_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1606870_9341679080_R04C01_Red.idat.gz 4.0 Mb (ftp)(http) IDAT
Processed data included within Sample table

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