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Sample GSM1606939 Query DataSets for GSM1606939
Status Public on May 19, 2015
Title AOCS_144_ICGC_DBPC_20130205_160
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 GSM6483123
Reanalyzed by GSE217673

Data table header descriptions
VALUE Average Beta

Data table
cg00000029 0.085261599
cg00000108 0.92913684
cg00000109 0.803687537
cg00000165 0.322708222
cg00000236 0.754899218
cg00000289 0.572144296
cg00000292 0.829043391
cg00000321 0.103724464
cg00000363 0.073422569
cg00000622 0.020489014
cg00000658 0.817247929
cg00000714 0.072014148
cg00000721 0.929568219
cg00000734 0.070251356
cg00000769 0.029634736
cg00000807 0.901037684
cg00000884 0.800070903
cg00000905 0.090441442
cg00000924 0.402010669
cg00000948 0.873878505

Total number of rows: 485005

Table truncated, full table size 10850 Kbytes.

Supplementary file Size Download File type/resource
GSM1606939_9341679080_R05C02_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1606939_9341679080_R05C02_Red.idat.gz 4.0 Mb (ftp)(http) IDAT
Processed data included within Sample table

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