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Sample GSM1606859 Query DataSets for GSM1606859
Status Public on May 19, 2015
Title AOCS_034_ICGC_DBPC_20130205_009
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 GSM6483071
Reanalyzed by GSE217673

Data table header descriptions
VALUE Average Beta

Data table
cg00000029 0.182088978
cg00000108 0.920396331
cg00000109 0.84883966
cg00000165 0.675068095
cg00000236 0.813868253
cg00000289 0.478215429
cg00000292 0.811013067
cg00000321 0.217193428
cg00000363 0.134657652
cg00000622 0.033837171
cg00000658 0.788634058
cg00000714 0.085414836
cg00000721 0.927974969
cg00000734 0.074103922
cg00000769 0.034161933
cg00000807 0.844688795
cg00000884 0.755488069
cg00000905 0.125648366
cg00000924 0.274319887
cg00000948 0.593552225

Total number of rows: 485005

Table truncated, full table size 10851 Kbytes.

Supplementary file Size Download File type/resource
GSM1606859_9305216078_R04C01_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1606859_9305216078_R04C01_Red.idat.gz 4.0 Mb (ftp)(http) IDAT
Processed data included within Sample table

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