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Sample GSM1606954 Query DataSets for GSM1606954
Status Public on May 19, 2015
Title AOCS_161_ICGC_DBDE_20130904_015
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 Aug 19, 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 GSM6483134

Data table header descriptions
VALUE Average Beta

Data table
cg00000029 0.283629689
cg00000108 0.900307567
cg00000109 0.89482857
cg00000165 0.690762421
cg00000236 0.819946072
cg00000289 0.504470542
cg00000292 0.774342414
cg00000321 0.54087804
cg00000363 0.162567288
cg00000622 0.018550008
cg00000658 0.806616059
cg00000714 0.089698707
cg00000721 0.915747955
cg00000734 0.068268129
cg00000769 0.040380393
cg00000807 0.862913891
cg00000884 0.800705675
cg00000905 0.128711278
cg00000924 0.490889103
cg00000948 0.87079407

Total number of rows: 485005

Table truncated, full table size 10851 Kbytes.

Supplementary file Size Download File type/resource
GSM1606954_9445229094_R04C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1606954_9445229094_R04C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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