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Sample GSM1606882 Query DataSets for GSM1606882
Status Public on May 19, 2015
Title AOCS_086_ICGC_DBPC_20130205_050
Sample type genomic
Source name Ascites
Organism Homo sapiens
Characteristics gender: Female
tissue: Ascites
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 May 19, 2015
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

Data table header descriptions
VALUE Average Beta

Data table
cg00000029 0.217112073
cg00000108 0.8829723
cg00000109 0.860921555
cg00000165 0.606240959
cg00000236 0.815481015
cg00000289 0.383614196
cg00000292 0.824830945
cg00000321 0.52547809
cg00000363 0.227914139
cg00000622 0.017821319
cg00000658 0.821173131
cg00000714 0.135345109
cg00000721 0.906571696
cg00000734 0.063151826
cg00000769 0.041892854
cg00000807 0.892619559
cg00000884 0.800010406
cg00000905 0.099651711
cg00000924 0.456433246
cg00000948 0.840137295

Total number of rows: 485005

Table truncated, full table size 10850 Kbytes.

Supplementary file Size Download File type/resource
GSM1606882_9298768174_R05C02_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1606882_9298768174_R05C02_Red.idat.gz 4.0 Mb (ftp)(http) IDAT
Processed data included within Sample table

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