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Sample GSM1606871 Query DataSets for GSM1606871
Status Public on May 19, 2015
Title AOCS_065_ICGC_DBPC_20130607_008
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 0.20303942
cg00000108 0.94309884
cg00000109 0.875383539
cg00000165 0.257469748
cg00000236 0.830821383
cg00000289 0.686619417
cg00000292 0.847147556
cg00000321 0.568174752
cg00000363 0.229296504
cg00000622 0.026612122
cg00000658 0.784995087
cg00000714 0.203088247
cg00000721 0.9465181
cg00000734 0.077037091
cg00000769 0.022879487
cg00000807 0.866512997
cg00000884 0.814298967
cg00000905 0.093102736
cg00000924 0.622182545
cg00000948 0.815825197

Total number of rows: 485005

Table truncated, full table size 10852 Kbytes.

Supplementary file Size Download File type/resource
GSM1606871_9341679080_R03C01_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1606871_9341679080_R03C01_Red.idat.gz 4.0 Mb (ftp)(http) IDAT
Processed data included within Sample table

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