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Sample GSM1606966 Query DataSets for GSM1606966
Status Public on May 19, 2015
Title AOCS_170_ICGC_DBDE_20131003_009
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 0.239762969
cg00000108 0.912955818
cg00000109 0.843198191
cg00000165 0.537357453
cg00000236 0.82292258
cg00000289 0.578895856
cg00000292 0.82420121
cg00000321 0.518359784
cg00000363 0.296315343
cg00000622 0.016366387
cg00000658 0.799513311
cg00000714 0.112175252
cg00000721 0.917150598
cg00000734 0.071355518
cg00000769 0.024016445
cg00000807 0.874322855
cg00000884 0.795332844
cg00000905 0.083287084
cg00000924 0.385861252
cg00000948 0.737361907

Total number of rows: 485005

Table truncated, full table size 10852 Kbytes.

Supplementary file Size Download File type/resource
GSM1606966_9445229158_R04C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1606966_9445229158_R04C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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