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Sample GSM1606945 Query DataSets for GSM1606945
Status Public on May 19, 2015
Title AOCS_150_ICGC_DBDE_20131003_003
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 0.296321915
cg00000108 0.893178704
cg00000109 0.781000059
cg00000165 0.545435575
cg00000236 0.81159254
cg00000289 0.450852926
cg00000292 0.707671859
cg00000321 0.421237704
cg00000363 0.227365437
cg00000622 0.024403811
cg00000658 0.804860961
cg00000714 0.105270119
cg00000721 0.883520255
cg00000734 0.064919236
cg00000769 0.03378513
cg00000807 0.826092053
cg00000884 0.764047622
cg00000905 0.125983159
cg00000924 0.480185406
cg00000948 0.660553248

Total number of rows: 485005

Table truncated, full table size 10845 Kbytes.

Supplementary file Size Download File type/resource
GSM1606945_9445229094_R04C01_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1606945_9445229094_R04C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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