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Sample GSM1606875 Query DataSets for GSM1606875
Status Public on May 19, 2015
Title AOCS_078_ICGC_DBPC_20130205_126
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 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 0.255462078
cg00000108 0.916458276
cg00000109 0.767112458
cg00000165 0.43726285
cg00000236 0.732071702
cg00000289 0.358821648
cg00000292 0.596596456
cg00000321 0.305690697
cg00000363 0.175840278
cg00000622 0.024359253
cg00000658 0.846993474
cg00000714 0.066671258
cg00000721 0.881613746
cg00000734 0.067433827
cg00000769 0.04393236
cg00000807 0.868875052
cg00000884 0.689102629
cg00000905 0.176314966
cg00000924 0.311429247
cg00000948 0.888236093

Total number of rows: 485005

Table truncated, full table size 10833 Kbytes.

Supplementary file Size Download File type/resource
GSM1606875_9298768174_R04C01_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1606875_9298768174_R04C01_Red.idat.gz 4.0 Mb (ftp)(http) IDAT
Processed data included within Sample table

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