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Sample GSM1606949 Query DataSets for GSM1606949
Status Public on May 19, 2015
Title AOCS_155_ICGC_DBPC_20130701_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 0.104133824
cg00000108 0.91033465
cg00000109 0.894536343
cg00000165 0.757575277
cg00000236 0.834097033
cg00000289 0.496314522
cg00000292 0.447393698
cg00000321 0.617958366
cg00000363 0.184759481
cg00000622 0.019116375
cg00000658 0.824519681
cg00000714 0.085109304
cg00000721 0.889394794
cg00000734 0.081642131
cg00000769 0.043631355
cg00000807 0.816474424
cg00000884 0.854425504
cg00000905 0.101177923
cg00000924 0.280081621
cg00000948 0.83595069

Total number of rows: 485005

Table truncated, full table size 10851 Kbytes.

Supplementary file Size Download File type/resource
GSM1606949_9445229094_R05C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1606949_9445229094_R05C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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