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Sample GSM1606935 Query DataSets for GSM1606935
Status Public on May 19, 2015
Title AOCS_141_ICGC_DBDE_20131003_002
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 0.2787607
cg00000108 0.92405206
cg00000109 0.881660139
cg00000165 0.611664313
cg00000236 0.857979359
cg00000289 0.664409395
cg00000292 0.668946113
cg00000321 0.51104743
cg00000363 0.209792152
cg00000622 0.02904365
cg00000658 0.810580664
cg00000714 0.102626111
cg00000721 0.962979271
cg00000734 0.073370498
cg00000769 0.048358362
cg00000807 0.857679635
cg00000884 0.807335319
cg00000905 0.089305503
cg00000924 0.464319087
cg00000948 0.868419204

Total number of rows: 485005

Table truncated, full table size 10851 Kbytes.

Supplementary file Size Download File type/resource
GSM1606935_9445229094_R02C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1606935_9445229094_R02C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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