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Sample GSM1606940 Query DataSets for GSM1606940
Status Public on May 19, 2015
Title AOCS_145_ICGC_DBPC_20130205_162
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 Nov 09, 2022
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
Reanalyzed by GSM6483124
Reanalyzed by GSE217673

Data table header descriptions
VALUE Average Beta

Data table
cg00000029 0.198086315
cg00000108 0.937025342
cg00000109 0.821299998
cg00000165 0.193003151
cg00000236 0.857760785
cg00000289 0.516328035
cg00000292 0.839175431
cg00000321 0.487305275
cg00000363 0.123536682
cg00000622 0.015880477
cg00000658 0.800246515
cg00000714 0.087763636
cg00000721 0.932229194
cg00000734 0.077406696
cg00000769 0.035310915
cg00000807 0.851890872
cg00000884 0.835605913
cg00000905 0.113470927
cg00000924 0.607732108
cg00000948 0.753381766

Total number of rows: 485005

Table truncated, full table size 10852 Kbytes.

Supplementary file Size Download File type/resource
GSM1606940_9341679082_R06C01_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1606940_9341679082_R06C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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