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Sample GSM1606876 Query DataSets for GSM1606876
Status Public on May 19, 2015
Title AOCS_079_ICGC_DBPC_20130205_039
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 GSM6483084
Reanalyzed by GSE217673

Data table header descriptions
VALUE Average Beta

Data table
cg00000029 0.134872264
cg00000108 0.918055987
cg00000109 0.845331372
cg00000165 0.676808317
cg00000236 0.85768719
cg00000289 0.531242058
cg00000292 0.850135335
cg00000321 0.596774203
cg00000363 0.190006953
cg00000622 0.016884177
cg00000658 0.767482063
cg00000714 0.112727147
cg00000721 0.921102629
cg00000734 0.075960532
cg00000769 0.045334199
cg00000807 0.808876755
cg00000884 0.791997988
cg00000905 0.081622368
cg00000924 0.355374772
cg00000948 0.843162324

Total number of rows: 485005

Table truncated, full table size 10851 Kbytes.

Supplementary file Size Download File type/resource
GSM1606876_9298768174_R05C01_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1606876_9298768174_R05C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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