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Sample GSM1606873 Query DataSets for GSM1606873
Status Public on May 19, 2015
Title AOCS_076_ICGC_DBPC_20130205_035
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 0.2175147
cg00000108 0.930287895
cg00000109 0.876973856
cg00000165 0.209176926
cg00000236 0.875665814
cg00000289 0.642413555
cg00000292 0.598933092
cg00000321 0.342266948
cg00000363 0.235695096
cg00000622 0.020738217
cg00000658 0.845744801
cg00000714 0.111262469
cg00000721 0.890592659
cg00000734 0.063932821
cg00000769 0.050050781
cg00000807 0.752390813
cg00000884 0.833779987
cg00000905 0.090236408
cg00000924 0.472276648
cg00000948 0.693501582

Total number of rows: 485005

Table truncated, full table size 10849 Kbytes.

Supplementary file Size Download File type/resource
GSM1606873_9341679070_R01C01_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1606873_9341679070_R01C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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