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Sample GSM1606895 Query DataSets for GSM1606895
Status Public on May 19, 2015
Title AOCS_094_ICGC_DBPC_20130205_067
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
E-mail(s) ann-marie.patch@qimrberghofer.edu.au
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
Relations
Reanalyzed by GSE217673

Data table header descriptions
ID_REF
VALUE Average Beta

Data table
ID_REF VALUE
cg00000029 0.18810986
cg00000108 0.920384574
cg00000109 0.880109989
cg00000165 0.578205886
cg00000236 0.805516474
cg00000289 0.543167292
cg00000292 0.780208329
cg00000321 0.593207791
cg00000363 0.124832065
cg00000622 0.02441348
cg00000658 0.830414195
cg00000714 0.222361717
cg00000721 0.91163886
cg00000734 0.075399354
cg00000769 0.031732134
cg00000807 0.873294989
cg00000884 0.75049454
cg00000905 0.195834154
cg00000924 0.484412337
cg00000948 0.882010094

Total number of rows: 485005

Table truncated, full table size 10851 Kbytes.




Supplementary file Size Download File type/resource
GSM1606895_9298768178_R06C01_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1606895_9298768178_R06C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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