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Sample GSM1606877 Query DataSets for GSM1606877
Status Public on May 19, 2015
Title AOCS_080_ICGC_DBPC_20130205_041
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 Aug 19, 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 GSM6483085

Data table header descriptions
ID_REF
VALUE Average Beta

Data table
ID_REF VALUE
cg00000029 0.135727689
cg00000108 0.936300534
cg00000109 0.827525637
cg00000165 0.254978327
cg00000236 0.827165566
cg00000289 0.531165887
cg00000292 0.783562939
cg00000321 0.210549958
cg00000363 0.079334441
cg00000622 0.028273373
cg00000658 0.811588265
cg00000714 0.059306495
cg00000721 0.902544158
cg00000734 0.068196303
cg00000769 0.044160821
cg00000807 0.861919729
cg00000884 0.835291702
cg00000905 0.137617094
cg00000924 0.138992483
cg00000948 0.848292391

Total number of rows: 485005

Table truncated, full table size 10851 Kbytes.




Supplementary file Size Download File type/resource
GSM1606877_9298768174_R06C01_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1606877_9298768174_R06C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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