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Sample GSM1606955 Query DataSets for GSM1606955
Status Public on May 19, 2015
Title AOCS_162_ICGC_DBDE_20130904_016
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
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

Data table header descriptions
ID_REF
VALUE Average Beta

Data table
ID_REF VALUE
cg00000029 0.129314112
cg00000108 0.946732053
cg00000109 0.816372771
cg00000165 0.691531382
cg00000236 0.793260096
cg00000289 0.481068674
cg00000292 0.866638388
cg00000321 0.512494325
cg00000363 0.197461813
cg00000622 0.021584702
cg00000658 0.821010019
cg00000714 0.077196017
cg00000721 0.918044869
cg00000734 0.06527774
cg00000769 0.027805535
cg00000807 0.816891566
cg00000884 0.682114781
cg00000905 0.129675397
cg00000924 0.194920976
cg00000948 0.832023505

Total number of rows: 485005

Table truncated, full table size 10849 Kbytes.




Supplementary file Size Download File type/resource
GSM1606955_9445229094_R05C02_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1606955_9445229094_R05C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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