GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1606858 Query DataSets for GSM1606858
Status Public on May 19, 2015
Title AOCS_034_ICGC_DBPC_20130205_007
Sample type genomic
Source name Ascites
Organism Homo sapiens
Characteristics gender: Female
tissue: Ascites
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 0.156001652
cg00000108 0.860431908
cg00000109 0.736042529
cg00000165 0.623183213
cg00000236 0.804189681
cg00000289 0.327333494
cg00000292 0.83908523
cg00000321 0.167654944
cg00000363 0.087737021
cg00000622 0.024295177
cg00000658 0.836811398
cg00000714 0.086996739
cg00000721 0.898863268
cg00000734 0.079199644
cg00000769 0.026333167
cg00000807 0.793928904
cg00000884 0.640189644
cg00000905 0.190034326
cg00000924 0.064311348
cg00000948 0.890819039

Total number of rows: 485005

Table truncated, full table size 10837 Kbytes.

Supplementary file Size Download File type/resource
GSM1606858_9305216078_R03C01_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1606858_9305216078_R03C01_Red.idat.gz 4.0 Mb (ftp)(http) IDAT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap