NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1606923 Query DataSets for GSM1606923
Status Public on May 19, 2015
Title AOCS_132_ICGC_DBPC_20130205_120
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 GSM6483119
Reanalyzed by GSE217673

Data table header descriptions
ID_REF
VALUE Average Beta

Data table
ID_REF VALUE
cg00000029 0.071220488
cg00000108 0.90661405
cg00000109 0.816858796
cg00000165 0.199806258
cg00000236 0.784634421
cg00000289 0.535171868
cg00000292 0.603671634
cg00000321 0.31023079
cg00000363 0.076170995
cg00000622 0.019095086
cg00000658 0.804961797
cg00000714 0.062721178
cg00000721 0.9008213
cg00000734 0.073906692
cg00000769 0.024112615
cg00000807 0.848155817
cg00000884 0.826453427
cg00000905 0.129916053
cg00000924 0.416039991
cg00000948 0.85075004

Total number of rows: 485005

Table truncated, full table size 10851 Kbytes.




Supplementary file Size Download File type/resource
GSM1606923_9341679080_R03C02_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1606923_9341679080_R03C02_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