NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1194476 Query DataSets for GSM1194476
Status Public on Jul 08, 2014
Title 8942334124_R01C01
Sample type genomic
 
Source name Tumor
Organism Homo sapiens
Characteristics tissue: pancreas
cellularity: 20
gender: Female
age: 72
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)
Data processing IDAT files were analysed in using minfi package and subset-quantile within array normalization (SWAN).Probes on chromosomes X and Y, probes with a detection P-value >0.01 in one or more samples and probes with SNP in the 10 last bases or with two or more SNP in the probe sequence were excluded from analysis. The differential methylation analysis was performed using 402,566 autosomal CpGs using the ‘dmpFinder’ minfi function.
 
Submission date Jul 23, 2013
Last update date Sep 11, 2014
Contact name Katia Nones
E-mail(s) katia.nones@qimrberghofer.edu.au
Phone +61 7 3845 3983
Organization name QIMR Berghofer MEdical Research Institute
Street address 300 Herston Road
City Brisbane
State/province QLD
ZIP/Postal code 4029
Country Australia
 
Platform ID GPL13534
Series (1)
GSE49149 Genome-wide DNA methylation patterns in pancreatic ductal adenocarcinoma (PDAC)

Data table header descriptions
ID_REF
VALUE Average Beta (GenomeStudio)

Data table
ID_REF VALUE
cg00000165 0.409073524
cg00000363 0.252067173
cg00001349 0.731925705
cg00001364 0.837726718
cg00001446 0.771535424
cg00001534 0.913523628
cg00001583 0.086880773
cg00002028 0.094612242
cg00002593 0.726498999
cg00002646 0.788253638
cg00002719 0.040322433
cg00002808 0.883685163
cg00002810 0.164897389
cg00002837 0.402606107
cg00003202 0.027720782
cg00003287 0.254048318
cg00003345 0.489150181
cg00003513 0.834593169
cg00003578 0.483073977
cg00003858 0.735499458

Total number of rows: 402496

Table truncated, full table size 9006 Kbytes.




Supplementary file Size Download File type/resource
GSM1194476_8942334124_R01C01_Grn.idat.gz 3.9 Mb (ftp)(http) IDAT
GSM1194476_8942334124_R01C01_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