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Sample GSM1194426 Query DataSets for GSM1194426
Status Public on Jul 08, 2014
Title 6285617073_R01C01
Sample type genomic
 
Source name Tumor
Organism Homo sapiens
Characteristics tissue: pancreas
cellularity: 20
gender: Male
age: 65
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 0.381664319
cg00000363 0.408810549
cg00001349 0.731700171
cg00001364 0.809165073
cg00001446 0.849805607
cg00001534 0.907082842
cg00001583 0.082389023
cg00002028 0.086438255
cg00002593 0.790002376
cg00002646 0.879032369
cg00002719 0.037041286
cg00002808 0.908340041
cg00002810 0.359177277
cg00002837 0.2533738
cg00003202 0.022008222
cg00003287 0.158342123
cg00003345 0.484736093
cg00003513 0.855176892
cg00003578 0.610825987
cg00003858 0.745260057

Total number of rows: 402496

Table truncated, full table size 9006 Kbytes.




Supplementary file Size Download File type/resource
GSM1194426_6285617073_R01C01_Grn.idat.gz 3.9 Mb (ftp)(http) IDAT
GSM1194426_6285617073_R01C01_Red.idat.gz 4.0 Mb (ftp)(http) IDAT
Processed data included within Sample table

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