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Sample GSM1194507 Query DataSets for GSM1194507
Status Public on Jul 08, 2014
Title 8942351064_R04C02
Sample type genomic
 
Source name Tumor
Organism Homo sapiens
Characteristics tissue: pancreas
cellularity: 16
gender: Male
age: 61
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 0.206815009
cg00000363 0.384458055
cg00001349 0.624176396
cg00001364 0.861117025
cg00001446 0.757827529
cg00001534 0.932940214
cg00001583 0.055643289
cg00002028 0.068973693
cg00002593 0.775309826
cg00002646 0.841264268
cg00002719 0.038543281
cg00002808 0.876391642
cg00002810 0.212740577
cg00002837 0.281397521
cg00003202 0.031430485
cg00003287 0.154935965
cg00003345 0.539873718
cg00003513 0.867530311
cg00003578 0.501385199
cg00003858 0.766982737

Total number of rows: 402496

Table truncated, full table size 9006 Kbytes.




Supplementary file Size Download File type/resource
GSM1194507_8942351064_R04C02_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1194507_8942351064_R04C02_Red.idat.gz 4.0 Mb (ftp)(http) IDAT
Processed data included within Sample table

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