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Sample GSM1194365 Query DataSets for GSM1194365
Status Public on Jul 08, 2014
Title 6229017109_R01C02
Sample type genomic
Source name Adjacent
Organism Homo sapiens
Characteristics tissue: pancreas
cellularity: Adjacent
gender: Male
age: 64
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
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
VALUE Average Beta (GenomeStudio)

Data table
cg00000165 0.281671383
cg00000363 0.234833566
cg00001349 0.60529898
cg00001364 0.864888607
cg00001446 0.810838197
cg00001534 0.896206165
cg00001583 0.050173704
cg00002028 0.072812393
cg00002593 0.676781908
cg00002646 0.880774267
cg00002719 0.049302607
cg00002808 0.916722387
cg00002810 0.179319563
cg00002837 0.384771474
cg00003202 0.03092455
cg00003287 0.376906274
cg00003345 0.548793
cg00003513 0.894359426
cg00003578 0.599180425
cg00003858 0.81568896

Total number of rows: 402496

Table truncated, full table size 9006 Kbytes.

Supplementary file Size Download File type/resource
GSM1194365_6229017109_R01C02_Grn.idat.gz 3.9 Mb (ftp)(http) IDAT
GSM1194365_6229017109_R01C02_Red.idat.gz 3.9 Mb (ftp)(http) IDAT
Processed data included within Sample table

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