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Sample GSM1194444 Query DataSets for GSM1194444
Status Public on Jul 08, 2014
Title 6285617075_R06C01
Sample type genomic
 
Source name Tumor
Organism Homo sapiens
Characteristics tissue: pancreas
cellularity: 19
gender: Male
age: 69
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 0.304110343
cg00000363 0.410473957
cg00001349 0.657328252
cg00001364 0.843868867
cg00001446 0.786851486
cg00001534 0.926639972
cg00001583 0.140031002
cg00002028 0.067970401
cg00002593 0.730203596
cg00002646 0.836014052
cg00002719 0.074736224
cg00002808 0.900943284
cg00002810 0.317971061
cg00002837 0.316878652
cg00003202 0.027283534
cg00003287 0.145619876
cg00003345 0.53277247
cg00003513 0.859319034
cg00003578 0.535693191
cg00003858 0.751031133

Total number of rows: 402496

Table truncated, full table size 9006 Kbytes.




Supplementary file Size Download File type/resource
GSM1194444_6285617075_R06C01_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1194444_6285617075_R06C01_Red.idat.gz 4.0 Mb (ftp)(http) IDAT
Processed data included within Sample table

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