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Sample GSM1194373 Query DataSets for GSM1194373
Status Public on Jul 08, 2014
Title 6229017109_R06C02
Sample type genomic
 
Source name Tumor
Organism Homo sapiens
Characteristics tissue: pancreas
cellularity: 22
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 0.274700167
cg00000363 0.336144126
cg00001349 0.737987685
cg00001364 0.869294741
cg00001446 0.798086009
cg00001534 0.923139099
cg00001583 0.272980192
cg00002028 0.078391967
cg00002593 0.604565118
cg00002646 0.880666305
cg00002719 0.149592319
cg00002808 0.881531784
cg00002810 0.369581251
cg00002837 0.289909087
cg00003202 0.022097318
cg00003287 0.138978875
cg00003345 0.452661291
cg00003513 0.876809904
cg00003578 0.503497407
cg00003858 0.689076092

Total number of rows: 402496

Table truncated, full table size 9006 Kbytes.




Supplementary file Size Download File type/resource
GSM1194373_6229017109_R06C02_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1194373_6229017109_R06C02_Red.idat.gz 4.0 Mb (ftp)(http) IDAT
Processed data included within Sample table

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