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Sample GSM1194432 Query DataSets for GSM1194432
Status Public on Jul 08, 2014
Title 6285617073_R04C02
Sample type genomic
 
Source name Adjacent
Organism Homo sapiens
Characteristics tissue: pancreas
cellularity: Adjacent
gender: Female
age: 63
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 0.271890501
cg00000363 0.284048763
cg00001349 0.63780096
cg00001364 0.826969696
cg00001446 0.815772876
cg00001534 0.911631893
cg00001583 0.071729632
cg00002028 0.089792727
cg00002593 0.697021507
cg00002646 0.850923727
cg00002719 0.08580523
cg00002808 0.898059951
cg00002810 0.203692309
cg00002837 0.40791283
cg00003202 0.033383639
cg00003287 0.229488237
cg00003345 0.527745761
cg00003513 0.898868518
cg00003578 0.647801037
cg00003858 0.793790862

Total number of rows: 402496

Table truncated, full table size 9006 Kbytes.




Supplementary file Size Download File type/resource
GSM1194432_6285617073_R04C02_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1194432_6285617073_R04C02_Red.idat.gz 4.0 Mb (ftp)(http) IDAT
Processed data included within Sample table

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