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Sample GSM1194528 Query DataSets for GSM1194528
Status Public on Jul 08, 2014
Title 8959312046_R04C01
Sample type genomic
 
Source name Tumor
Organism Homo sapiens
Characteristics tissue: pancreas
cellularity: 47
gender: Female
age: 71
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 0.440386088
cg00000363 0.217392868
cg00001349 0.75341198
cg00001364 0.879730892
cg00001446 0.808856828
cg00001534 0.941484351
cg00001583 0.080358402
cg00002028 0.088658165
cg00002593 0.692872368
cg00002646 0.774217658
cg00002719 0.223316306
cg00002808 0.895558234
cg00002810 0.357478753
cg00002837 0.16684927
cg00003202 0.021490334
cg00003287 0.128078905
cg00003345 0.485054337
cg00003513 0.818835625
cg00003578 0.462495826
cg00003858 0.780681697

Total number of rows: 402496

Table truncated, full table size 9006 Kbytes.




Supplementary file Size Download File type/resource
GSM1194528_8959312046_R04C01_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1194528_8959312046_R04C01_Red.idat.gz 4.0 Mb (ftp)(http) IDAT
Processed data included within Sample table

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