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Sample GSM1194386 Query DataSets for GSM1194386
Status Public on Jul 08, 2014
Title 6229017121_R01C01
Sample type genomic
Source name Tumor
Organism Homo sapiens
Characteristics tissue: pancreas
cellularity: 24
gender: Male
age: 78
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 0.40192609
cg00000363 0.274845162
cg00001349 0.753229047
cg00001364 0.855686991
cg00001446 0.728680261
cg00001534 0.901500112
cg00001583 0.161821082
cg00002028 0.077013195
cg00002593 0.770866499
cg00002646 0.82007083
cg00002719 0.200164401
cg00002808 0.882692471
cg00002810 0.325015985
cg00002837 0.329528608
cg00003202 0.030054301
cg00003287 0.129747097
cg00003345 0.445412963
cg00003513 0.821572544
cg00003578 0.515569808
cg00003858 0.768653964

Total number of rows: 402496

Table truncated, full table size 9006 Kbytes.

Supplementary file Size Download File type/resource
GSM1194386_6229017121_R01C01_Grn.idat.gz 3.9 Mb (ftp)(http) IDAT
GSM1194386_6229017121_R01C01_Red.idat.gz 3.9 Mb (ftp)(http) IDAT
Processed data included within Sample table

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