|
| Status |
Public on Jul 08, 2014 |
| Title |
6229017109_R04C02 |
| Sample type |
genomic |
| |
|
| Source name |
Tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: pancreas
cellularity: 14
gender: Male
age: 74
|
| 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) |
|
