|
| Status |
Public on Feb 27, 2015 |
| Title |
Pancreatic carcinoma ICGC_0139 |
| Sample type |
genomic |
| |
|
| Source name |
Primary Tumour
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Primary Tumour
disease: Pancreatic Adenocarcinoma
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nucleic acids were then extracted using the Qiagen Allprep® Kit in accordance with the manufacturers instructions with purification of DNA and RNA from the same sample. DNA was quantified using Qubit HS DNA Assay (Invitrogen). Throughout the process, all samples were tracked using unique identifiers.
|
| Label |
cy3/cy5
|
| Label protocol |
DNA was assayed using Illumina SNP BeadChips as per manufacturer’s instructions (Illumina, San Diego CA) (HumanOmni1-Quad or HumanOmni2.5-8 BeadChips).
|
| |
|
| Hybridization protocol |
As per manufacturer’s instructions (Illumina, San Diego CA)
|
| Scan protocol |
Arrays were scanned on iScan
|
| Description |
Raw data for arrays used for copy number analysis using GAP (Popova, et al 2009)
|
| Data processing |
Data was extracted using Genotyping module (v1.8.4) in Genomestudio v2010.3 (Illumina, San Diego CA) to calculate B-allele frequencies (BAF) and logR values.
|
| |
|
| Submission date |
Sep 17, 2014 |
| Last update date |
Feb 27, 2015 |
| 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 |
GPL16104 |
| Series (1) |
| GSE61502 |
Whole Genome Sequencing Informs Therapeutic Selection for Pancreatic Cancer |
|
