|
| Status |
Public on Aug 17, 2016 |
| Title |
25 |
| Sample type |
RNA |
| |
|
| Source name |
body/tail of pancreas
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: pancreatic tumor
Stage: 2b
grouped stage: LNM
|
| Biomaterial provider |
Baki Topal (Department of Abdominal Surgical Oncology, University Hospitals Leuven, KU Leuven)
|
| Treatment protocol |
NA
|
| Growth protocol |
Snap-frozen tissue samples were stored in liquid nitrogen and/or at -80C in RNALater (Qiagen) until further use.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted using the RNeasy Mini kit (Qiagen) according the manufacturer's instructions. Only samples with an RNA integrity number (RIN) of >7.0 were used.
|
| Label |
biotin
|
| Label protocol |
RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Using the NuGEN Ovation Pico WTA System, an amount of 2 ng of total RNA was amplified and converted to cDNA. An amount of 5 ug of cDNA was fragmented and labeled with biotin using the NuGEN Encore Biotin Module.
|
| |
|
| Hybridization protocol |
A mixture of fragmented biotinylated cDNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U219 arrays, followed by staining and washing in a GeneChip Fluidics Station 450 (Affymetrix) according to the manufacturer's procedures.
|
| Scan protocol |
To assess the raw probe signal intensities, chips were scanned using a GeneChip Scanner 3000 (Affymetrix).
|
| Description |
PDAC
|
| Data processing |
Data were normalized using RMA as implemented in the xps package of Bioconductor. Expression values are represented on a log2-scale.
|
| |
|
| Submission date |
Oct 08, 2014 |
| Last update date |
Aug 17, 2016 |
| Contact name |
Rekin's Janky |
| E-mail(s) |
Nucleomics.Bioinformatics@vib.be
|
| Organization name |
VIB
|
| Department |
Nucleomics Core
|
| Street address |
Herestraat 49 Box 816
|
| City |
Leuven |
| ZIP/Postal code |
B-3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL13667 |
| Series (1) |
| GSE62165 |
Prognostic relevance of molecular subtypes and master regulators in pancreatic ductal adenocarcinoma |
|
