|
Status |
Public on Aug 17, 2016 |
Title |
290 |
Sample type |
RNA |
|
|
Source name |
body/tail of pancreas
|
Organism |
Homo sapiens |
Characteristics |
tissue: pancreatic tumor Stage: 4 grouped stage: Advanced
|
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.
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|
|
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.
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|
|
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 |
|