|
| Status |
Public on Jan 09, 2013 |
| Title |
D-10578/1-BT |
| Sample type |
RNA |
| |
|
| Source name |
PaCa, bad prognosis
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
age: 75 years
tissue: pancreatic ductal adenocarcinoma (PDAC)
tumor stage: T3N0M0
tumor grade: 3
Stage: 2a
prognosis: bad
|
| Biomaterial provider |
University hospital, Leuven
|
| Growth protocol |
Biopsies were taken peroperatively and stored in RNAlater (-80°C) until RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the instructions of the manufacturer.
|
| 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). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturer's protocol (Affymetrix).
|
| |
|
| Hybridization protocol |
A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 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 |
bad
|
| Data processing |
Data were normalized using RMA as implemented in the Affy package of Bioconductor. Expression values are represented on a log2-scale.
|
| |
|
| Submission date |
Dec 17, 2012 |
| Last update date |
Jan 09, 2013 |
| Contact name |
Rekin's Janky |
| E-mail(s) |
[email protected]
|
| Organization name |
VIB
|
| Department |
Nucleomics Core
|
| Street address |
Herestraat 49 Box 816
|
| City |
Leuven |
| ZIP/Postal code |
B-3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE42952 |
Molecular markers associated with outcome and metastasis in human pancreatic cancer |
|
