|
| Status |
Public on Dec 18, 2012 |
| Title |
P104 |
| Sample type |
RNA |
| |
|
| Source name |
PDAC_P_104
|
| Organism |
Homo sapiens |
| Characteristics |
patient code: 104
gender: Female
age: 72
tumor grade: 3
t-stage: 3
n-stage: 1
ajcc classif. (2002): 2b
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using a protocol combining Trizol/chloroform extraction, followed by column chromatography with the RNeasy Mini kit (Qiagen).
|
| Label |
biotin
|
| Label protocol |
Per sample, ideally an amount of 5-10 ng of total RNA spiked with four bacterial RNA transcripts (Affymetrix) was converted and amplified to double stranded cDNA in a 2-cycle cDNA reverse transcription reaction. Subsequently the sample was converted to antisense cRNA and labeled with biotin through an in vitro transcription reaction according to the manufacturer’s protocol (Affymetrix).
|
| |
|
| Hybridization protocol |
Purified fragmented biotinylated cRNA and hybridization controls (Affymetrix) were mixed, hybridized on Affymetrix HG U133 Plus 2.0 arrays, and subsequently stained and washed in the GeneChip fluidics station 450 (Affymetrix).
|
| Scan protocol |
To assess the raw probe signal intensities, chips were scanned using the GeneChip scanner 3000 (Affymetrix).
|
| Description |
Gene expression data of non-tumor pancreatic control tissue of pancreatic ductal adenocarcinoma patient
|
| Data processing |
To decide whether a signal was significantly above background, the MAS 5.0 algorithm was applied to calculate probe set detection calls. Robust Multichip Average (RMA) was applied to probe sets that had a present detection call in at least 4 out of 6 CCD samples. Using limma, the average expression value for each experimental condition was estimated. Based on these estimates, the contrasts CTC vs. T, CTC vs. P, CTC vs. G, T vs. P, T vs. G, and P vs. G were estimated. For each contrast it was tested whether it was significantly different from 0 using a moderated t-statistic (implemented in limma).
|
| |
|
| Submission date |
Oct 21, 2009 |
| Last update date |
Dec 19, 2012 |
| 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 (2) |
| GSE18670 |
Pancreatic cancer circulating tumor cells express a cell motility gene signature that predicts survival after surgery |
| GSE42952 |
Molecular markers associated with outcome and metastasis in human pancreatic cancer |
|
