|
| Status |
Public on Jun 13, 2009 |
| Title |
T40875 |
| Sample type |
RNA |
| |
|
| Source name |
pancreas
|
| Organism |
Homo sapiens |
| Characteristics |
patient: 40875
sample: tumor
|
| Treatment protocol |
Pairs of normal and tumor tissue samples were obtained at the time of surgery from resected pancreas of 36 pancreatic cancer patients. The tissue samples were snap-frozen in liquid nitrogen immediately upon surgical removal and maintained at −85°C. For histological evaluation, sections were stained with haematoxylin and eosin. The resected cancer specimens were not microdissected.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the frozen tissue samples in two steps: RNA isolation using the TriReagent (Sigma) protocol, followed by RNA clean-up performed as described in the RNeasy (Qiagen) protocol. Briefly, tissues were homogenized in TriReagent (1 mL of TriReagent per 50-100mg of tissue). Then, RNA was precipitated from the aqueous phase with addition of isopropanol at half the volume of the original TriReagent volume and centrifugated at 12000 × g for 10 min. RNA was cleaned using an RNeasy column according to the manufacturer’s instructions (RNeasy Mini Kit, Qiagen) and eluted in 100 µL of RNase-free water. RNA sample quantitation was performed by means of spectrophotometry (Genequant, Pharmacia), while RNA quality (integrity) control was done with microfluidics technology (2100 Bioanalyser, Agilent Technologies).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
|
| |
|
| Hybridization protocol |
The fragmented cRNA was hybridized to the oligonucleotide microarray, which was washed and stained with streptavidin-phycoerythrin.
|
| Scan protocol |
Scanning was performed with an Affymetrix Microarray Scanner.
|
| Description |
Gene expression data from surgical samples
|
| Data processing |
Affymetrix GeneChip Operating Software (GCOS) Version 1.4 was used for low-level scanning data processing. The data was subsequently normalized using the RMA algorithm using the Bioconductor 1.9 package (http://www.bioconductor.org/) running under R version 1.9.1.
|
| |
|
| Submission date |
Mar 31, 2009 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Liviu Badea |
| E-mail(s) |
[email protected]
|
| Organization name |
ICI
|
| Department |
Research
|
| Lab |
AI and Bioinformatics
|
| Street address |
8-10 Averescu Blvd.
|
| City |
Bucharest |
| ZIP/Postal code |
011455 |
| Country |
Romania |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE15471 |
Whole-Tissue Gene Expression Study of Pancreatic Ductal Adenocarcinoma |
|
| Relations |
| Reanalyzed by |
GSE51798 |
| Reanalyzed by |
GSE119087 |
