|
Status |
Public on Jun 13, 2009 |
Title |
N51677 |
Sample type |
RNA |
|
|
Source name |
pancreas
|
Organism |
Homo sapiens |
Characteristics |
patient: 51677 sample: normal
|
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 |
GSE119087 |