|
| Status |
Public on Oct 18, 2007 |
| Title |
Liver vehicle rep2 |
| Sample type |
RNA |
| |
|
| Source name |
cirrhotic liver, vehicle treatment
|
| Organism |
Rattus norvegicus |
| Characteristics |
Strain:Wistar, Gender: male, Tissue: cirrhotic liver, Induction of cirrhosis: CCl4
|
| Treatment protocol |
Cirrhosis was induced by inhalation of CCl4 administered twice weekly. Control and cirrhotic rats were fed ad libitum with standard feed and water containing Phenobarbital (0.3 g/L) as drinking fluid
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from frozen liver with Trizol reagent (Life Technologies, Rockville, MD). The extracted total RNA was purified with the RNeasy kit (Qiagen).
|
| Label |
Biotin
|
| Label protocol |
Twenty µg of total RNA was used to synthesize double-strand cDNA with SuperScript II reverse transcriptase (Life Technologies) and a T7-(dT)24 primer (Metabion, Germany). Then, biotinylated cRNA was synthesized from the double-stranded cDNA using the RNA Transcript Labeling kit (Enzo Life Sciences) and was purified and fragmented.
|
| |
|
| Hybridization protocol |
The fragmented cRNA was hybridized to the oligonucleotide microarray, which was washed and stained with streptavidin-phycoerythrin as described in the Affymetrix GeneChip Expression Analysis Manual (Affymetrix, Santa Clara, CA)
|
| Scan protocol |
Scanning was performed with an Agilent Microarray Scanner (Agilent Technologies)
|
| Description |
NA
|
| Data processing |
GeneChip analysis was performed with libraries from the Bioconductor project. The starting point for all the analysis was the CEL files generated by the Affymetrix software. Each CEL file contains data on the intensity at each probe on the GeneChip. To import CEL file data into the Bioconductor system, we used the ReadAffy function of the “affy” package. Next, we used the RMA approximation for background adjustment, normalization, and summarization using the median polish algorithm . The RMA measures were computed using the RMA function from the affy package.
|
| |
|
| Submission date |
Feb 01, 2007 |
| Last update date |
Oct 18, 2007 |
| Contact name |
Manuel Morales-Ruiz |
| E-mail(s) |
[email protected]
|
| Phone |
34932275400 (2667)
|
| Organization name |
Hospital Clinic
|
| Department |
Biochemistry and Molecular Genetics
|
| Street address |
Villarroel 170
|
| City |
Barcelona |
| ZIP/Postal code |
08036 |
| Country |
Spain |
| |
|
| Platform ID |
GPL1355 |
| Series (1) |
| GSE6929 |
Angiogenesis inhibitors ameliorates inflammatory infiltrate, fibrosis and portal pressure in cirrhotic rats |
|
