|
| Status |
Public on Jul 29, 2009 |
| Title |
Liver Study4 24h Vehicle_Control dose 0 - rep 2 |
| Sample type |
RNA |
| |
|
| Source name |
Male Wistar Rat Liver
|
| Organism |
Rattus norvegicus |
| Characteristics |
gender: Male
tissue: Liver
strain: Wistar
treatment: Vehicle_Control
dose amount (mg_per_kg_per_day): 0
sampling time (hours): 24
|
| Treatment protocol |
Eight-week-old male Wistar rats were dosed orally (gavage) once daily with the indicated dose of either test compound or vehicle (citric acid buffer) and sacrificed by carbon dioxide asphyxiation 24 hrs after the last dosing. The livers of all animals were excised immediately and a tissue slice which consisted of ca. ¼ from the bottom of the left lateral lobe was placed in RNALater (Ambion, TX, USA) at 4°C for 24 hrs to allow penetration of the tissue and then stored at -20°C until further processing for gene expression analysis.
|
| Growth protocol |
All animals received ethical care as specified by Swiss law and in accordance with the 'Guide for the care and use of laboratory animals' published by the NIH. The test facility is fully accredited by the Association for Assessment and Accreditation of Laboratory Animal Care International (AAALAC). The study was based on guidelines proposed by the ICH (International Conference on Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use) and the CPMP (Committee for Proprietary Medicinal Products of the EMEA [European Agency for the Evaluation of Medicinal Products]) and the OECD.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat U34a Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
|
| Description |
Gene expression data from rat liver, vehicle control
|
| Data processing |
MAS 5 data summarization was carrried out using the simpleaffy package in Bioconductor (call.exprs function). Values were calculated on a linear scale, afterwards a quantile normalization was applied across all arrays.
|
| |
|
| Submission date |
Jul 28, 2009 |
| Last update date |
Jul 28, 2009 |
| Contact name |
Adrian B Roth |
| Organization name |
Roche
|
| Department |
NCS
|
| Lab |
90-518a
|
| Street address |
Grenzacherstr 124
|
| City |
Basel |
| ZIP/Postal code |
4070 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL85 |
| Series (1) |
| GSE17388 |
Gene expression analysis of rat livers treated with pharmaceutical development compounds |
|
