|
| Status |
Public on Apr 20, 2018 |
| Title |
Liver_CO_D_28d_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
liver, Corn oil, 0 mg/kg/day, 28 days
|
| Organism |
Rattus norvegicus |
| Characteristics |
compound abbreviation: CO
cpound full name: Corn oil
compound dose [mg/kg]: 0
timepoint [days]: 28
treatment group: CO_D_28d
tisue: liver
replicate: 3
quality ok?: Yes
|
| Treatment protocol |
Adults animals were assigned to dose groups (five to six rats/group) by randomization acc. to performing Laboratory SOPs. Substances or corresponding vehicle controls were administered by daily gastric gavage for up to 14, 28 or 90 days, and animals were sacrificed one day after the last application.
|
| Growth protocol |
Male Han Wistar rats from appropriate suppliers, e.g. Charles River Laboratories, were kept according to relevant SOPs at the performing laboratories.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen liver sections were grinded in a Mixer Mill MM 200 (Retsch GmbH and Co. KG, Haan, Germany) using precooled stainless steel balls. After adjusting the volume to 1ml with RLT lysis buffer, total RNA was isolated using Qiagen RNAeasy spin column kits, including a DNase digestion step according to the manufacturer’s instructions. A volume of lysate corresponding to 7mg of tissue was loaded per RNeasy spin column. The final product was quality controlled by gel analysis using RNA 6000 Nano chips on an Agilent 2100 Bioanalyzer (Agilent Technologies GmbH, Berlin, Germany). All samples had a RIN of 9-10. RNA concentrations were determined using a Nanodrop spectrophotometer.
|
| Label |
biotin
|
| Label protocol |
Starting from 300ng total RNA, Biotin-labeled cRNA samples for hybridization on Affymetrix RaGene_2.0_ST arrays were prepared according to the protocol supplied with the GeneChip ® WT PLUS Reagent Kit for Affymetrix GeneChip Whole Transcript (WT) Expression Arrays (P/N 703174 Rev.2, Affymetrix Inc., Santa Clara, CA) .
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| |
|
| Hybridization protocol |
3μg fragmented ssDNA was hybridized for 16 h at 45°C. The microarrays were washed and stained with streptavidin-phycoerythrin (SAPE, Molecular Probes) on the Affymetrix Fluidics Station 450 according to the manufacturer’s instructions.
|
| Scan protocol |
The fluorescent images of the GeneChips were captured with the Affymetrix GeneChip Scanner 3000.
|
| Data processing |
Microarray data has been processed with the R/Bioconductor package “affy” version 1.44.1 modified by Brainarray lab for Gene ST support. Brainarray Custom CDF ragene20st version 19.0.0 was used for summarization. Raw data was normalized using RMA as implemented in the “affy” package.
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| |
|
| Submission date |
Apr 21, 2015 |
| Last update date |
Apr 20, 2018 |
| Contact name |
Jonathan Moggs |
| E-mail(s) |
[email protected]
|
| Organization name |
Novartis
|
| Street address |
Fabrikstrasse 2
|
| City |
Basel |
| ZIP/Postal code |
4056 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL20091 |
| Series (2) |
| GSE68128 |
Chronic subacute (incl. one subchronic study) exposure of Wistar rats to (non-)carcinogenic compound |
| GSE68387 |
IMI MARCAR Project: towards novel biomarkers for cancer risk assessment |
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