|
| Status |
Public on Aug 12, 2006 |
| Title |
Rat liver, untreated (control), extrated 48 hours after treatment (no treatment in this case), biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Rat liver, left lateral lobe
|
| Organism |
Rattus norvegicus |
| Characteristics |
Male Sprague-Dawley (Crl:CD(SD)IGS Br
Age: between 5 and 6 weeks old
|
| Biomaterial provider |
Scantox, Lille Skensved, Denmark
|
| Treatment protocol |
The animals were sacrificed 48 hours after treatment and organs were frozen for later analysis. Tissue samples of the left lateral lobe of the liver were snap frozen in liquid nitrogen, transferred to dry ice and stored at approximately -80?C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen liver samples were homogenized in 2 ml TRIzol® reagent (Invitrogen ; Life Technologies, Scotland) using an Ultra Turrax T25 basic homogenizer (IKA Labortechnik; IKA-Werke, Staufen, Germany). Chloroform (400 ?l) was added and homogenized samples were shaken vigorously by hand for 15 seconds. Phase separation was achieved by centrifugation for 15 min at 10,000 × g at 4°C. Total RNA from the aqueous phase was purified using the RNeasy 96 Qiagen vacuum system following the “Clean-up” procedure.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Rat 230 version 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned on GeneChip® Scanner 3000 7G 4C
|
| Description |
Gene expression data from rat liver 48 hours after treatment with compound.
|
| Data processing |
The data were analyzed with RMA. R was used with the affy package. Expresso with the following settings (bgcorrect.method=rma, normalize.method = quantiles.robust, pmcorrect.method=pmonly, summary.method=liwong) was used to normalize
|
| |
|
| Submission date |
Aug 11, 2006 |
| Last update date |
Aug 09, 2011 |
| Contact name |
Jeppe Skytte Spicker |
| E-mail(s) |
skytte@cbs.dtu.dk
|
| Organization name |
Danish University of Technology
|
| Department |
CBS
|
| Street address |
Building 208
|
| City |
Lundtofte |
| ZIP/Postal code |
XXXX |
| Country |
Denmark |
| |
|
| Platform ID |
GPL1355 |
| Series (1) |
| GSE5509 |
Expression data from Rat liver 48 hours after treated with different toxic compounds. |
|
| Relations |
| Reanalyzed by |
GSE31289 |
