|
| Status |
Public on Aug 23, 2007 |
| Title |
Eker Kidney C d14 biological rep2 23 |
| Sample type |
RNA |
| |
|
| Source name |
Kidney cortex and outer medulla_Eker_time mached vehicle control (AA)_d14_biological replicate2
|
| Organism |
Rattus norvegicus |
| Characteristics |
Genotype: Eker
Gender: male
Age: 10-14 weeks
|
| Biomaterial provider |
MD Anderson Cancer Center, Smithville, Texas, USA
|
| Treatment protocol |
Daily gavaged with 0,1M sodium bicarbonate. After 14 days: Anesthesia with pentobarbital, exsanguination subsequent to retrograde perfusion with PBS. Kidney collection and storage in RNAlater.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction of total RNA was performed according to the manufacturer's instructions: RNeasy Midi Kit (Qiagen, Cat No. 75144)
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Affymetrix, USA; GeneChip® Expression Analysis, GeneChip sample Cleanup Module, 701194 Rev.1)
|
| |
|
| Hybridization protocol |
According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays , and hybridized cRNA was stained using Phycoerythrin-conjugated Streptavidin
|
| Scan protocol |
The stained Genechips were scanned with the GCS3000 Scanner according to the manufacturer’s instructions, using GCOS software Vers 1 (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 4, 701028 rev1)
|
| Description |
total RNA from kidney cortex and outer medulla
|
| Data processing |
Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity of 100.
|
| |
|
| Submission date |
Sep 27, 2006 |
| Last update date |
Aug 23, 2007 |
| Contact name |
Daniel R. Dietrich |
| E-mail(s) |
[email protected]
|
| Phone |
0049-7531-883518
|
| Fax |
0049-7531-883170
|
| Organization name |
University of Konstanz
|
| Department |
Environmental Toxicology
|
| Street address |
Jakob-Burckhardt-Str. 25
|
| City |
Konstanz |
| ZIP/Postal code |
78467 |
| Country |
Germany |
| |
|
| Platform ID |
GPL341 |
| Series (1) |
| GSE5923 |
Expression data from Aristolochic Acid and Ochratoxin A treated Tsc2 mutant (Eker) and corresponding wild type rats |
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