Daily gavaged with OTA (210µg_ kg BW), dissolved in 0,1M sodium bicarbonate. After 14 days: Anesthesia with pentobarbital, exsanguination subsequent to retrograde perfusion with PBS. Kidney collection and storage in RNAlate
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
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
