stain: Wistar gender: male age: adult brain status: brain damage (BD) ventilation type: high tidal volume ventilation (HT)
Extracted molecule
total RNA
Extraction protocol
Total RNA of right lung tissue was extracted using Trizol® Reagent (Invitrogen GmbH, Karslruhe, Germany). DNase treatment was carried out, using DNA Free Kit (Ambion / Life Technologies GmbH, Darmstadt). RNA yield, quality, and integrity were assessed by agarose gel electrophoresis and spectrophotometry. RNA concentration was assessed by 260/280 measurements using the Infinite® 200 PRO NanoQuant (Tecan Group Ltd., CH), and RNA integrity was measured by Agilent Bioanalyzer 2100 System (Agilent, Böblingen, Germany). 1 µg RNA was transcribed to cDNA according to the protocol provided with the High Capacity cDNA Reverse Transcription kit (Life Technologies GmbH, Darmstadt, Germany). Recombinant ribonuclease inhibitor was added to prevent RNase-mediated degradation.
Label
biotin
Label protocol
Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
Hybridization protocol
Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.
Scan protocol
Affymetrix GeneArray Scanner3000
Description
BD_HT_24
Data processing
The data were analyzed with a commercial software called JMP Genomics, version 5, from SAS. Gene expression profiling was performed using arrays of RaGene10stv1-type from Affymetrix. A Custom CDF Version 14 with entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization.