animal: rat 4 gender: male strain: spontaneously hypertensive rats (SHR) age: 16 weeks tissue: Blood treatment: before MCA occlusion time: control
Treatment protocol
Stroke was induced by thread occlusion of the middle cerebral artery (MCAo) using a silicon-coated thread which was maneuvered through the internal carotid until resistance was felt and a drop in cerebral blood flow noted on Laser Doppler; Whole blood (250µl) was drawn from the lateral tail vein (1ml syringe, 26G needle) into 500 international units of heparin (500IU, Pfizer) at 0 (immediately before anesthesia induction), 1, 2, 3, and 6 hours post MCA occlusion. The 24 hour sample was taken by heart puncture immediately following anesthetic overdose
Growth protocol
Eight male 16 week old spontaneously hypertensive rats were maintained under standard housing conditions with a normal light/dark cycle with ad libitum access to normal rat chow and water for two weeks before stroke induction.
Extracted molecule
total RNA
Extraction protocol
RNA was prepared from the whole blood cell pellets using the PAXgene Blood RNA Kit (PreAnalytiX #762174, Qiagen).
Label
biotin
Label protocol
The Encore Biotine module (NuGen, San Carlos, CA, USA; cat#4200-12) was used for fragmentation and labelling. Gene hybridisation was performed using the Affymetrix GeneChip Expression 3’ Amplification Reagent Hybridisation Controls kit (Affymetrix, Santa Clara, CA, USA; cat#900454)
Hybridization protocol
Samples were randomly hybridized to the GeneChip® RatGene 1.0 ST arrays (Affymetrix, Santa Clara CA, USA; cat#9011730).
Scan protocol
GeneChips were scanned using the Fluidics control station (Affymetrix GeneChip Fluidics Station 450, Affymetrix, Santa Clara, CA, USA)
Description
gene expression data from SHR rat blood before MCA occlusion
Data processing
For gene expression, pairwise comparisons were made between neighboring time points of the experiment using linear models, and the resulting F-statistic was used to identify genes whose expression varied the most across the time course of the experiment. Models were constructed, and significance testing was performed using the R package limma Genes with expression varying the most over time were ranked by p-value of the F statistic, with a cut-off of 5x10^-7
