strain: Wistar stress: High wall shear stress WSS replicate: 11 tissue: aorta from region with High WSS
Treatment protocol
No special treatment of rats - different regions of aorta were compared
Growth protocol
Male Wistar rats under constant environmental temperature (21°C) and 12h:12h light/dark cycle, witg free access to standard rodent chow and water.
Extracted molecule
total RNA
Extraction protocol
With guidance from the CFD simulations, portions of the entire artery from high and low WSS regions, respectively, were cut out under RNase free conditions and directly put in pre-chilled Lysing Matrix D tubes (MP Biomedicals, Illkirch, France) containing Trizol (Invitrogen, Paisley, Scotland, UK). In order to yield significant amounts of RNA, tissue pieces from the specific high and low WSS regions from five animals were pooled for each sample (a total of 28 pools; 14 paired samples of high and low WSS regions). Samples were homogenized with FastPrep. Total RNA was isolated using RNeasy Mini kit (Qiagen, Maryland, USA), including DNase treatment for elimination of potential DNA contamination. RNA integrity was analyzed by the use of an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Paolo Alto, CA, USA) and quantified using NanoDrop (NanoDrop products, Wilmington, DE, USA).
Label
biotin
Label protocol
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Hybridization protocol
RNA samples were hybridized at the Karolinska Institute microarray core facility. Affymetrix Rat Gene 1.1 ST Array Plate system and protocols were used.
Scan protocol
RNA samples were scanned at the Karolinska Institute microarray core facility. Affymetrix Rat Gene 1.1 ST Array Plate system and protocols were used.
Description
Rat aorta from region with High WSS
Data processing
Raw data from cel-files was pre-processed using the RMA-algorithm. Gene annotation was downloaded from the Affymetrix web page (version RaGene-1_1-st-v1.na31.rn4). Probe sets without annotation and probe sets with mean expression level below 4 were omitted from analysis, resulting in the analysis of 13968 genes.
