Post-confluent cells were treated with 10 fM Shiga toxin-2 (Stx2) for 24 and compared to untreated cells
Growth protocol
Primary human dermal neonatal microvascular endothelial cells (HMVEC) isolated from a single donor were maintained in EGM-2MV medium (Lonza) and grown in a humidified incubator with 5% CO2 at 37°C.
Extracted molecule
total RNA
Extraction protocol
Total cellular RNA was purified by cesium chloride ultracentrifugation, as described previously (Chirgwin et al, 1979, Biochemistry)
Label
biotin
Label protocol
According to the standard protocol of Affymetrix
Hybridization protocol
According to the standard protocol of Affymetrix
Scan protocol
According to the standard protocol of Affymetrix
Description
Gene expression data from untreated human microvascular endothelial cells
Data processing
Raw signal intensities were pre-processed using 13 different computational methods. The base affy package was used to compute MAS5.0, RMA, dChip.PM, and dChip.PM-MM summary expression measures. GCRMA, PLIER, VSN, mgMOS, mmgMOS, q.FARMS, l.FARMS, and the method of Choe et al, were computed using Bioconductor packages or packages made freely available by the package developers. PDNN summary expression measures were determined using PerfectMatch v2.3. All pre-processing methods were used in their default implementations. Probe sets were then filtered to remove those called 'absent' by the affy package, and then submitted to Cyber-T for statistical analysis.
