strain: C57/B6 gender: male tissue: liver genotype/variation: SKO (Shp2hep-/-, or Shp2fl/fl:Alb-Cre+)
Extracted molecule
total RNA
Extraction protocol
RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
Label
biotin
Label protocol
Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays
Hybridization protocol
Standard illumina hybridization protocol
Scan protocol
Standard Illumina scanning protocol
Description
replicate 2 8615501094_D
Data processing
Microarray data were collected and analyzed in three steps. First, we obtained the sample probe file of all samples using illumina’s GenomeStudio software after expression intensities were calculated and quality controlled with a detection p value set to < 0.05 for each gene probed on the array for all hybridizations. Second, we used hierarchical clustering methods to detect outliers in all samples. From this analysis, no outliers were detected. Finally, we further analyzed the expression data for differentially expressed genes using Agilent’s GeneSpring GX 11.5 software with quantile normalization, log transformation, and statistical analysis. Microarray data were collected and analyzed in three steps. First, we obtained the sample probe file of all samples using illumina’s GenomeStudio software after expression intensities were calculated and quality controlled with a detection p value set to < 0.05 for each gene probed on the array for all hybridizations. Second, we used hierarchical clustering methods to detect outliers in all samples. From this analysis, no outliers were detected. Finally, we further analyzed the expression data for differentially expressed genes using Agilent’s GeneSpring GX 11.5 software with quantile normalization, log transformation, and statistical analysis.
