Whole transcriptome analysis was performed with 2-3 biological replicates per experimental group, with each sample pooled from 4 mice. Total RNA using RiboPure kit (Ambion, Austin, TX), amplified using TargetAmp 2-Round Biotin-aRNA Amplification Kit (Cambio, Cambridge, UK) and whole genome expression profiled using Single-Color MouseWG-6_V2BeadChip with direct hybridization assay (Illumina, San Diego, CA). Cy3 fluorscence emissions were imaged using iScan system (Illumina).
Signal intensities generated using GenomeStudio 2011 software (Illumina) were background corrected and subjected to variance stabilizing transformation (VST) implemented in the Lumi package from R/Bioconductor 45 (link). Quantile normalised signal intensities were used for differential expression analysis implemented in Limma 46 . Probes below a Benjamini-Hochberg derived adjusted p-value of 0.1 were deemed significant. Microarray data are deposited with ArrayExpress and available under accession code E-MTAB-3067.
Signal intensities generated using GenomeStudio 2011 software (Illumina) were background corrected and subjected to variance stabilizing transformation (VST) implemented in the Lumi package from R/Bioconductor 45 (link). Quantile normalised signal intensities were used for differential expression analysis implemented in Limma 46 . Probes below a Benjamini-Hochberg derived adjusted p-value of 0.1 were deemed significant. Microarray data are deposited with ArrayExpress and available under accession code E-MTAB-3067.