For genome-wide expression analysis, total RNA was extracted using Trizol reagent (Invitrogen) and labeled and hybridized to Agilent Whole Mouse Genome Oligo 4X44K Microarrays (one-color platform) according to the manufacturer's protocols.
miRNAs profile was analyzed by Agilent (Santa Clara, CA, USA) Human miRNA microarray platform (v.3) according to manufacturer's instructions, scanned with Agilent Scanner G2505 and analyzed by Feature Extraction (v10.5) software to obtain raw data.
It suggests that a standard set of microRNAs would be needed to compare the performances between microRNA microarray platforms designed according to different miRBase versions.
The microarray platform was designed according to the 2006 version genome annotation, whereas the RNA-Seq data were analysed using the 2008 version genome annotation.
All genes represented in the ORESTES microarray platform were grouped according to biological process as described by public databases GeneCards® [ 43] and Gene ontology [ 44].
Fifty ng of RNA were converted to cDNA then to biotinylated cRNA, labelled with Cy3 and hybridized to Mouse-6 Expression BeadChips (Illumina) on the Integragen Illumina microarray platform (Evry, France), according to the Illumina procedures.
Profiling on the individual microarray platforms was done according to manufacturer's specifications.
