Mouse genechip microarrays mogene 1

RNA was isolated and purified from the thymuses of 10 day old wild type and CD2-MYC/Runx2 double transgenic mice using an RNeasy Mini Kit as per the manufacturer's instructions (Qiagen, UK) with mechanical lysis using a pellet pestle in a microfuge tube (Sigma). RNA purity was assessed using a Nanodrop 2000 Spectrophotometer (Thermo Scientific), and integrity verified using the Agilent 2100 Bioanalyser with RNA 6000 Nano Reagents kit (Agilent Biotechnologies) as per the manufacturer's protocol. Whole genome expression profiling was performed using Affymetrix mouse GeneChip microarrays (MoGene-1) in triplicate as per the manufacturer's protocol (Affymetrix, UK). Data analysis was carried out using the Partek Genomic Suite (Partek Inc., St. Louis, MO, USA). Briefly, after Robust Multichip Average normalisation [76] (link) with GC content pre-background adjustment, the differentially expression analysis was performed using ANOVA. Multiple testing correction was done using the ‘q value’ cut-off [77] with gene changes of p<0.05 considered significant. Graphical representations of data were prepared using CLC Genomics Workbench 4.

RNA was isolated and purified from the thymuses of 10‐day‐old wild‐type and CD2‐MYC/Runx2 transgenic mice as previously described.2 Microarray analysis was based on a previously archived dataset (GEO accession number GSE80254). Briefly, whole genome expression profiling was performed using Affymetrix mouse GeneChip microarrays (MoGene‐1) in triplicate as per the manufacturer's protocol (Affymetrix, UK). Data analysis was carried out using Partek Genomics Suite (Partek Inc, St. Louis, MO). After Robust Multichip Average normalization20 with GC content pre‐background adjustment, differential expression analysis was performed using ANOVA. Multiple testing correction was performed and “q‐value” cut‐offs selected21 with gene changes of q < 0.05 considered significant. Graphical representations of data were prepared using CLC Genomics Workbench 4.2