Differentially expressed genes selected using ANOVA yield good classifiers for undifferentiated MSCs and their lineages. The x-axis represents the different samples and the y-axis represent log intensity values. Assuming that high transcript levels correlate with strong protein expression, we filtered the post hoc analysis results for genes showing strong intensity for putative positive markers of MSCs. The filtering criterion was mean signal intensity (MSI)—the average signal intensity for a particular condition—of more than 1000 units. Based on analysis of genes with known expression levels, Illumina reported the intensity of 1000 units to correspond to a concentration of 10 pM of RNA. Similarly for differentiation markers, we identified genes with statistical significance between cells of that lineage and other lineages from the post hoc test. All putative markers show a strong up-regulation compared with the expression in other lineages. (A-D) Putative markers for undifferentiated MSCs and MSC-derived adipocytes, chondrocytes, and osteocytes as predicted by the microarray data. (E-H) Quantitative RT-PCR (qRT-PCR) validation of some of these markers. Relative quantification was calculated using the comparative Ct method. Expression of a gene in one lineage was compared with the expression of the same gene in pooled RNA from other lineages. This approach enabled a better comparison of qRT-PCR data with the array data and also indicated the specificity of these markers in a particular lineage. The tables show relative quantification (RQ) values of expression of these genes in the respective lineage compared with their expression in all other lineages.