Quantitative RT-PCR validations of 12 differentially expressed genes.

We selected 12 significantly differentially expressed genes that had average fold change greater than 1.5 and mean expression levels greater than 150 in the P1 dataset, and validated changes using quantitative RT-PCR. A total of 30 ASD and 30 control samples from the P1 population were run in replicates of four on the Biomark real time PCR system (Fluidigm, CA) using nanoliter reactions and the Taqman system (Applied Biosystems, CA). We were limited to 60 samples because the other 39 samples did not have enough RNA for qRT-PCR. The housekeeping gene used for qRT-PCR normalization was GAPDH (Hs9999905_m1). The values shown are for 30 ASD and 30 control samples from the P1 population, and fold changes refer to ASD/Control. P-values were calculated using Welch's t-test. For microarray data, p-values and fold changes were recalculated using the available samples. Eleven of 12 genes (all except ZMAT1) were successfully validated.