Transcript and differential exon level changes in T-REx-293 cells after Tat-SF1 depletion

In order to identify genes with different overall transcript levels or differential exon levels (alternative processing) between the groups Control and Tat-SF1KD, we studied 11 hybridizations on the HumanExon10ST array using mixed model analysis of variance. 526 genes with significant transcript level differences between the groups and 1397 genes with significant differential exon levels were found, including 99 genes with both transcript and exon level differences (p<0.01). Total RNA from cells under 2 different conditions were collected: control cells and Tat-SF1 KD cells. Cells stably expressing an empty vector or a GFP-specific shRNA composed the control group. Two different shRNAs specific to Tat-SF1 composed the Tat-SF1 KD group. Biological triplicates were isolated from each of the above samples, resulting in a total of 12 samples. One sample (Empty Vector, biological replicate 3) did not pass quality control metrics, and was excluded from the analysis, leaving 11 final samples.