RNA-seq analysis to examine the effect of the Ube2e1 and Ube2e1 knockdown on gene expression profile in 3T3-L1 pre-adipocyte cells

UBE2E2 and UBE2E1 are both members of the same family of E2 conjugating enzymes raising the question of whether they are functionally redundant, particularly given that genetic targeting of both genes inhibited adipogenesis, in vitro. To explore this question, we sought to test for molecular redundancy using transcriptomics analyses. We performed comparative transcriptomics analyses of 3T3-L1 cells in which we targeted either Ube2e2 or Ube2e1. To investigate the cooperative function of Ube2e1 and Ube2e2 in the regulation of adipogenic differentiation, we transduced 3T3-L1 cells with previously validated shRNA retroviruses. We established 3T3-L1 cell lines in which each target gene was knocked down after puromycin selection. Three different stable 3T3-L1 cell lines (shUbe2e1, shUbe2e2, and Scramble) were treated with or without an adipogenic cocktail for 12 hours. We then performed a comparative gene expression profiling analysis using RNA-seq data obtained from six different groups, each with three biological replicates.