Identifying gene expression changes in fibroblasts treated with an inhibitor targeting MLL1-MENIN complex and depleted for MEN1 gene during reprogramming using RNA-seqeuncing

Here we investigated the effects of MLL1-MENIN inhibition and MENIN depletion on somatic cell reprogramming. Overall design: For samples 1-6, dH1f human fibroblasts were infected with lentiviral vectors expressing OCT4, SOX2, KLF4 and c-MYC and one day later treated with VTP50469 (1 uM) for 6 days. Control cells for the VTP50469 treatment were treated with DMSO. For samples 7-12, dH1f cells were not infected with the reprogramming vectors but were treated with the chemicals at the same concentrations for 6 days. For samples 13-18, dH1f human fibroblasts expressing Cas9 and non-targeting (NT1) and gRNA targeting MEN1 gene were infected with lentiviral vectors expressing OCT4, SOX2, KLF4 and c-MYC. For samples 19-24, dH1f cells were not infected with the reprogramming vectors. Total RNA was collected after 6 days of growth from all of the samples.