Transcriptional changes in experimentally-induced basal to squamous cell carcinoma transition (BST) upon treatment with small molecule inhibitors [ASZ_RNAseq_inhibitor]

Basal cell carcinoma may undergo BST spontaneously or upon Hedgehog targeting therapy. We identified that either modulation of Ras/MAPK or TGFb signaling or c-FOS induction could drive BST. Enhanced EGFR signaling has been implicated during BST. Here, we analyze transcriptional profiles upon c-FOS induction when cells are treated with EGFR signaling inhibitors afatinib (5uM) and UO126 (10uM). Overall design: Methods: mRNA profiles of ASZ transfected with doxycycline-inducible empty vector (ctrl) or c-FOS containing vector (c-FOS) upon Dox treatment (24h) followed by EGFR signaling inhibitor treatments (6h) or DMSO control, were generated by deep sequencing, in duplicate, using Illumina HiSeq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Homer.