Transcriptional changes in experimentally-induced basal to squamous cell carcinoma transition (BST) [ASZ_RasV12_TGFbR1_RNAseq]

Basal cell carcinoma may undergo BST spontaneously or upon Hedgehog targeting therapy. We identified that modulation of Ras/MAPK or TGFb signaling drive BST. Here, we induce Ras/MAPK and/or abrogate TGFb signaling to induce BST. Alternatively we drive c-FOS to induce BST. Here, we analyze transcriptional profiles upon Ras/MAPK activation and/or TGFb signaling abrogation. Methods: mRNA profiles of ASZ transfected with non-silencing (NS) or TGFbR1-targeting shRNA (TGFbR1kd) upon DMSO or Dox/4OHT treatment, 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.