Gene Expression in Wild Type and TTP Delta ARE Knock-in Mice using RNA-seq

Purpose: The goals of this study are to compare NGS-derived skin transcriptome profiling (RNA-seq) in wild type mice with TTP delta ARE knock-in mutants. Methods: Skin mRNA profiles of approximately 27 week old wild-type (WT) and TTP delta ARE knock-in mice were generated by deep sequencing, with five biological replicates, using Illumina sequencers. The skin RNA samples were prepared from skin biopsies from treated but not papillomatous skin from mice treated with a standard DMBA-TPA protocol for 20 weeks. The sequence reads that passed quality filters were mapped to mm10 with STAR Aligner followed by featureCounts and DESeq2 anlysis. Results: We observed 1144 statistically differentially expressed genes (232 and 912 up- and down-regulated genes in TTP delta ARE mice, respectively, with fold changes >2 and FDR<0.05. Conclusions: Regulated overexpression of TTP by a stablizing deletion in the 3'UTR of its mRNA causes many changes in gene expression in mice subjected to a standard skin papilloma protocol. Overall design: Skin mRNA profiles of wild type (WT) and knockin (KI) mice were generated by deep sequencing, in quintuplicate.