Next Generation Sequencing Quantitative Analysis of Wild Type, CDK8-/-, CDK19-/-, and CDK8-/-CDK19-/- mouse instestinal organoids transcriptomes

Purpose: The goals of this study were to compare gene expression profiles of mouse intestinal epithelium organoids with intact or disrupted CDK8 and CDK19 genes. Methods: mRNA profiles of all organoid genotypes, in biological triplicates, were generated by deep sequencing using the BGISEQ SE50 50 million single-end, 50bp reads per sample. The sequence reads that passed quality filters were aligned to the mouse genome, quantified, and differential gene expression (DGE) analysis was performed using DEseq2. Results: Using an optimized data analysis workflow, we mapped about 50 million sequence reads per sample to the mouse genome (GRCm38.p6) and identified differentially expressed genes. This mild changes in overall gene expression, preferentially enriched in tissue specif genes. The transcription profile showed an overlap between those present in a CFTR KO context. Conclusions: CDK8/19 knockout causes tissue specif expression alteration. Intestinal organoids presented a CFTR-like phenotype after removal of both genes Differential gene expression of RNAseq profiles of wild-type (WT) and wild Type, CDK8-/-, CDK19-/-, and CDK8-/-CDK19-/- mouse intestinal organoids. The effect of Senexin B as a CDK8/19 inhibitor on the transcriptome was also studied.