RNA-seq of intestinal stem cells

The impact of Mll1 removal on intestinal stem cells expressing an oncogenic form of beta-catenin (beta-cateninGOF) was analysed in 4 pairs of sorted intestinal stem cells of Lgr5-CreERT2; beta-cateninGOF;Mll1+/- (control) and Lgr5-CreERT2; beta-cateninGOF;Mll1-/- (knockout) at 10 days after tamoxifen-induced mutagenesis. Using 75-base-pair reads, around 30 million reads per sample with comparable unique mapped reads (73-78%) were obtained. To analyze differentially expressed genes, we applied DESeq2 analysis to the RNA-seq dataset. Differentially expressed genes in beta-cateninGOF; Mll1-/- versus beta-cateninGOF; Mll1+/- stem cells showed both up- and downregulation of genes at a false discovery rate (FDR) of 10%. This included a global increase in the expression of goblet cell-specific genes. Downregulated genes included specific markers of Paneth cells, indicating that ablation of Mll1 shifted the Paneth-like identity of beta-cateninGOF stem cells towards a goblet cell fate. The stem cell transcriptome further revealed that beta-cateninGOF; Mll1-/- stem cells exhibited a decreased expression of several transcription factors and stem cell genes. mRNA profiles of beta-cateninGOF; Mll1+/- (control) and beta-cateninGOF; Mll1-/- (knockout) stem cells were generated by deep sequencing in quadruplicates