RNA-seq of sorted intestinal stem and Paneth cells

The impact of Mll1 removal on the intestinal stem cells and its direct effect on neighbouring Paneth cells was evaluated in sorted intestinal stem and Paneth cells from Mll1FC/+; Lgr5-eGFP-CreERT2/+ (control) and Mll1FC/FC; Lgr5-eGFP-CreERT2/+ (knockout) mice, 4 and 10 days after tamoxifen-induced mutagenesis. Using 75-base-pair reads, 30 million reads per sample with comparable unique mapped reads for stem (70-77%) and Paneth (60-76%) cells were obtained. To analyze differentially expressed genes, we applied DESeq2 analysis to the RNA-seq dataset. Analysis by DAVID and GSEA at a false discovery rate (FDR) of 5% was conducted.The stem cell transcriptome revealed that Mll1 knockout stem cells exhibited a decreased expression of several transcription factors and stem cell genes. Additionally, Mll1 ablation in stem cells had an impact on Paneth cells. Downregulation of Paneth cell specific markers indicated a loss of Paneth cell identity. Overall design: mRNA profiles of sorted stem and Paneth cells from Mll1FC/+; Lgr5-eGFP-CreERT2 (control) and Mll1FC/FC; Lgr5-eGFP-CreERT2 (knockout) mice, 4 and 10 days after tamoxifen were generated by deep sequencing.