Tissue specific gene expression of epithelial tuft cells from small intestine and gallbladder in mouse

Rare chemosensory epithelial cells called tuft cells have known roles in small intestinal regulation of type 2 cytokine producing Group 2 innate lymphoid cells. To understand the phenotype of tuft cells in another tissue, the extrahepatic biliary tree, we performed RNAseq analysis on tuft cells and non-tuft epithelial cells from small intestine and gallbladder of the mouse. Overall design: IL-25+ and IL-25- epithelial cells were sorted from reporter mice into Dynabead mRNA Direct Micro Purification kit lysis buffer (Thermofisher); mRNA was isolated according to the manufacturer's protocol. Amplified cDNA was prepared using the NuGen Ovation RNA-Seq system V2 kit according to the manufacturer's protocol (NuGen Technologies). Sequencing libraries were generated using the Nextera XT library preparation kit with multiplexing primers according to manufacturer's protocol (Illumina). Library fragment size distributions were assessed using the Bioanalyzer 2100 and the DNA high-sensitivity chip (Agilent Technologies). Library sequence quality was assessed by sequencing single-end 50 bp reads using the Illumina MiSeq platform and pooled for high-throughput sequencing on the Illumina HiSeq 4000 by using equal numbers of uniquely mapped reads (Illumina). Twelve samples per lane were multiplexed. Sequencing yielded a median read depth of 89.2 million reads per sample.