Expression profiling by high throughput sequencing
To understand the diversity of cellular states within mouse intestinal epithelial tissue, we obtained whole intestines from wild type mice, dissagregated the samples, sorted into single cells and profiled them by single-cell RNA-seq.
To understand normal tissue homeostasis, untreated cells were profiled, while to investiage the impact of enteric pathogens on epithelial cells, mice infected with both Salmonella Enterica and the parasitic worm H. polygyrus were profiled using both 3'-droplet-based and full length plate-based single-cell RNAseq. RANKL-mediated differentiation of organoid cultures were used to sequence the rare intestinal M cell, these were then compared to M cells obtained from the in vivo follicle associated epithelium (FAE).
Please note that the FAE_UMIcounts.txt file has been updated on May 7th 2020.