Analysis by RNA-seq of the transcriptional profile of three sub-populations of mouse colon epithelial cells (Lgr5+ columnar basal cells, goblet cells, enterocytes).

In this dataset, we report the analysis by RNA-sequencing (RNA-seq) of the transcriptional profile of three sub-populations of epithelial cells contained in the mouse colonic epithelium: 1) Epcam+/Cd44+/Kit-neg cells, which correspond to a population of epithelial cells located at the bottom of colonic crypts and enriched in Lgr5+ columnar basal cells (CBCs); 2) Epcam+/Cd44+/Kit+ cells, which correspond to a population of epithelial cells located at the bottom of colonic crypts and enriched in goblet cells; 3) Epcam+/Cd44-neg/Cd66-high cells, which correspond to a population of epithelial cells located at the top of colonic crypts and enriched in mature enterocytes (Rothenberg et al., Gastroenterology, 142:1195-1205, 2012). All three populations included in the study (Epcam+/Cd44+/Kit-neg, Epcam+/Cd44+/Kit+, Epcam+/Cd44-neg/Cd66-high) were sorted by fluorescence activated cell sorting (FACS), starting from adult colonic tissues of female C57BL/6J mice (The Jackson Laboratory: stock #000664). For each of the three populations, three independent replicates were generated, each sorted from an independent mouse, for a total of 9 samples, representative of 3 independent mice. Colonic crypts were detached from colon tissues using EDTA (5 mM) and then dissociated into single-cell suspensions using DNAse-I (100 units/ml) and Collagenase-III (200 units/ml). Single-cell suspensions were stained with monoclonal antibodies against differentially expressed surface antigens (Epcam, Cd44, Kit, Cd66a, Cd3, Cd16/Cd32, Cd31, Cd45) and sorted using a FACSAria-III machine (Becton Dickinson), after exclusion of dead cells (DAPI+), cell doublets (serial gating based on FSC-A vs. FSC-H and SSC-A vs. SSC-W profiles) and cells of non-epithelial lineages (Cd3+, Cd16/Cd32+, Cd31+, Cd45+).