Wnt/PCP-primed intestinal stem cells directly differentiate into enteroendocrine or Paneth cells

We performed 7 single-cell RNAseq experiments to identify progenitor cell populations in the small intestine. To also capture rare intestinal cell populations such as stem cells and secretory cells we not only analyzed crypt cells from wildtype mice but also used two reporter mouse lines: i) the FltpZV/+ mouse line of which we mixed live crypt cells with Fltp Venus reporter (FVR) positive cells at different ratios and ii) Foxa2-Venus fusion (FVF) reporter mice. The FVF-enriched samples are part of another manuscript (link to GEO# will be provided). Using this FACS-based enrichment strategy, we could identify a Paneth cell-primed ISC population and potential progenitor populations for all intestinal lineages. To assess the role of Wnt/PCP signaling for enteroendocrine and Paneth cell differentiation, we performed 4 single-cell RNAseq experiments from crypt cells of Celsr1crsh/+; FltpZV/ZV compound mutant mice. When comparing control and mutant cells we found specific transcriptional alterations in the Paneth cell lineage. 7 single-cell RNA-seq experiments were performed using 10X Genomics technology to generate single cell transcriptomic profiles of small intestinal epithelial crypt cells from control wildtype and FltpZV/+ mouse line. 4 samples single-cell RNA-seq experiments were performed using 10X Genomics technology to generate single cell transcriptomic profiles of small intestinal epithelial crypt cells from a Flattop (Fltp)-Venus-Reporter (FVR) Celsr1(crsh) hemizygous mouse line. Cells were sampled from the small intestine of adult mice. Cells were sorted to enrich for FVR positive cells.