Purification column

Isolation of Foxl1+ cells using fluorescent-activated cell sorting was performed using Foxl1–Cre;Rosa–YFP mice. Small intestines were dissected and washed thoroughly with PBS. Intestinal villi were scraped using a coverslip and the remaining tissue was incubated in 30 mmol/L EDTA plus 1.5 mmol/L dithiothreitol and Hank's balanced salt solution on ice for 20 minutes and subsequently incubated in 30 mmol/L EDTA at 37° for 8 minutes to completely remove the epithelium. After vigorous washes, the remaining mesenchymal fraction was collected and cut into small pieces. The mesenchymal tissue was collected by centrifugation and resuspended in 7 mg/mL Dispase II/0.05% trypsin solution (Sigma-Aldrich, St. Louis, MO) at 37° until the solution became cloudy and the mesenchyme was dissociated. A single-cell suspension was obtained by collecting the supernatant and washing with Hank's balanced salt solution before cell sorting using a BD influx instrument (BD Biosciences, San Jose, CA). For RNA isolation, YFP+ cells were lysed and total RNA was isolated by column purification (Agilent Technologies). Messenger RNA (mRNA) was isolated using Poly(A) mRNA isolation magnetic beads and an mRNA sequencing library prepared using the NEBNext RNA library prep kit (New England BioLabs, Inc, Ipswich, MA). RNA sequencing was performed on an Illumina HiSeq instrument.