library_construction_protocol: Colonic epithelial cells and lymphocytes were isolated via mechanical disruption and enzymatic digestion. Briefly, colonic biopsies were twice shaken at 250 revolutions per minute (rpm) for 30 minutes at 37°C in 7mL RPMI 1640 (Fisher Scientific) supplemented with 1% dialyzed fetal bovine serum (Biowest), 2mM EDTA (Corning), and 1.5 mM MgCl2 (Thermo Fisher Scientific). Cells were filtered through a 40mM filter (Fisher Scientific), centrifuged, and pooled for subsequent analysis. This fraction was considered the epithelial fraction. Subsequently, the remaining tissue was digested in two sequential shakes at 250rpm at 37°C for 30 minutes in 15mL RPMI 1640 supplemented with 20% fetal bovine serum and 1mg/mL collagenase type IV, from Clostridium histolyticum (Sigma-Aldrich). After each digestion, the solution was filtered, centrifuged, and then combined for downstream experimentation. This fraction was considered the lamina propria fraction.x Cells were centrifuged and resuspended to a final concentration in RPMI 1640 medium supplemented with 10% FBS and 1% penicillin/streptomycin, and the suspensions were loaded into a Chromium Controller (10x Genomics, Inc.) under conditions to generate an anticipated yield of 1,000-10,000, depending on yield of cells from the tissue. Single-cell 5' RNA-seq libraries, as well as V(D)J libraries, were generated for each sample according to the manufacturer's instructions (Chromium Single Cell 5' Library Construction Kit V1 Chemistry, Single Cell V(D)J Enrichment Kit for Human T-cells, and Single Cell V(D)J Enrichment Kit for Human B-cells, all from 10x Genomics Inc). 5' libraries were sequenced to a minimum depth of 50,000 reads per cell for 5' gene expression libraries, or 5,000 reads per cell for V(D)J libraries