Intestinal tissue sample was processed within 3 hours of collection with epithelial stripping followed by collagenase digestion to generate a single cell suspension and submitted to single cell RNA sequencing.
Cells were loaded on a 10x Chromium controller and processed following the NextGEM v3.1 dual-index 3' Chemistry (10x Genomics, CG000315_ChromiumNextGEMSingleCell3-_GeneExpression_v3.1(DualIndex)_RevF.pdf). Libraries were sequenced on an Illumina HiSeq with the following read configuration: R1 (cell barcode and UMI): 28bp, i7 index: 10bp, i5 index: 10bp, R2 (insert): 90bp.