Biopsy samples from proximal and distal sites were enzymatically digested within 3 hours of collection with collagenase/dispase to generate a single cell suspension and submitted to single cell RNA sequecing as described in the design.
Cells were loaded on a 10x Chromium controller and processed following the 10x Chromium single cell 3' v2 chemistry protocol (10x Genomics, CG000108_AssayConfiguration_SC3v2).  Libraries were sequenced on an Illumina HiSeq with the following read configuration: R1 (cell barcode and UMI): 26bp, i7 index: 8bp, R2 (insert): 98bp.