Intestinal resection samples were embedded in OCT and snap frozen. Tissues were sectioned in a cryostat and placed on a Visium slide for RNA capture and spatial transcriptomics.
Sections were placed on a Visium Spatial Gene Expression slide (10x Genomics, 1000184), methanol fixed and permeabilized for 24 minutes based on optimization results obtained on intestinal tissues with the Visium Spatial Tissue Optimization Slide & Reagent Kit (10x Genomics, 1000193). Libraries were then constructed according to the manufacturer's instructions and sequenced at a targeted depth of 50 000 reads per spatial spot on a sequencer (Illumina) with the following read configuration: Read 1 (spatial barcode and UMI): 28bp, Read 2 (insert): 90bp, Index 1/2: 10bp.