Bulk RNAseq expression data of colon biopsies from intestinal mucosa of non-IBD controls and patients with Crohn's disease or ulcerative colitis

Ulcerative colitis and Crohn’s disease are chronic inflammatory intestinal diseases with perplexing heterogeneity in manifestations and response to treatment. While the molecular basis for this heterogeneity remains uncharacterized, single-cell technologies allow us to explore the transcriptional states within tissues at an unprecedented resolution which could further understanding of these complex diseases. Here, we apply single-cell RNA-sequencing to human inflamed intestine and show that the largest differences among patients are present within the myeloid compartment including macrophages and neutrophils. Using spatial transcriptomics in human tissue at single-cell resolution (CosMx Spatial Molecular Imaging) we spatially localized each of the macrophage and neutrophil subsets identified by single-cell RNA-sequencing and unravel further macrophage diversity based on their tissue localization. Finally, single-cell RNA-sequencing combined with single-cell spatial analysis reveals a strong communication network involving macrophages and inflammatory fibroblasts. Our data sheds light on the cellular complexity of these diseases and points towards the myeloid and stromal compartments as important cellular subsets for understanding patient-to-patient heterogeneity. Barcoded RNAseq libraries were prepared from total RNA using a TruSeq stranded mRNA kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Libraries were subjected to single-end sequencing (100 bp) on a HighSeq-3000 platform (Illumina, CA, USA) at the Translational Medicine and Genomics group (Boehringer-Ingelheim GmbH & Co, Biberach, Germany). Quality filtering and adapter trimming was performed using Skewer version 2.2.8 Reads were mapped against the human reference genome using the STAR aligner version 2.5.2a. The genome used was GRCh38.p10, and gene annotation was based on Gencode version 27 (EMBL-EBI, Hinxton, UK). Read counts per gene were obtained using RSEM version 1.2.31 and the Ensembl GTF annotation file (EMBL-EBI, Hinxton, UK).