Transcriptomic profiles of biopsy-derived colon epithelial organoids from pediatric patients with ulcerative colitis

Colon epithelial organoid lines were developed from pediatric patients with endoscopically active ulcerative colitis, inactive ulcerative colitis, and those without endoscopic or histologic evidence of colon inflammation (non-IBD controls). From each organoid line, RNA was processed from undifferentiated organoids (spheroids) and parallel organoids differentiated for 3 days (colonoids). Paired-end sequencing of poly-A enriched RNA libraries was carried out on the Illumina NovaSeq PE150 platform and the reads were aligned to the human reference hg38 genome. To determine differentially expressed genes, transcripts with Log2FC ≥ ±1, FDR P ≤ 0.1 were considered statistically significant. Bulk RNA-sequencing of colon epithelial organoid lines from eight pediatric patients with active UC, inactive UC, and non-IBD controls.