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. Overall design: Bulk RNA-sequencing of colon epithelial organoid lines from eight pediatric patients with active UC, inactive UC, and non-IBD controls.

本数据集的结肠上皮类器官系分别源自三类儿童受试者：内镜下活动性溃疡性结肠炎（ulcerative colitis, UC）患者、非活动性溃疡性结肠炎患者，以及无内镜或组织学结肠炎症证据的非炎症性肠病对照者（non-IBD controls）。针对每一株类器官系，分别对未分化类器官（球状体，spheroids）与诱导分化3天的平行培养类器官（结肠类器官，colonoids）提取并处理RNA。采用Illumina NovaSeq PE150测序平台，对聚腺苷酸富集RNA文库开展双端测序，并将测序读段比对至人类参考基因组hg38。为鉴定差异表达基因，本研究将Log2倍数变化（Log2FC）绝对值≥1、错误发现率校正P值（FDR P）≤0.1的转录本判定为具有统计学显著性。实验整体设计：对8名活动性UC、非活动性UC患儿及非炎症性肠病对照者的结肠上皮类器官系进行批量RNA测序（bulk RNA-sequencing）。