Inflammatory hematopoiesis contributes to intestinal inflammation and is modulated by common therapy

This Zenodo repository contains the analysis scripts and processed outputs associated with our study of inflammatory hematopoiesis in Crohn’s disease. The codebase includes end-to-end workflows for single-nucleus multiome (RNA + ATAC), bulk RNA-seq, and ATAC-seq analyses, encompassing quality control, genotype-based demultiplexing (Souporcell/Demuxafy), Seurat/Signac preprocessing, MiloR differential abundance testing, pseudo-bulk differential expression (muscat/edgeR), chromVAR motif analysis, and enhancer-based gene regulatory network inference using SCENIC+. In addition to reproducible analysis scripts, this repository provides processed differential expression tables, differentially accessible peak annotations, chromVAR motif activity results, and SCENIC+ eRegulon activity matrices and network summaries used to generate the main and extended figures of the manuscript. These resources enable full transparency and reproducibility of the transcriptional and epigenetic analyses underlying the identification of cytokine-associated progenitor reprogramming and treatment-responsive regulatory programs in human Crohn’s disease.