DOI: 10.5281/zenodo.18703964
title: Human Inflammatory Bowel Disease-on-a-chip for modelling disease progression, cancer initiation, and sex-specific effects - shallow pass sequencing

description: Shallow Whole Genome Sequencing FASTQ Files and Snakemake Bioinformatics Pipeline

Associated with: Özkan et al., Human Inflammatory Bowel Disease-on-a-chip for modelling disease progression, cancer initiation, and sex-specific effects, Nat. Biomed. Eng. (2026)

This repository contains shallow whole genome sequencing FASTQ files and the associated Snakemake-based bioinformatics pipeline used in the study by Özkan et al. (2026). The sequencing data were generated from Healthy and Inflammatory Bowel Disease (IBD) human Colon Organ Chips constructed using primary patient-derived epithelial and stromal cells. Chips were exposed to experimental perturbations including carcinogen treatment (ENU), and genomic copy number alterations were assessed to model early cancer progression in vitro.

Raw sequence reads were aligned to the human reference genome (GRCh38) and processed using standard best-practice workflows (BWA, GATK, Picard). Copy number profiling was performed using shallow whole genome sequencing approaches as described in the manuscript. The provided Snakemake workflow reproduces the processing steps used for alignment, quality filtering, duplicate handling, and downstream copy number analysis.

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We grant access to this dataset to make the results presented in the corresponding research paper verifiable and replicable (“Human Inflammatory Bowel Disease-on-a-chip for modelling disease progression, cancer initiation, and sex-specific effects" published in Nat. Biomed. Eng.).

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