Human Inflammatory Bowel Disease-on-a-chip for modelling disease progression, cancer initiation, and sex-specific effects - shallow pass sequencing

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.

Access and License

If you would like to request access to these files, please fill out the Non-Commercial Research and Academic Use form.

You need to satisfy these conditions in order for this request to be accepted:

• 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.).
• This dataset may further be used for research purposes only. Commercial use is not permitted.
• As part of your access to the dataset, you represent and warrant that you shall comply with all applicable federal, state, and institutional regulations and policies governing the handling and use of human-derived data. You further agree that you shall not attempt to: (i) identify, re-identify, or otherwise depseudonymize the data set; and (ii) you shall not further share, distribute, publish, or otherwise disseminate the data set without the author's prior written approval. Any authorized use of the dataset must include proper acknowledgement of the originating investigators and institution.

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ALL DATA AND FILES ARE PROVIDED “AS IS.” THERE IS NO REPRESENTATION OR WARRANTY, EXPRESS OR IMPLIED, REGARDING THE DATA’S ACCURACY, COMPLETENESS OR USE. THERE ARE NO EXPRESS OR IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, OR THAT THE USE OF THE DATA OR FILES WILL NOT INFRINGE ANY PATENT, COPYRIGHT, TRADEMARK, OR OTHER PROPRIETARY RIGHTS.

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