Code repository for our paper.
We present a single cell dateset on IBD, including 12 patients (6 Chron's Disease and 6 Ulcerative colitis patients) and 6 healthy controls for:
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Analysis of samples by health
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Analysis of samples together
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Comparison with publicly available data
You can inspect our dataset easily, by using our ShinyApp here. Please visit our webpage for further information.
Ulcerative colitis and Crohn’s disease are chronic inflammatory intestinal diseases with perplexing heterogeneity in disease manifestation and response to treatment. While the molecular basis for this heterogeneity remains uncharacterized, single-cell technologies allow us to explore the transcriptional states within tissues at an unprecedented resolution which could further understanding of these complex diseases. Here, we apply single-cell RNA-sequencing to human inflamed intestine and show that the largest differences among patients are present within the myeloid compartment including macrophages and neutrophils. Using spatial transcriptomics in human tissue at single-cell resolution (CosMx Spatial Molecular Imaging) we spatially localize each of the macrophage and neutrophil subsets identified by single-cell RNA-sequencing and unravel further macrophage diversity based on their tissue localization. Finally, single-cell RNA-sequencing combined with single-cell spatial analysis reveals a strong communication network involving macrophages and inflammatory fibroblasts. Our data sheds light on the cellular complexity of these diseases and points towards the myeloid and stromal compartments as important cellular subsets for understanding patient-to-patient heterogeneity.
Analyisis of our data: htmls with code and results of the analyisis of
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01_Samples_by_health: samples analyzed separately for HC and IBD -
02_Samples_together: samples analysed together
Other datasets: codes used for the different analysis in our publication
source: source codes needed for the analysis