A spatial transcriptomics dataset of pancreas sections in donors with normal glucose tolerance and type 2 diabetes
Description
Understanding the spatial distribution of gene expression in the pancreas is essential for establishing the molecular basis of pancreatic function in healthy and disease contexts. The 10x Genomics Visium platform offers a robust method for quantifying gene expression within a spatial context. Here, we report spatial transcriptomic profiling from pancreas samples obtained from three donors with type 2 diabetes (T2D) and three donors with normal glucose tolerance (NGT). Our analysis identified a major technical challenge: substantial transcript bleed of highly abundant genes (e.g., INS and GCG) into adjacent tissue regions. We demonstrate that this bleed can be computationally corrected using probabilistic models. Our analysis highlights the importance of incorporating bleed-correction techniques in preprocessing of spatial transcriptomic profiling. In summary, this study provides a dataset, methods, and resources to investigate the spatial regulation of gene expression in normal and T2D-affected human pancreas.
Files
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Additional details
Related works
- Is supplement to
- Dataset: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001188.v3.p1 (URL)
- Dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE264331 (URL)