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Data availability
All pancreatic islet sequencing data have been uploaded to PANC-DB (https://hpap.pmacs.upenn.edu/) and the interactive session can be accessed on the cellxgene database hosted on PANC-DB (https://faryabi16.pmacs.upenn.edu/view/T1D_T2D_public.h5ad/). The raw islet sequencing data in the form of FASTQ files for each HPAP sample can be obtained from the PANC-DB database. The processed data can be downloaded in two formats, RDS or h5ad, which can be loaded for analysis using Seurat12 and Scanpy19 pipelines.
Code availability
The scripts used for data processing and analysis of the scRNA-seq data are available on GitHub (https://github.com/faryabiLab/HPAP-scRNA-seq-Workflow-2022). The cellxgene interactive tool with HPAP data can be accessed via the cellxgene database (https://faryabi16.pmacs.upenn.edu/view/T1D_T2D_public.h5ad/)
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Acknowledgements
We thank the Vahedi, Faryabi and Kaestner lab members for discussions. This work was supported by National Institute of Health grants UC4 DK112217, U01DK112217 (A.N., K.H.K., R.B.F. and G.V.), R01HL145754, U01DK127768 and U01DA052715 and awards from the Burroughs Wellcome Fund, the Chan Zuckerberg Initiative, W. W. Smith Charitable Trust, the Penn Epigenetics Institute and the Sloan Foundation (G.V.).
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Nature Metabolism thanks Yan Li and Benoit Gauthier for their contribution to the peer review of this work.
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Patil, A.R., Schug, J., Naji, A. et al. Single-cell expression profiling of islets generated by the Human Pancreas Analysis Program. Nat Metab 5, 713–715 (2023). https://doi.org/10.1038/s42255-023-00806-x
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DOI: https://doi.org/10.1038/s42255-023-00806-x