Single cell expression map of pancreatic islets using data from HPAP, IIDP and Prodo v3.4

Single Cell Expression Map of Pancreatic Islets (v3.4)

Dataset ID: islet_of_Langerhans_scRNA_v3-4
Source: PanKbase  
Tissue: Islet of Langerhans  
Species: Human (Homo sapiens)  
Platform: 10x Genomics  
Total Cells: 448,935  

Summary

This dataset represents a curated and integrated single-cell RNA sequencing map of the human islet of Langerhans, derived from samples contributed by HPAP, IIDP, and Prodo. It provides insights into pancreatic islet biology and includes metadata annotations across age, sex, and disease state (diabetes).

File Description

- RDS file containing the Seurat object with integrated expression and metadata.

Secondary Citations and Source Acknowledgments

This work used data acquired from the [Human Pancreas Analysis Program (HPAP)](https://hpap.pmacs.upenn.edu/) (RRID:SCR_016202), supported by the Human Islet Research Network (HIRN; RRID:SCR_014393), with funding from:
- UC4-DK112217  
- U01-DK123594  
- UC4-DK112232  
- U01-DK123716

Related Publications:
- PMID: 31127054
- PMID: 36206763
- PMID: 35228745
- PMID: 37188822

Additional islet samples and tissues were provided by the Integrated Islet Distribution Program (IIDP) (RRID:SCR_014387), funded by NIH Grant #2UC4DK098085.

Data from the following studies were used:

1] S. N. Shapira, A. Naji, M. A. Atkinson, A. C. Powers, and K. H. Kaestner, "Understanding islet dysfunction in type 2 diabetes through multidimensional pancreatic phenotyping: The Human Pancreas Analysis Program," Cell Metab., vol. 34, no. 12, pp. 1906–1913, Dec. 2022, doi: 10.1016/j.cmet.2022.09.013.
[2]    K. H. Kaestner, A. C. Powers, A. Naji, HPAP Consortium, and M. A. Atkinson, "NIH Initiative to Improve Understanding of the Pancreas, Islet, and Autoimmunity in Type 1 Diabetes: The Human Pancreas Analysis Program (HPAP)," Diabetes, vol. 68, no. 7, pp. 1394–1402, Jul. 2019, doi: 10.2337/db19-0058.
[3]    A. R. Patil, J. Schug, A. Naji, K. H. Kaestner, R. B. Faryabi, and G. Vahedi, "Single-cell expression profiling of islets generated by the Human Pancreas Analysis Program," Nat. Metab., vol. 5, no. 5, pp. 713–715, May 2023, doi: 10.1038/s42255-023-00806-x.
[4]    M. Fasolino et al., "Single-cell multi-omics analysis of human pancreatic islets reveals novel cellular states in type 1 diabetes," Nat. Metab., vol. 4, no. 2, pp. 284–299, Feb. 2022, doi: 10.1038/s42255-022-00531-x.
[5]    B. Marquina-Sanchez et al., "Single-cell RNA-seq with spike-in cells enables accurate quantification of cell-specific drug effects in pancreatic islets," Genome Biol., vol. 21, no. 1, p. 106, Dec. 2020, doi: 10.1186/s13059-020-02006-2.
[6]    X. Tang et al., "SARS-CoV-2 infection induces beta cell transdifferentiation," Cell Metab., vol. 33, no. 8, pp. 1577-1591.e7, Aug. 2021, doi: 10.1016/j.cmet.2021.05.015.
[7]    S. Shrestha et al., "Combinatorial transcription factor profiles predict mature and functional human islet α and β cells," JCI Insight, vol. 6, no. 18, p. e151621, Sep. 2021, doi: 10.1172/jci.insight.151621.
[8]    G. Basile et al., "Excess pancreatic elastase alters acinar-β cell communication by impairing the mechano-signaling and the PAR2 pathways," Cell Metab., vol. 35, no. 7, pp. 1242-1260.e9, Jul. 2023, doi: 10.1016/j.cmet.2023.05.007.
[9]    W. Xu et al., "Architecture of androgen receptor pathways amplifying glucagon-like peptide-1 insulinotropic action in male pancreatic β cells," Cell Rep., vol. 42, no. 5, p. 112529, May 2023, doi: 10.1016/j.celrep.2023.112529.
[10]    R. B. Kang et al., "Single-nucleus RNA sequencing of human pancreatic islets identifies novel gene sets and distinguishes β-cell subpopulations with dynamic transcriptome profiles," Genome Med., vol. 15, no. 1, p. 30, May 2023, doi: 10.1186/s13073-023-01179-2.
[11]    K. Bandesh et al., "Single-cell decoding of human islet cell type-specific alterations in type 2 diabetes reveals converging genetic- and state-driven β-cell gene expression defects," Jan. 22, 2025, Genomics. doi: 10.1101/2025.01.17.633590.
[12]    J. S. Stancill, M. Y. Kasmani, W. Cui, and J. A. Corbett, "Single Cell RNAseq Analysis of Cytokine-Treated Human Islets: Association of Cellular Stress with Impaired Cytokine Responsiveness," Function, vol. 5, no. 4, p. zqae015, Jul. 2024, doi: 10.1093/function/zqae015.
[13]    E. K. Sokolowski et al., "Multi-omic human pancreatic islet endoplasmic reticulum and cytokine stress response mapping provides type 2 diabetes genetic insights," Cell Metab., vol. 36, no. 11, pp. 2468-2488.e7, Nov. 2024, doi: 10.1016/j.cmet.2024.09.006.

License

CC-BY 4.0 International

Citation

Please cite this dataset using the DOI generated by Zenodo, all the Source Acknowledgment grants listed above, and the 13 primary studies that generated the data.