HCA Data Explorer

A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure

Updated August 31, 2022

Although the function of the mammalian pancreas hinges on complex interactions of distinct cell types, gene expression profiles have primarily been described with bulk mixtures. Here we implemented a droplet-based, single-cell RNA-seq method to determine the transcriptomes of over 12,000 individual pancreatic cells from four human donors and two mouse strains. Cells could be divided into 15 clusters that matched previously characterized cell types: all endocrine cell types, including rare epsilon-cells; exocrine cell types; vascular cells; Schwann cells; quiescent and activated stellate cells; and four types of immune cells. We detected subpopulations of ductal cells with distinct expression profiles and validated their existence with immuno-histochemistry stains. Moreover, among human beta- cells, we detected heterogeneity in the regulation of genes relating to functional maturation and levels of ER stress. Finally, we deconvolved bulk gene expression samples using the single-cell data to detect disease-associated differential expression. Our dataset provides a resource for the discovery of novel cell type-specific transcription factors, signaling receptors, and medically relevant genes.

Allon M KleinHarvard Medical Schoolallon_klein@hms.harvard.edu
Douglas A MeltonHarvard Universitydmelton@harvard.edu
Itai YanaTechnion - Israel Institute of Technologyitai.yanai@nyumc.org
Maayan Baron1
Adrian Veres2
Samuel L Wolock3
Aubrey L Faust2
Renaud Gaujoux1
Amedeo Vetere4
Jennifer Hyoje Ryu2
Bridget K Wagner4
Shai S Shen-Orr1
Allon M Klein3
Douglas A Melton2
Itai Yana1
1Technion - Israel Institute of Technology
2Harvard University
3Harvard Medical School
4Broad Institute
Mallory Ann Freeberg

To reference this project, please use the following link:

https://explore.data.humancellatlas.org/projects/f86f1ab4-1fbb-4510-ae35-3ffd752d4dfc
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Analysis Portals

UCSC Cell BrowserUCSC Cell Browser

Project Label

HumanMousePancreas

Species

2 species

Sample Type

specimens

Anatomical Entity

pancreas

Organ Part

Unspecified

Selected Cell Types

pancreatic PP cell

Disease Status (Specimen)

Unspecified

Disease Status (Donor)

2 disease statuses

Development Stage

3 development stages

Library Construction Method

inDrop

Nucleic Acid Source

single cell

Paired End

true

File Format

3 file formats

Cell Count Estimate

12.4k

Donor Count

14
fastq.gz38 file(s)tar1 file(s)xlsx1 file(s)