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| Status |
Public on Jun 26, 2021 |
| Title |
Generation of Human Islet Cell-Type-Specific Identity Genesets |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Generation of mature cells with stable functional identities is crucial for developing cell-based replacement therapies. Current global efforts to produce insulin-secreting beta-like cells to treat diabetes are hampered by the lack of tools to reliably assess cellular identity. We conducted a thorough single-cell transcriptomics meta-analysis to generate robust genesets defining the identity of human adult alpha-, beta-, gamma- and delta-cells. After extensive validation, we showed the efficacy of the novel genesets to define changes in islet cell identity, whether during embryonic development or in different experimental setups aimed at developing new functional glucose-responsive insulin-secreting cells, such as through pluripotent stem-cell differentiation or islet cell reprogramming protocols. Finally, we evaluated whether the perturbed metabolic conditions typical of diabetes influence islet cell identity. We observed that alpha-cells from diabetic donors exhibit an altered phenotype. In conclusion, these novel genesets represent valuable tools that robustly benchmark gain and loss in islet cell identity traits.
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| Overall design |
Human islets from 3 independent non-diabetic donors (RRID: SAMN11633049, SAMN11963659, SAMN12227196) were dissociated and labelled with cell-surface antibodies. Cells were sorted on a Moflo Astrios (Beckman Coulter) system. Populations gated as gamma- or delta-cells in 2D12 vs. 2B4 plots were further gated in a CD9 vs. FSC-H plot. For gamma-cells, all CD9+ cells were complemented to 15000 cells with CD9- cells. For delta-cells, 15000 CD9+ and FSC-HLOW cells were sorted. Each population was processed as an independent experiment using the Chromium single cell gene expression protocol v3 (10x Genomics). A median of 55000, 100bp paired-end reads per cell were sequenced using Illumina Hiseq4000. Data were mapped against the Homo sapiens transcriptome reference 38 (GRCh38) using 10x Genomics Cell Ranger v3.0.2.
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| Contributor(s) |
van Gurp L, Fodoulian L, Oropeza D, Furuyama K, Brú Tarí E, Rodríguez I, Thorel F, Herrera PL |
| Citation(s) |
34294685, 35440614 |
| Submission date |
May 17, 2020 |
| Last update date |
Apr 20, 2022 |
| Contact name |
Léon van Gurp |
| E-mail(s) |
leonvgurp@gmail.com
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| Phone |
+41 22 379 5223
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| Organization name |
University of Geneva
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| Department |
Genetic Medicine and Development
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| Lab |
group Herrera
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| Street address |
Rue Michel Servet 1
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| City |
Geneva |
| State/province |
Geneva |
| ZIP/Postal code |
1206 |
| Country |
Switzerland |
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| Platforms (1) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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| Samples (6)
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| GSM4557280 |
Single cell RNA sequencing of human pancreatic islet cells enriched for gamma and epsilon cells - donor 1 |
| GSM4557281 |
Single cell RNA sequencing of human pancreatic islet cells enriched for delta cells - donor 1 |
| GSM4557282 |
Single cell RNA sequencing of human pancreatic islet cells enriched for gamma and epsilon cells - donor 2 |
| GSM4557283 |
Single cell RNA sequencing of human pancreatic islet cells enriched for delta cells - donor 2 |
| GSM4557284 |
Single cell RNA sequencing of human pancreatic islet cells enriched for gamma and epsilon cells - donor 3 |
| GSM4557285 |
Single cell RNA sequencing of human pancreatic islet cells enriched for delta cells - donor 3 |
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| Relations |
| BioProject |
PRJNA633387 |
| SRA |
SRP262056 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE150724_Donor1_barcodes.tsv.gz |
36.1 Kb |
(ftp)(http) |
TSV |
| GSE150724_Donor1_genes.tsv.gz |
117.0 Kb |
(ftp)(http) |
TSV |
| GSE150724_Donor1_matrix.mtx.gz |
73.3 Mb |
(ftp)(http) |
MTX |
| GSE150724_Donor2_barcodes.tsv.gz |
31.7 Kb |
(ftp)(http) |
TSV |
| GSE150724_Donor2_genes.tsv.gz |
117.0 Kb |
(ftp)(http) |
TSV |
| GSE150724_Donor2_matrix.mtx.gz |
56.4 Mb |
(ftp)(http) |
MTX |
| GSE150724_Donor3_barcodes.tsv.gz |
4.7 Kb |
(ftp)(http) |
TSV |
| GSE150724_Donor3_genes.tsv.gz |
117.0 Kb |
(ftp)(http) |
TSV |
| GSE150724_Donor3_matrix.mtx.gz |
11.2 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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