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| Status |
Public on Jun 24, 2016 |
| Title |
A single-cell transcriptome atlas of the human pancreas |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
To understand organ (dys)function it is important to have a complete inventory of its cell types and the corresponding markers that unambiguously identify these cell types. This is a challenging task, in particular in human tissues, because unique cell-type markers are typically unavailable, necessitating the analysis of complex cell type mixtures. Transcriptome-wide studies on pancreatic tissue are typically done on pooled islet material. To overcome this challenge we sequenced the transcriptome of thousands of single pancreatic cells from deceased organ donors with and without type 2 diabetes (T2D) allowing in silico purification of the different cell types. We identified the major pancreatic cell types resulting in the identification of many new cell-type specific and T2D-specific markers. Additionally we observed several subpopulations within the canonical pancreatic cell types, which we validated in situ. This resource will be useful for developing a deeper understanding of pancreatic biology and diabetes mellitus.
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| Overall design |
Human cadaveric pancreata were used to extract islets of Langerhans, which were kept in culture until single-cell dispersion and FACS sorting. Single-cell transcriptomics was performed on live cells from this mixture using CEL-seq or on cells stained for CD63, CD13, TGFBR3 or CD24 and CD44. The RaceID algorithm was used to identify clusters of cells corresponding to the major pancreatic cell types and to mine for novel cell type-specific genes as well as subpopulations within the known pancreatic cell types.
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| Contributor(s) |
Muraro MJ, Dharmadhikari G, Grün D, de Koning E, van Oudenaarden A |
| Citation(s) |
27345837 |
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| Submission date |
May 03, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Mauro Muraro |
| E-mail(s) |
m.muraro@scdiscoveries.com
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| Organization name |
Single Cell Discoveries
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| Street address |
Uppsalalaan, 8
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| City |
Utrecht |
| State/province |
Utrecht |
| ZIP/Postal code |
3584 CT |
| Country |
Netherlands |
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| Platforms (2) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (18)
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| GSM2142253 |
Donor number 10, CD63+ sorted cells |
| GSM2142254 |
Donor number 10, live sorted cells, library 1 |
| GSM2142255 |
Donor number 10, live sorted cells, library 2 |
| GSM2142256 |
Donor number 17, CD13+ sorted cells |
| GSM2142257 |
Donor number 17, CD24+ CD44+ live sorted cells |
| GSM2142258 |
Donor number 17, live sorted cells, library 1 |
| GSM2142259 |
Donor number 17, live sorted cells, library 2 |
| GSM2142260 |
Donor number 17, TGFBR3+ sorted cells |
| GSM2142261 |
Donor number 2, exocrine fraction, live sorted cells |
| GSM2142262 |
Donor number 3 live sorted cells, library 1 |
| GSM2142263 |
Donor number 3 live sorted cells, library 2 |
| GSM2142264 |
Donor number 3 live sorted cells, library 3 |
| GSM2142265 |
Donor number 3 live sorted cells, library 4 |
| GSM2142266 |
Donor number 3, exocrine fraction, live sorted cells |
| GSM2142267 |
Donor number 7 live sorted cells, library 1 |
| GSM2142268 |
Donor number 7 live sorted cells, library 2 |
| GSM2142269 |
Donor number 7 live sorted cells, library 3 |
| GSM2142270 |
Donor number 7 live sorted cells, library 4 |
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| Relations |
| BioProject |
PRJNA320424 |
| SRA |
SRP074299 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE81076_D2_3_7_10_17.txt.gz |
5.3 Mb |
(ftp)(http) |
TXT |
| GSE81076_cel-seq_barcodes.csv.gz |
424 b |
(ftp)(http) |
CSV |
| GSE81076_readme_demultiplexing_Cel-seq_data.rtf |
57.1 Kb |
(ftp)(http) |
RTF |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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