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| Status |
Public on Dec 31, 2021 |
| Title |
Transcriptional profiling of pancreatic somatostatin and beta-cells from zebrafish [scRNA-seq] |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Pancreas contains a collection of different types of endocrine cells. Each endocrine cell secretes a specific hormone. Using reporter lines for two hormones, insulin and somatostatin1.1, we observe the presence of bi-hormonal cells in zebrafish pancreas. To characterize the cells at transcriptional level, we performed next-generation RNA-Sequencing on FACS sorted cells expressing sst1.1, ins, or both sst1.1 and ins.
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| Overall design |
We used fluorescence-activated cell sorting (FACS) coupled with next generation RNA-Sequencing to profile sst1.1+ somatostatin, ins+ beta- and sst1.1+ ins+ cells from 30 dpf animals. Cells were sorted directly into lysis buffer and cDNA prepared using Smart-Seq2. Sequencing was performed on llumina NextSeq500. Reads were splice-aligned to the zebrafish genome, GRCz11, using HISAT2. Featurecounts was used to assign reads to exons thus eventually getting counts per gene.
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| Contributor(s) |
Singh SP |
| Citation(s) |
35088828 |
| |
| Submission date |
Jun 17, 2020 |
| Last update date |
Apr 01, 2022 |
| Contact name |
Sumeet Pal Singh |
| E-mail(s) |
sumeetpalsingh@gmail.com
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| Phone |
+32-473-125019
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| Organization name |
ULB
|
| Department |
IRIBHM
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| Lab |
Regeneration and Stress Biology
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| Street address |
Route de Lennik 808, Anderlecht
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| City |
Brussels |
| ZIP/Postal code |
1070 |
| Country |
Belgium |
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| Platforms (1) |
| GPL20828 |
Illumina NextSeq 500 (Danio rerio) |
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| Samples (186)
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| This SubSeries is part of SuperSeries: |
| GSE152697 |
Transcriptional profiling of pancreatic somatostatin and beta-cells from zebrafish |
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| Relations |
| BioProject |
PRJNA640143 |
| SRA |
SRP267693 |
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