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| Status |
Public on Nov 29, 2018 |
| Title |
Modelling pancreatic beta-cell inflammation in zebrafish identifies a natural product for human beta-cell protection |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
To assess the effect of chronic inflammation on the beta-cells transcriptome, we conducted RNA-sequencing, from 3 months old zebrafish transgenic line Tg(ins:IL1B) animals and WT siblings
The total RNA from FACS sorted Beta-cells was isolated using Quick-RNA MicroPrep kit (R1050 Zymo Research) and following the manufacturer instructions. The sequencing was made on llumina HiSeq2500 in 2x75bp paired-end mode. method
Results:Two replicates for controls and two for IL1B expressing beta cells were sequenced. About 40 million sequence reads per sample were mapped to the Zebrafish genome. We identify around 19 thousand genes per sample. Approximately 6% of the genes were differentially expressed. 1,245 genes with a FDR of 5 showed a fold change ≥0.7 and adjusted p-value <0.05.
Conclusions: Hierarchical clustering by Pearson correlation of differentially expressed genes uncovered the expression of alpha-cell related genes in beta-cells. This provides a possible impairment of beta-cell identity reflected in RNA expression profiles.
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| Overall design |
Beta-cell mRNA profiles of 3 month old wild type (WT) and Tg(ins:IL1B; cryaa:mCherry) Zebrafihs, were generated by deep sequencing, in duplicate, using llumina HiSeq2500.
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| Contributor(s) |
Delgadillo-Silva L, Akhtar N, Ninov N |
| Citation(s) |
30679186 |
| |
| Submission date |
Nov 28, 2018 |
| Last update date |
Feb 18, 2019 |
| Contact name |
Luis Fernando Delgadillo Silva |
| E-mail(s) |
delgadillo.silva@gmail.com
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| Organization name |
CRTD
|
| Lab |
Ninov
|
| Street address |
Fetscherstraße 105
|
| City |
Dresden |
| ZIP/Postal code |
01307 |
| Country |
Germany |
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| Platforms (2) |
| GPL14875 |
Illumina HiSeq 2000 (Danio rerio) |
| GPL20828 |
Illumina NextSeq 500 (Danio rerio) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA507363 |
| SRA |
SRP171016 |
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