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| Status |
Public on Dec 26, 2018 |
| Title |
RNA profiling of the liver and gut tissues in zebrafish (Danio rerio) [mRNA] |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Compared to other fish models, miRNAs are currently most extensively studied and identified in zebrafish. Approximately 415 dre-miRNAs have been identified and several articles have studied some aspect of miRNA function in zebrafish such as their role in basic development and in disease pathways. However, this field of research is in its infancy and the function of several dre-miRNAs, as well as their tissue-specific expression profile, are yet to be defined. In this study, the liver and gut were dissected (wildtype/untreated fish), total and small RNA were extracted, mRNA and miRNA libraries constructed and subjected to high throughput sequencing (HTS) using standard approaches. We carried out differential expression (DE) analysis and compared liver miRNA expression to gut using established bioinformatics pipelines. Through bioinformatics analysis, known and putative novel miRNAs were identified. Finally, we constructed a “miRNA matrix” that connects both total RNA-Seq and miRNA-Seq.
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| |
|
| Overall design |
Examination of transcriptome in an in vivo model organism in two defined tissues, liver and gut.
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| |
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| Contributor(s) |
Ludivine R, Hardiman G |
| Citation(s) |
30386173 |
| Submission date |
Dec 22, 2017 |
| Last update date |
Mar 26, 2021 |
| Contact name |
Gary Hardiman |
| E-mail(s) |
hardiman@musc.edu, g.hardiman@qub.ac.uk, glen@musc.edu
|
| Organization name |
Medical University of South Carolina
|
| Department |
Medicine
|
| Street address |
135 Cannon Street
|
| City |
Charleston |
| State/province |
SC |
| ZIP/Postal code |
SC |
| Country |
USA |
| |
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| Platforms (1) |
| GPL14875 |
Illumina HiSeq 2000 (Danio rerio) |
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| Samples (4)
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| This SubSeries is part of SuperSeries: |
| GSE108437 |
RNA profiling of the liver and gut tissues in zebrafish (Danio rerio) |
|
| Relations |
| BioProject |
PRJNA427283 |
| SRA |
SRP127390 |
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