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| Status |
Public on Jun 12, 2018 |
| Title |
Tbx5 paralogues during zebrafish development |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: The goals of this study were to compare the effect on the transcriptome of loss of the Tbx5 paralogues in zebrafish.
Methods: Whole embryos were injected with morpholinos targetting either Tbx5a, Tbx5b, or both at the single cell stage. At either 18 or 21 hpf, embryos were pooled and RNA was extracted from the whole embryo. Transcriptomes were generated using Illumina HiSeq 2500.
Results: The preliminary experiment produced 632 million reads and a list of 494 differentially expressed genes (detected using Cuffdiff), of which 454 were unique. This final triplicate sequencing gave 309.4 million reads. When using Cuffdiff to produce differential gene expression lists, a list of 162 differentially expressed genes were identified.
Conclusions: This study is a detailed analysis of the different transcriptomes of zebrafish deficient in the Tbx5 paralogues and the differential gene expression that occurs as a result of downregulation of the paralogues, both individually and separately.
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| Overall design |
Whole embryo RNA sequencing of pooled zebrafish embryos at 18hpf and 21hpf in wildtype, Tbx5a- and Tbx5b-deficient embryos.
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| Contributor(s) |
Boyle Anderson EA, Ho RK |
| Citation(s) |
30532148 |
| |
| Submission date |
Jun 11, 2018 |
| Last update date |
Dec 12, 2018 |
| Contact name |
Erin A Boyle Anderson |
| Organization name |
University of Chicago
|
| Department |
Committee on Development, Regeneration and Stem Cell Biology
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| Lab |
Ho lab
|
| Street address |
1057 E 57th St
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL18413 |
Illumina HiSeq 2500 (Danio rerio) |
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| Samples (30)
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| Relations |
| BioProject |
PRJNA475603 |
| SRA |
SRP150270 |
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