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| Status |
Public on Feb 10, 2017 |
| Title |
Trancriptome study of zebrafish mutant fn10a |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We conducted functional analysis on zebrafish mutant fn10a by polyA+, 100bp paired end, strand-specific RNA-seq. By comparing the transcriptome of fn10a mutants and their wildtype siblings or wildtype controls, we revealed a transcriptome-wide RNA splicing deficiency and a large amount of intron-retaining transcripts, which resulted in compromised nonsense-mediated RNA decay and activation of the p53 pathway in fn10a mutants. 2 biological replicates were performed to consolidate the findings. We also conducted subcellular RNA-seq between fn10a mutants and wildtype siblings, to investigate the localization of intron retaining transcripts.
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| Overall design |
The wild-type control group (WT-control group) of 36-hpf embryos was generated from mating crosses between wild-type TL zebrafish, while fn10a mutants (mutant group) and siblings (WT-sibling group) were generated from mating crosses of fn10a heterozygote zebrafish. RNA-seq of 36hpf embryos for fn10a mutants, their wildtype siblings and wildtype TL. RNA-seq of cytoplasm RNA and nuclear RNA from 36hpf embryos for fn10a mutants and their wildtype siblings.
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| Contributor(s) |
Li C, Xiong J, Yan S |
| Citation(s) |
27899647 |
| Submission date |
Feb 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Shouyu Yan |
| E-mail(s) |
Yan.Shouyu@gmail.com
|
| Organization name |
Peking University
|
| Department |
Institution of Molecular Medicine
|
| Street address |
5#, Yiheyuan Road
|
| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platforms (1) |
| GPL14875 |
Illumina HiSeq 2000 (Danio rerio) |
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| Samples (10)
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| Relations |
| BioProject |
PRJNA312615 |
| SRA |
SRP070566 |
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