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| Status |
Public on Jul 18, 2017 |
| Title |
Expression profiling of the retina of pde6c, a zebrafish model of retinal degeneration |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Retinal degeneration often affects the whole retina even though the disease-causing gene is specifically expressed in the light-sensitive photoreceptors. These retinal defects can potentially be determined by gene-expression profiling of the whole retina. In this study, we measured the gene-expression profile of retinas microdissected from a zebrafish pde6cw59 (pde6c) mutant. Its retinas display not only photoreceptor degeneration but also issues in other cell types starting from 4 days postfertilization (dpf). To capture these initial changes, we subjected pde6c and wild-type (WT) retinas at 5 dpf to RNA sequencing (RNA-Seq) on the Illumina HiSeq 2000 platform. The sequencing analyses indicate that the RNA-Seq dataset was of high quality. We also validated the RNA-Seq results by Reverse Transcription Quantitative Polymerase Chain Reaction (RT-qPCR) of seven phototransduction genes. We found that the fold changes of these genes measured by RT-qPCR highly correlated to those measured by RNA-Seq. Therefore, our RNA-Seq dataset likely captures the molecular changes in the whole pde6c retina. This dataset will facilitate the characterization of the molecular defects in the pde6c retina at the initial stage of retinal degeneration
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| Overall design |
3 samples of pde6c mutant and 3 samples of wild type animals are analyzed.
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| Contributor(s) |
Zhang L, Zhang X, Zhang G, Pang CP, Leung YF, Zhang M, Zhong W |
| Citation(s) |
29231925 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 GM113242 |
Novel statistical tools for cell line specific epigenetic analysis |
UNIVERSITY OF GEORGIA RESEARCH FOUNDATION, INC |
Wenxuan Zhong |
| R01 GM122080 |
Deciphering the Regulatory Role of Small RNAs on Alternative Splicing |
UNIVERSITY OF GEORGIA RESEARCH FOUNDATION, INC |
PING MA |
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| Submission date |
Jul 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Nadejda Beliakova-bethell |
| Organization name |
University of California San Diego
|
| Street address |
9500 Gilman Dr, La Jolla
|
| City |
San Diego |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platforms (1) |
| GPL14875 |
Illumina HiSeq 2000 (Danio rerio) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA394760 |
| SRA |
SRP112616 |
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