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| Status |
Public on Feb 08, 2018 |
| Title |
Transcripts within Rod Photoreceptors of the Zebrafish Retina |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Purpose: The purpose of this study was to identify transcripts of rod photoreceptors of the zebrafish, an important animal model for vision science. Methods: Zebrafish rods, and non-rod retinal cells of the XOPS:eGFP transgenic line, were separated by cell dissociation and fluorescence-activated cell sorting (FACS), followed by RNA-seq. Validation studies used qPCR and in situ hybridization. Some transcripts were examined in sorted retinal cell populations of larval and juvenile retinas and regenerated adult retinas, and in a zebrafish model for rod degeneration. Results: At a false discovery rate of <0.01, 597 transcripts were upregulated in rods vs. non-rod retinal cells, and 1032 were downregulated. 13,324 total transcripts were detected in rods, including many not previously known to be expressed by rods. Transcripts enriched in rods from adult retinas were also enriched in rods from larval and juvenile retinas, and were also enriched in regenerated rods. Many transcripts enriched in rods were upregulated in retinas of wildtype retinas vs. those of a zebrafish model for rod degeneration. Conclusions: We report the generation of an RNA-seq dataset describing the rod transcriptome of the zebrafish, which is now available as a resource for further studies of rod photoreceptor biology and comparative transcriptomics.
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| Overall design |
8 samples analyzed: 4 GFP+ (FACS-sorted rods), 4 GFP- (FACS-sorted non-rods from retina); the two retinas from each of four fish contributed to each sample.
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| Contributor(s) |
Stenkamp DL, Sun C |
| Citation(s) |
29422031 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 EY012146 |
Patterning Genes in Retinal Development |
UNIVERSITY OF IDAHO |
Deborah L Stenkamp |
| R21 EY026814 |
Synapses in Regenerated Retina |
UNIVERSITY OF IDAHO |
Deborah L Stenkamp |
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| |
| Submission date |
Jun 15, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Deborah Lynn Stenkamp |
| E-mail(s) |
dstenkam@uidaho.edu
|
| Phone |
208-885-8963
|
| Organization name |
University of Idaho
|
| Department |
Biological Sciences
|
| Street address |
875 Perimeter Drive, MS 3051
|
| City |
Moscow |
| State/province |
Idaho |
| ZIP/Postal code |
83844-3051 |
| Country |
USA |
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| Platforms (1) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA390613 |
| SRA |
SRP109268 |
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