PUBLICATION
Expression profiling of the retina of pde6c, a zebrafish model of retinal degeneration
- Authors
- Zhang, L., Zhang, X., Zhang, G., Pang, C.P., Leung, Y.F., Zhang, M., Zhong, W.
- ID
- ZDB-PUB-171213-14
- Date
- 2017
- Source
- Scientific data 4: 170182 (Journal)
- Registered Authors
- Keywords
- none
- Datasets
- GEO:GSE101544
- MeSH Terms
-
- Animals
- Cyclic Nucleotide Phosphodiesterases, Type 6/genetics*
- Microarray Analysis
- Retina/metabolism*
- Retinal Degeneration/genetics*
- Transcriptome
- Zebrafish
- Zebrafish Proteins/genetics*
- PubMed
- 29231925 Full text @ Sci Data
Citation
Zhang, L., Zhang, X., Zhang, G., Pang, C.P., Leung, Y.F., Zhang, M., Zhong, W. (2017) Expression profiling of the retina of pde6c, a zebrafish model of retinal degeneration. Scientific data. 4:170182.
Abstract
Retinal degeneration often affects the whole retina even though the disease-causing gene is specifically expressed in the light-sensitive photoreceptors. The molecular basis of the retinal defect 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. This retinal-degeneration model not only displays cone degeneration caused by a cone-specific mutation, but also other secondary cellular changes starting from 4 days postfertilization (dpf). To capture the underlying molecular changes, we subjected pde6c and wild-type (WT) retinas at 5 dpf/ 120 h postfertilization (hpf) to RNA sequencing (RNA-Seq) on the Illumina HiSeq 2,000 platform. We also validated the RNA-Seq results by Reverse Transcription Quantitative Polymerase Chain Reaction (RT-qPCR) of seven phototransduction genes. Our analyses indicate that the RNA-Seq dataset was of high quality, and effectively captured 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.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping