Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA.
Department of Statistics, University of Georgia, 101 Cedar St, Athens, GA 30602, USA.
Sci Data. 2017 Dec 12;4:170182. doi: 10.1038/sdata.2017.182.
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 pde6c (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.
视网膜变性通常会影响整个视网膜，尽管致病基因是特异性地在光敏感的光感受器中表达的。整个视网膜的基因表达谱分析可以确定视网膜缺陷的分子基础。在这项研究中，我们测量了从斑马鱼 pde6c（pde6c）突变体中分离的视网膜的基因表达谱。这种视网膜变性模型不仅显示出由特定于视锥细胞的突变引起的视锥细胞变性，而且还显示出其他从受精后 4 天（dpf）开始的次级细胞变化。为了捕获潜在的分子变化，我们将 pde6c 和野生型（WT）视网膜在受精后 5 天/ 120 小时（hpf）时进行 RNA 测序（RNA-Seq）在 Illumina HiSeq 2000 平台上。我们还通过反转录定量聚合酶链反应（RT-qPCR）验证了七个光转导基因的 RNA-Seq 结果。我们的分析表明，RNA-Seq 数据集质量很高，有效地捕获了整个 pde6c 视网膜的分子变化。该数据集将有助于在视网膜变性的初始阶段对 pde6c 视网膜的分子缺陷进行表征。
