Effect of Phb2 depletion in retinal photoreceptors on gene expression in the bulk retina of C57BL/6J mice

To explore the functions for Phb2 gene in early retinal degeneration, we performed RNA-seq analysis on the bulk retinas from control and photoreceptor-specific knockout Phb2 mice at 6 weeks of age. Compared with control mice, there were 778 differentially expressed genes (log2 |fold change|> 1, log10 adjusted p-values < 0.05) identified to be associated with distinct biological processes. 585 genes were significantly upregulated and 192 genes were significantly downregulated in photoreceptor cell-specific knockout Phb2 mice. The KEGG pathways analysis of up-regulated and down-regulated genes and ranking the enrichment pathways according to the corrected p-value.To explore the critical signaling pathways that might be affected by knockout Phb2 in retinal photoreceptors, we performed RNA-seq analysis on 6-week-old C57BL/6J photoreceptor cell-specific knockout Phb2 mice and control mice. Compared with control mice, there were 778 differentially expressed genes (log2 |fold change|> 1, log10 adjusted p-values < 0.05) identified to be associated with distinct biological processes. 585 genes were significantly upregulated and 192 genes were significantly downregulated in photoreceptor cell-specific knockout Phb2 mice. The KEGG pathways analysis of up-regulated and down-regulated genes and ranking the enrichment pathways according to the corrected p-value. retina were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.RNA libraries were prepared for sequencing using standard Illumina protocols为探究Phb2基因在视网膜早期退行性病变中的功能，我们对6周龄对照组小鼠及光感受器细胞特异性敲除Phb2小鼠的全视网膜开展了RNA测序（RNA-seq）分析。与对照组小鼠相比，本研究共鉴定得到778个差异表达基因（log₂|折叠变化|>1，log₁₀校正P值<0.05），这些基因与多种不同的生物学过程密切相关。在光感受器细胞特异性敲除Phb2小鼠中，共有585个基因显著上调，192个基因显著下调。我们针对上调及下调基因开展了京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes，KEGG）通路富集分析，并基于校正后的P值对富集通路进行排序。 为探究视网膜光感受器细胞中Phb2敲除可能影响的关键信号通路，我们对6周龄C57BL/6J品系光感受器细胞特异性敲除Phb2小鼠及对照组小鼠开展了RNA测序分析。与对照组小鼠相比，本研究共鉴定得到778个差异表达基因（log₂|折叠变化|>1，log₁₀校正P值<0.05），这些基因与多种不同的生物学过程密切相关。在光感受器细胞特异性敲除Phb2小鼠中，共有585个基因显著上调，192个基因显著下调。我们针对上调及下调基因开展了KEGG通路富集分析，并基于校正后的P值对富集通路进行排序。 实验过程中，我们摘取小鼠视网膜，置于干冰上快速冷冻后，使用Trizol试剂提取总RNA；取1 μg总RNA，采用Illumina TruSeq RNA样本制备试剂盒构建测序文库，测序文库的制备严格遵循Illumina标准实验流程。