Department of Biological Sciences, University of Delaware, Newark, DE, USA.
Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE, USA.
Methods Mol Biol. 2025;2848:37-58. doi: 10.1007/978-1-0716-4087-6_3.
Several protocols have been established for the generation of lens organoids from embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs), and other cells with regenerative potential in humans or various animal models. It is important to examine how well the regenerated lens organoids reflect lens biology, in terms of its development, homeostasis, and aging. Toward this goal, the iSyTE database (integrated Systems Tool for Eye gene discovery; https://research.bioinformatics.udel.edu/iSyTE/ ), a bioinformatics resource tool that contains meta-analyzed gene expression data in wild-type lens across different embryonic, postnatal, and adult stages, can serve as a resource for comparative analysis. This article outlines the approaches toward effective use of iSyTE to gain insights into normal gene expression in the mouse lens, enriched expression in the lens, and differential gene expression in select mouse gene-perturbation cataract/lens defects models, which in turn can be used to evaluate expression of key lens-relevant genes in lens organoids by transcriptomics (e.g., RNA-sequencing (RNA-seq), microarrays, etc.) or other downstream methods (e.g., RT-qPCR, etc.).
已经建立了几种从胚胎干细胞 (ESCs)、诱导多能干细胞 (iPSCs) 和人类或各种动物模型中具有再生潜力的其他细胞生成晶状体类器官的方案。重要的是要检查再生的晶状体类器官在其发育、动态平衡和衰老方面反映晶状体生物学的程度。为此，iSyTE 数据库（综合眼基因发现系统工具；https://research.bioinformatics.udel.edu/iSyTE/）是一个生物信息学资源工具，其中包含了不同胚胎、出生后和成年阶段野生型晶状体的元分析基因表达数据，可以作为比较分析的资源。本文概述了有效利用 iSyTE 的方法，以深入了解小鼠晶状体中的正常基因表达、晶状体中富集的表达以及在特定的小鼠基因干扰白内障/晶状体缺陷模型中的差异基因表达，这反过来又可以用于通过转录组学（例如 RNA 测序 (RNA-seq)、微阵列等）或其他下游方法（例如 RT-qPCR 等）评估关键晶状体相关基因在晶状体类器官中的表达。
