High-throughput RNA-sequencing-based transcriptomic profiles of embryonic lens development for cataract gene discovery

We applied previously established in silico whole-embryo body (WB)-subtraction-based approach to identify "lens-enriched" genes. These new RNA-seq datasets on embryonic stages E10.5, E12.5, E14.5 and E16.5 confirmed high expression of established cataract-linked genes and identified several new potential regulators in the lens. Finally, we present lens stage-specific UCSC Genome Brower annotation-tracks; these are publicly accessible through iSyTE (https://research.bioinformatics.udel.edu/iSyTE/) and enable a user-friendly visualization of lens gene expression/enrichment to help prioritize genes from high-throughput data from cataract cases. RNA-sequencing datasets of microdissected embyonic eye lens samples from stages embryonic day E10.5, E12.5, E14.5 and E16.5 were generated. To estimate lens enriched genes we generated control "whole-embryo body (WB)" datasets. The lens enriched genes were used for enrichment level based clustering to identify gene clusters exhibiting distinct lens enrichment patterns across E10.5 to E16.5 developmental window. This new lens RNA-seq data and its accessibility through iSyTE 2.0 serves as a new integrative resource for prioritization of lens defects and/or cataract-linked candidate genes identified by other high-throughput analyses such as exome-seq and GWAS.我们采用此前已建立的基于计算机模拟（in silico）全胚胎体（whole-embryo body, WB）消减的方法，以鉴定"晶状体富集基因"。本研究针对胚胎发育阶段E10.5、E12.5、E14.5及E16.5的样本生成了全新的RNA测序（RNA-seq）数据集，验证了已报道的与白内障相关基因的高表达情况，并鉴定出若干全新的晶状体潜在调控因子。最后，我们提供了晶状体发育阶段特异性的UCSC基因组浏览器（UCSC Genome Browser）注释轨道；这些资源可通过iSyTE（https://research.bioinformatics.udel.edu/iSyTE/）公开获取，能够以友好的用户界面可视化展示晶状体基因的表达/富集情况，助力从白内障病例的高通量数据中筛选优先候选基因。本研究生成了取自胚胎发育日E10.5、E12.5、E14.5及E16.5阶段的显微切割胚胎眼晶状体样本的RNA测序数据集。为评估晶状体富集基因，我们同时构建了对照的"全胚胎体（whole-embryo body, WB）"数据集。我们基于富集水平对晶状体富集基因进行聚类分析，以鉴定出在E10.5至E16.5的发育窗口内呈现独特晶状体富集模式的基因簇。这套全新的晶状体RNA测序数据及其通过iSyTE 2.0的开放获取渠道，将作为一套全新的整合资源，用于对通过其他高通量分析（如exome-seq、GWAS）鉴定出的晶状体缺陷或白内障相关候选基因进行优先级筛选。