RNA-Seq transcriptome analysis of whole newborn lenses from FVB/N, Le-Cre and P0-3.9GFPCre mice

Here we report RNA-Seq data from RNA isolated from newborn lenses from FVB/N control mice as well as from newborn lenses of two different transgenic mouse lines (Le-Cre and P0-3.9GFPCre). Sequence reads of 51 bp were obtained from an illumine HiSeq 2000 system and mapped to the C57BL/6 reference genome (assembly GRCm38 (mm10)) using GSNAP software. Adapters and poor-quality regions were trimmed using Trimmomatic-0.36 software. Gene and isoform abundance was quantified using RSEM-1.3.0 software. Differential expression analysis was completed using DESeq2-1.10.1 software. For differential expression we used a cutoff value of equal to or greater than 1.5-fold change with an adjusted p value ≤ 0.05. The transcriptomes of both Le-Cre and P0-3.9GFPCre lenses closely matched the FVB/N control lenses. However, Le-Cre lenses exhibited deregulation of 15 murine genes, several of which are associated with apoptosis. In contrast, P0-3.9GFPCre lenses only deregulated two murine genes. Lens mRNA profiles of newborn wild type FVB/N strain, Le-Cre and P0-3.9GFPCre mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.

本研究报道了来自FVB/N对照小鼠新生晶状体，以及两种不同转基因小鼠品系（Le-Cre与P0-3.9GFPCre）新生晶状体中提取的RNA对应的RNA测序（RNA-Seq）数据。研究采用Illumina HiSeq 2000测序平台获取了51 bp的测序读段，使用GSNAP软件将读段比对至C57BL/6参考基因组（组装版本GRCm38（mm10））；通过Trimmomatic-0.36软件对测序接头与低质量区域进行剪切过滤；利用RSEM-1.3.0软件对基因及其转录本亚型的表达丰度进行定量分析；并采用DESeq2-1.10.1软件完成差异表达分析。本研究设置的差异表达筛选阈值为：表达变化倍数≥1.5倍，校正后P值≤0.05。结果显示，Le-Cre与P0-3.9GFPCre转基因小鼠的晶状体转录组均与FVB/N对照小鼠的晶状体转录组高度相似。但Le-Cre转基因小鼠的晶状体中存在15个小鼠基因的表达失调，其中多个基因与细胞凋亡相关；相比之下，P0-3.9GFPCre转基因小鼠的晶状体中仅存在2个小鼠基因的表达失调。本研究采用Illumina HiSeq 2000平台，对新生野生型FVB/N品系、Le-Cre及P0-3.9GFPCre小鼠的晶状体mRNA进行了深度测序，每组设置3次生物学重复。