MicroRNA-sequencing from the striatum of ELAVL4 (HuD) KO mice and wild type littermate adult mice

Purpose: The goals of this study are to determine how deletion of the RNA-binding protein HuD affects the levels of microRNAs in the striatum of Elav4 (HuD) KO using miRNA-seq Methods: Total RNA from striatum of male adult Elavl4 (HuD) KO and wild-type (WT) littermates (n=3 per genotype) crossbred to C57Bl/6 for more than 10 generations were analyzed by small RNA sequencing, in triplicate, using an Illumina NextSeq platorm. The percentage of the number of bases with Q >30 for all 6 samples were >93%. Results: Using an optimized data analysis workflow (see diagram below), about 6.3 million sequence reads per HuD KO sample and 3.3 million per WT sample were mapped miRBase v22. The expression level (Reads count) of miRNAs were calculated using miRDeep2. The number of identified miRNA per group was calculated based on the mean of CPM in group > 1. Conclusions: We found 309 miRNAs from 54 unique families (FC>1.75- and p<0.05) were significantly upregulated while 161 miRNAs from 143 unique families (FC<0.55 and p<0.05) were significantly downregulated in the striatum of HuD KO mice vs WT samples. Striatal miRNA profiles of adult male wild type (WT) and Elavl4 -/- (HuD KO) mice研究目的：本研究旨在通过微小RNA测序（miRNA-seq）技术，探究RNA结合蛋白HuD的敲除对Elavl4（HuD）敲除（KO）小鼠纹状体中微小RNA（miRNAs）表达水平的影响。 实验方法：选取经与C57Bl/6小鼠回交超过10代的成年雄性Elavl4（HuD）敲除（KO）小鼠及其同窝野生型（WT）仔鼠（每个基因型组n=3），提取其纹状体总RNA，采用Illumina NextSeq测序平台进行三次重复小RNA测序。所有6个样本的碱基质量值Q>30的占比均超过93%。 实验结果：采用优化后的数据分析流程（详见下图），HuD KO组每个样本约630万条测序读段、WT组每个样本约330万条测序读段均可比对至miRBase v22数据库。使用miRDeep2软件计算微小RNA的表达水平（读段计数）。每组中鉴定到的微小RNA数量以该组每百万读段计数（CPM）的平均值大于1为标准进行统计。 实验结论：与WT样本相比，HuD KO小鼠纹状体中共有309个来自54个独特家族的微小RNA表达显著上调（折叠变化FC>1.75且P<0.05），161个来自143个独特家族的微小RNA表达显著下调（FC<0.55且P<0.05）。本数据集涵盖成年雄性野生型（WT）及Elavl4^-/-（HuD KO）小鼠的纹状体微小RNA表达谱。