RNA sequencing facilitates quantitative analysis of siRNA circHIPK2 transfected neural stem cells and siRNA circCon transfected neural stem cells transcriptomes

We report the application of Illumina paired-end RNA-seq approach for transcriptome of siRNA circHIPK2 transfected neural stem cells and siRNA circCon transfected neural stem cells . By removing sequence-dependent bias and amplification noise using UMI-tools. The mapped reads of each sample were assembled using StringTie. After the final transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. By obtaining a total of million paired-end reads of sequence from neural stem cells , we generated transcriptome profiles of siRNA circHIPK2 transfected neural stem cells and siRNA circCon transfected neural stem cells , respectively. We found 201 differentially expressed genes (DEGs) between siRNA circHIPK2 transfected neural stem cells and siRNA circCon transfected neural stem cells. This study provides a detailed analysis of the underlying mechanisms of stroke，such as neuronal injury and long-term effect, generated by RNA-seq technology.

本研究报告了Illumina双端RNA测序（Illumina paired-end RNA-seq）技术在转染靶向circHIPK2的小干扰RNA（siRNA circHIPK2）的神经干细胞，以及转染对照小干扰RNA（siRNA circCon）的神经干细胞的转录组分析中的应用。本研究通过UMI工具（UMI-tools）去除序列依赖性偏差与扩增噪声，随后使用StringTie软件对每个样本的比对序列读段进行组装。在最终转录组构建完成后，结合StringTie与edgeR软件包估算所有转录本的表达水平。通过从神经干细胞中获取总计百万条双端序列读段，本研究分别构建了转染siRNA circHIPK2的神经干细胞与转染siRNA circCon的神经干细胞的转录组谱。本研究在两组转染细胞间筛选得到201个差异表达基因（differentially expressed genes, DEGs）。本研究借助RNA测序技术，对脑卒中的潜在发病机制——包括神经元损伤与远期效应——展开了详尽分析。