High-throughput RNA sequencing analysis of human nasopharyngeal carcinoma cell line HK1 transfected with E2F1 siRNA or E2F3 siRNA

Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are using RNA sequencing analysis to evaluate the effects of si-E2F1 (or E2F3) on the mRNA of human nasopharyngeal carcinoma cell line HK1. Methods: Human nasopharyngeal carcinoma cell line HK1 was transfected with a control non-targeting siRNA to cells or transfected with siRNA targeting E2F1 (or E2F3) for 48 hours in DMEM medium (with 10% serum). Total RNA were extracted and detected by Illumina high-throughput RNA sequencing data analysis. 3 independent biological replicates were plated, transfected in parallel for each control and siRNA. Results: Log-fold changes of up- or down-regulated mRNAs between the control and experiment group were selected with a significance threshold of p<0.05. Conclusions: Our study describes the mRNA changes of human nasopharyngeal carcinoma cell line HK1 transfected with E2F1 (or E2F3) siRNA. Overall design: Human nasopharyngeal carcinoma cell line HK1 mRNA profiles of “control” (cells was transfected with a control non-targeting siRNA) and “si-E2F1”(cells was transfected with E2F1 siRNA) and “si-E2F3”(cells was transfected with E2F3 siRNA) were generated by RNA sequecning, using Illumina high-throughput sequencing service (Microanaly, Shanghai, China).

研究目的：下一代测序（Next-generation sequencing, NGS）已彻底革新了基于系统生物学视角的细胞通路分析。本研究旨在通过RNA测序分析，评估si-E2F1（或E2F3）对人鼻咽癌细胞系HK1的mRNA表达的影响。
实验方法：将人鼻咽癌细胞系HK1分为三组，分别转染对照非靶向小干扰RNA（small interfering RNA, siRNA）、靶向E2F1或E2F3的siRNA，于含10%胎牛血清的DMEM培养基中培养48小时。随后提取总RNA，采用Illumina高通量RNA测序技术进行数据分析与检测。每组设置3次独立生物学重复，对照与各siRNA转染组均平行开展实验。
实验结果：筛选对照组与实验组间差异上调、下调mRNA的对数倍数变化值，设定显著性阈值为p<0.05。
研究结论：本研究揭示了转染E2F1（或E2F3）siRNA的人鼻咽癌细胞系HK1的mRNA表达变化特征。
整体实验设计：以人鼻咽癌细胞系HK1为研究模型，分别设置对照组（转染对照非靶向siRNA）、si-E2F1组（转染E2F1靶向siRNA）与si-E2F3组（转染E2F3靶向siRNA），通过位于中国上海的Microanaly公司提供的Illumina高通量测序服务完成RNA测序，获取各组的mRNA表达谱。