Transcriptome Analysis of HMGB1 knock-out iSLK BAC16 cell (2)

Purpose: RNA sequencing (RNA-seq) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis. In addition, we have already registered the transcriptome analysis results of HMGB1 KO iSLK BAC16 cell in GSE157275, and this registration is to reproduce it. Overall design: HMGB1 WT or KO iSLK BAC16 cells transcriptome were analyzed by RNA seq. cells were or were not induced KSHV lytic replication with doxycycline and sodium butyrate.研究目的：RNA测序（RNA-seq）已彻底革新了基于系统生物学的细胞通路分析研究。本研究旨在对比新一代测序（Next-Generation Sequencing, NGS）来源的转录组谱分析（RNA-seq）技术与微阵列、定量反转录聚合酶链反应（quantitative reverse transcription polymerase chain reaction, qRT–PCR）技术，并优化适用于高通量数据分析的实验方案。此外，我们已将高迁移率族蛋白B1（High Mobility Group Box 1, HMGB1）敲除的iSLK BAC16细胞的转录组分析结果提交至GSE157275数据集，本次数据提交旨在复现该研究成果。 整体实验设计：本研究通过RNA测序分析HMGB1野生型（wild type, WT）或敲除（knock out, KO）的iSLK BAC16细胞的转录组；部分细胞经多西环素（doxycycline）与丁酸钠（sodium butyrate）诱导卡波西肉瘤相关疱疹病毒（Kaposi's sarcoma-associated herpesvirus, KSHV）裂解性复制，其余细胞未作诱导处理。