Experimental and Computational Workflow for RNA Sequencing in Mycobacterium tuberculosis : From Total RNA to Differentially Expressed Genes.
Experimental and Computational Workflow for RNA Sequencing in Mycobacterium tuberculosis : From Total RNA to Differentially Expressed Genes.
复制标题
结核分枝杆菌 RNA 测序的实验和计算工作流程：从总 RNA 到差异表达基因。
DOI：
10.1007/978-1-0716-1460-0_21
复制
发表时间：
2021
期刊：
影响因子：
--
通讯作者：
Sherman,DavidR
中科院分区：
文献类型：
--
作者：
Ma,Shuyi;JonesJr,RichardM;Gleason,NatalieS;Farrow-Johnson,Jessica;Sherman,DavidR
细菌中的RNA测序（RNAseq）已成为许多应用的变革性工具，包括鉴定致病机制，环境适应和药物反应。RNA-seq可实现的分析输出类型在很大程度上取决于样品制备、测序和数据处理步骤中的几个关键技术参数。在本章中，我们将描述将结核分枝杆菌样品加入测序文库的过程，选择合适的测序平台，并进行与基因表达定量兼容的数据处理。我们还将讨论每个参数如何影响结果。下面描述的方案产生一致的高产率。本章应告知影响测序输出的技术考虑因素，并使读者能够根据自己的实验目标决定最佳参数。
RNA sequencing (RNAseq) in bacteria has become a transformative tool for many applications, including the identification of mechanisms that contribute to pathogenesis, environmental adaptation, and drug response. The kinds of analysis outputs achievable from RNA-seq depend heavily on several key technical parameters during the sample preparation, sequencing, and data processing steps. In this chapter, we will describe the process of preparingMycobacterium tuberculosissamples into sequencing libraries, selecting the appropriate sequencing platform, and performing data processing compatible with gene expression quantification. We will also discuss how each parameter could affect outcomes. The protocols described below produce consistently high yields. This chapter should inform on the technical considerations that impact sequencing output and enable the reader to decide on the best parameters to implement based on their own experimental goals.