计算生物学
转录组
生物
基因
转录因子
基因表达谱
基因表达
生物信息学
抄写(语言学)
小桶
RNA序列
DNA微阵列
基因调控网络
微阵列分析技术
核糖核酸
生物信息学
基因表达调控
微阵列
系统生物学
计算机科学
转录调控
作者
Antonio Rodríguez-García,Alberto Sola-Landa,Rosario Pérez-Redondo
出处
期刊:Methods of Molecular Biology
日期:2021-01-01
卷期号:2296: 263-278
标识
DOI:10.1007/978-1-0716-1358-0_16
摘要
The term coupled transcriptomics is coined to describe a design of an RNA-seq experiment intended for both differential expression analysis and genome-wide determination of the transcription start sites (TSS). The minimal requirements for the first analysis are two experimental conditions with at least two biological replicates enabling statistical tests. The second analysis involves the bioinformatics comparison of the data generated from a control RNA-seq library with another library enriched in primary transcripts using Terminator™ 5'-phosphate-dependent exonuclease, in an experiment denominated differential RNA-seq (dRNA-seq). Usually, dRNA-seq is carried out with specific protocols for library construction, different of those used for common differential expression analysis. Our experimental design allows to use the same data for both analyses, reducing the number of libraries to be generated and sequenced. This is a guide for designing a coupled transcriptomics experiment and for the subsequent bioinformatics procedures. The proposed methods can be applied to the detection and study of small RNA genes.
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