Transcriptome Analysis

Transcriptomics is the comprehensive study of the transcriptome, which measures the complete set of RNA transcripts produced by the genome under specific circumstances or in a particular cell. It reflects the active biological processes occurring within a cell or tissue and provides rich insights into cellular characteristics. The rapid developments in next generation sequencing technologies and analysis methods have had a great impact on the quality of assembled transcriptome, in addition to an increase in the accuracy of gene expression quantification. RNA-sequencing (RNA-seq) has become an integral component of transcriptome analysis to detect and quantify transcriptome-wide gene expression. The advent of third generation sequencing technologies has exhibited great potential to study and unravel the complex and dynamic nature of the whole transcriptome including the annotation and identification of long noncoding RNA transcriptome. Single-cell RNA sequencing (scRNA-seq) has revolutionized transcriptomics by enabling the analysis of gene expression at the resolution of individual cells, thus revealing insights into understanding of cell types and complex cellular heterogeneity in tissues. Spatial transcriptomics uniquely retains the spatial location of gene expression within tissue sections, unlike bulk RNA-seq and scRNA-seq. This chapter provides an overview of various transcriptomic technologies and the various steps integral to the transcriptomic analysis. Furthermore, we also provide a few case studies illustrating the impact of transcriptome analysis.