RNA-seq : The Pros and Cons of Bulk & Single Cell Transcriptomics

Abstract

RNA sequencing (RNA-seq) has revolutionized the study of gene expression by enabling the identification of differentially expressed features (such as genes) across biological samples. Two commonly employed methodologies are bulk and single-cell RNA sequencing (scRNA-seq), each with its distinct advantages and limitations. THis presentation will detail the pros and cons of these and other emerging approaches.

Bulk RNA-seq is a well-established technique that enables transcriptome profiling in a population of cells. This method yields an average expression profile of the sample and can effectively capture changes in gene expression at the population level. Bulk RNA-seq offers a high sample throughput and lower cost per sample compared to scRNA-seq, but lacks the ability to discern the cellular heterogeneity and may not detect rare cell types or subpopulations.

On the other hand, scRNA-seq offers unprecedented insights into the cellular heterogeneity, cell-to-cell variability, and gene expression dynamics by profiling RNA expression at the individual cell level. scRNA-seq can effectively identify rare cell types and subpopulations that may be obscured in bulk analysis. scRNA-seq has lower throughput and is more expensive.

The choice of RNA-seq methodology depends on the scientific question and the experimental design. I will discuss emerging RNA-seq technologies, such as long-read sequencing and spatial transcriptomics, which aim to bridge the gap between bulk and scRNA-seq and enhance the accuracy and sensitivity of transcriptomic profiling.