AAT Bioquest

What are the different types of RNA-seq?

Posted August 10, 2023


The different types of RNA-seq include: mRNA sequencing, RNA exome capture sequencing, total RNA sequencing, small RNA sequencing, and targeted RNA sequencing. mRNA-Seq is a highly sensitive and accurate technique of quantifying gene expression. It can identify both known and novel gene fusions, novel transcript isoforms, and allele-specific expression. Targeted RNA-seq is a highly accurate technique for sequencing transcripts of interest. It provides both qualitative and quantitative data. Targeted RNA-seq can be carried out through amplicon-based approaches or enrichment. Enrichment assays have the ability to detect both known and novel gene fusions in many sample types. Small RNA-seq is a method to isolate and sequence small RNA molecules (e.g. miRNAs). Small RNA-seq can query thousands of small RNA and miRNA sequences with high sensitivity and wide dynamic range. Additionally, one can characterize variations (e..g isomiRs) with single-base resolution. Total RNA-Seq is used for whole-transcriptome analysis, and detects coding and multiple forms of noncoding RNA. This can measure gene and transcript abundance and identify novel and known features of the transcriptome. Total RNA-seq displays accurate analysis for normal or low-quality samples. RNA exome capture sequencing captures only the coding regions of the transcriptome. It allows higher throughput and requires lower sequencing depth than non-exome capture techniques. Sequence-specific capture of the RNA exome is not reliant on the presence of a poly-A tail. Thus, this technique is ideal for low-quality samples or limited starting material.  

Additional resources

Editorial: RNA-Seq Analysis: Methods, Applications and Challenges

Gene Expression Analysis & Genotyping

StrandBrite™ Green Fluorimetric RNA Quantitation Kit *High Selectivity*

Portelite™ Fluorimetric RNA Quantitation Kit*Optimized for Cytocite™ and Qubit™ Fluorometers*