Methodologies for Transcript Profiling Using Long-Read Technologies

Frontiers in Genetics
Spyros OikonomopoulosJiannis Ragoussis

Abstract

RNA sequencing using next-generation sequencing technologies (NGS) is currently the standard approach for gene expression profiling, particularly for large-scale high-throughput studies. NGS technologies comprise high throughput, cost efficient short-read RNA-Seq, while emerging single molecule, long-read RNA-Seq technologies have enabled new approaches to study the transcriptome and its function. The emerging single molecule, long-read technologies are currently commercially available by Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT), while new methodologies based on short-read sequencing approaches are also being developed in order to provide long range single molecule level information-for example, the ones represented by the 10x Genomics linked read methodology. The shift toward long-read sequencing technologies for transcriptome characterization is based on current increases in throughput and decreases in cost, making these attractive for de novo transcriptome assembly, isoform expression quantification, and in-depth RNA species analysis. These types of analyses were challenging with standard short sequencing approaches, due to the complex nature of the transcriptome, which consists of variable lengths...Continue Reading

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Methods Mentioned

BETA
RNA-seq
PCR
size fractionation
Smart-seq2
cDNA
ICE
nucleic acid sequencing
pull down
Rolling Circle
scRNA-Seq

Related Concepts

Alleles
Antigens, Tumor-Associated, Carbohydrate
Gene Expression
Genes
Poly A
RNA
RNA Splicing
Ribosomal RNA
Research Methodology
Gene Function

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