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Related Concept Videos

RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
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Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

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Targeted sequencing for gene discovery and quantification using RNA CaptureSeq.

Tim R Mercer1, Michael B Clark2, Joanna Crawford3

  • 11] Garvan Institute of Medical Research, Sydney, New South Wales, Australia. [2].

Nature Protocols
|April 8, 2014
PubMed
Summary
This summary is machine-generated.

RNA Capture Sequencing (CaptureSeq) enhances RNA sequencing (RNAseq) by targeting specific genes. This method improves gene discovery, transcript assembly, and quantification for complex eukaryotic transcriptomes.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Eukaryotic transcriptomes are large, complex, and have a wide dynamic range, leading to sparse sequencing coverage in standard RNA sequencing (RNAseq).
  • Sparse coverage in RNAseq hinders accurate isoform assembly and quantification of gene expression.

Purpose of the Study:

  • To describe a detailed protocol for RNA Capture Sequencing (CaptureSeq).
  • To enable sensitive gene discovery, robust transcript assembly, and accurate gene quantification through targeted RNAseq.

Main Methods:

  • Design of oligonucleotide probes for capturing targeted genes or regions of interest.
  • Experimental capture of targeted RNA using probes.
  • Assembly and quantification of captured transcripts.

Main Results:

  • RNA Capture Sequencing (CaptureSeq) provides enhanced sequencing coverage for selected genes.
  • The protocol facilitates sensitive gene discovery and robust transcript analysis.
  • The entire process, from probe design to final analysis, can be completed efficiently.

Conclusions:

  • RNA Capture Sequencing is an effective method to overcome limitations of standard RNAseq for analyzing complex transcriptomes.
  • This targeted RNAseq approach offers improved accuracy and sensitivity for gene expression studies.