Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

RNA-seq

RNA-seq

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.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Loss of O-antigen due to <i>wbbL</i> mutations is common and associated with increased mortality in <i>Escherichia coli</i> bloodstream infections.

Science advances·2026

Same author

Power and sample-size estimation in human microbiome research.

Med (New York, N.Y.)·2026

Same author

Species and strain diversity in Staphylococcus drive divergent host responses in human skin.

bioRxiv : the preprint server for biology·2026

Same author

Deep single-cell decoding of human pancreatic islets reveals T2D β-cell gene expression defects.

The EMBO journal·2026

Same author

Distinct biochemical phenotypes of HIV exposed infants driven by antiviral medication.

medRxiv : the preprint server for health sciences·2026

Same author

PD-L1 is an intrinsic switch for natural killer cell-mediated, TRAIL-dependent antiviral function.

Cell reports·2026

Same journal

Salinity-driven microbial adaptation of hydrocarbon-degrading communities in coastal sediments.

mSphere·2026

Same journal

Tools for genetic manipulation of the endemic fungal pathogen <i>Emergomyces africanus</i> and application of a fluorescent reporter strain in infection models.

mSphere·2026

Same journal

Cysteine-S-nitrosylation inhibits ROP5-mediated immune evasion in <i>Toxoplasma gondii</i>.

mSphere·2026

Same journal

Inheritance of four-membrane-bound structures in the "apicoplast-minus" <i>Plasmodium falciparum</i>.

mSphere·2026

Same journal

mSphere of Influence: The bacterial growth law-revisiting the old to discover the new.

mSphere·2026

Same journal

Preclinical characterization of immune responses induced by a candidate gonococcal native outer membrane vesicle vaccine.

mSphere·2026

See all related articles

Search research articles

Related Experiment Video

Updated: May 10, 2025

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

TEAL-Seq: targeted expression analysis sequencing.

Georgia Doing¹, Priya Shanbhag¹, Isaac Bell¹

¹The Jackson Laboratory for Genomic Medicine Farmington, Farmington, Connecticut, USA.

|April 22, 2025

Summary

This summary is machine-generated.

We developed targeted expression analysis sequencing (TEAL-seq) for sensitive, species-specific gene expression analysis in microbial communities. This method overcomes challenges like low biomass and host RNA, offering a cost-effective and adaptable solution for microbiome research.

Keywords:

metagenomics skin microbiome targeted sequencing

More Related Videos

3' End Sequencing Library Preparation with A-seq2

3' End Sequencing Library Preparation with A-seq2

Published on: October 10, 2017

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Published on: March 12, 2021

Related Experiment Videos

Last Updated: May 10, 2025

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

3' End Sequencing Library Preparation with A-seq2

3' End Sequencing Library Preparation with A-seq2

Published on: October 10, 2017

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Published on: March 12, 2021

Area of Science:

Microbiology
Genomics
Molecular Biology

Background:

Metagenome sequencing characterizes microbial communities but struggles with quantifying gene expression due to variable abundances and low biomass.
Host RNA and low microbial biomass complicate accurate assessment of microbial activity within complex environments.

Purpose of the Study:

To develop a sensitive and specific method for analyzing gene expression in targeted microbial species within complex communities.
To address limitations of existing methods in detecting species-specific activity in microbiomes.

Main Methods:

Developed "targeted expression analysis sequencing" (TEAL-seq) using highly multiplexed custom probe pools for species-specific gene expression analysis.
Applied TEAL-seq with molecular inversion probes and a linear pre-amplification step to laboratory cultures and human nasal swabs.
Targeted ~1,700 core and accessory genes of *Staphylococcus aureus* and *S. epidermidis*.

Main Results:

TEAL-seq demonstrated high specificity (>90% reads on target) even with complex background DNA/RNA.
Inferred expression levels from TEAL-seq showed excellent correlation with bulk RNA-seq.
Profiling was successful from as little as 1 ng of total RNA, demonstrating effectiveness with low biomass samples.

Conclusions:

TEAL-seq provides a cost-effective, sensitive, and adaptable strategy for analyzing microbial gene expression in any community.
The method enables detection across a greater dynamic range compared to bulk metatranscriptomic profiling.
TEAL-seq facilitates the study of microbial activity and interactions in diverse natural environments.