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Related Concept Videos

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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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Related Experiment Video

Updated: Jan 13, 2026

A Novel Microdissection Approach to Recovering Mycobacterium tuberculosis Specific Transcripts from Formalin Fixed Paraffin Embedded Lung Granulomas
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Transcript-Capture sequencing enriches mRNA of Mycobacterium tuberculosis from host samples.

Eleanor I Lamont1, Richard M Jones1,2, Jessica Assadi1

  • 1Department of Microbiology, University of Washington, Seattle, WA 98195, United States.

NAR Molecular Medicine
|January 12, 2026
PubMed
Summary

We developed Transcript-Capture Seq to analyze bacterial gene expression in infections. This method significantly increases bacterial mRNA detection in patient samples, revealing the complete bacterial transcriptome in tuberculosis patients.

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Area of Science:

  • Microbiology
  • Genomics
  • Infectious Diseases

Background:

  • Bacterial gene expression at infection sites is difficult to study due to low bacterial mRNA levels in clinical samples.
  • Understanding bacterial activity in vivo is crucial for diagnosing and treating infections like tuberculosis.

Purpose of the Study:

  • To develop a novel method for enriching bacterial RNA from host samples for Next Generation Sequencing (NGS).
  • To analyze the complete bacterial transcriptome from clinical samples, specifically in tuberculosis patients.
  • To investigate the in vivo physiological state and gene expression of Mycobacterium tuberculosis (Mtb) in patients.

Main Methods:

  • Transcript-Capture Seq utilizes custom biotinylated probes to enrich bacteria-specific RNA from mixed host-bacterial samples.
  • The enriched RNA is then analyzed using Next Generation Sequencing (NGS).
  • The method was applied to both tuberculosis infection models and sputum samples from tuberculosis patients.

Main Results:

  • Transcript-Capture Seq achieved a >200-fold increase in bacterial mRNA reads from mixed samples.
  • The study generated the first complete in vivo bacterial transcriptome of Mtb from patient sputum using NGS.
  • Mtb in patient sputum showed upregulated genes related to host lipid utilization and zinc limitation, mirroring in vitro log-phase growth.

Conclusions:

  • Transcript-Capture Seq enables comprehensive analysis of bacterial transcriptomes directly from clinical samples.
  • This technique provides a valuable snapshot of bacterial activity in vivo, aiding the study of infection physiology.
  • The findings offer insights into Mtb's adaptation and activity within tuberculosis patients, potentially impacting treatment strategies.