Dual RNA Sequencing
What Is Dual RNA Sequencing?
Dual RNA sequencing (Dual RNA-seq) profiles the transcriptomes of both a host and its infecting microbe—bacteria, fungi, parasites, or viruses—in a single experiment. By depleting ribosomal RNA from both organisms and using strand-specific library preparation, Dual RNA-seq captures:
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Host mRNAs that orchestrate immune responses, signaling cascades, and tissue repair
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Pathogen transcripts that drive virulence, metabolic adaptation, and stress responses
This unified approach reveals how pathogens manipulate host gene expression and how hosts deploy defenses. At AUGenomics, we optimize rRNA-depletion chemistries for mixed samples, apply UMI-enabled, strand-specific workflows, and balance library complexity to ensure accurate quantitation even in low-biomass infections.
Advantages of Dual RNA Sequencing
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Comprehensive Dual Transcriptomes: Capture host and pathogen mRNAs in one workflow—no need for separate sequencing runs.
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Balanced Sensitivity: Tailored rRNA depletion ensures reliable detection of low-abundance transcripts on both sides.
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Strand Specificity: Precisely assign antisense transcripts and small RNAs to the correct organism and orientation.
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Custom Reference Alignment: Dual indexing against combined host–pathogen genomes minimizes mapping ambiguity and supports novel transcript discovery.
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Low-Input & Challenging Samples: Robust on 50–100 ng total RNA from infected tissues, co-cultures, or biofluids with low pathogen load.
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Actionable Insights: Concurrently identify host biomarkers of infection severity and pathogen virulence factors for translational research.
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Scalable & Cost-Effective: One experiment yields two data sets, saving >30% on reagents and run time compared to separate assays.
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Infection Dynamics: Track temporal gene expression in both host and pathogen during acute or chronic infection.
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Immune Response Profiling: Quantify host cytokine, chemokine, and signaling cascades alongside pathogen counter-measures.
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Pathogen Adaptation: Identify microbial genes and RNAs upregulated in vivo versus in vitro conditions.
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Therapeutic Target Discovery: Pinpoint interaction nodes—receptors, transcription factors, virulence regulators—for vaccine or drug development.
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Microbiome–Host Studies: Profile gene expression in complex communities (gut, skin, lung) together with host tissue responses.
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Co-evolution & Symbiosis: Investigate mutualistic interactions in plant or animal symbiont systems.
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High-Content Screening: Evaluate effects of antibiotics, antivirals, immunomodulators, or gene-editing interventions in co-culture assays.
Our workflows are designed for sensitivity and balance, ensuring both host and pathogen transcripts are captured and quantified accurately—even in low-biomass infections.
What is Dual RNA Sequencing Used For?
Dual RNA Sequencing with AUGenomics
Sample Submission
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Accepted Sample Types: Infected cells or tissues (human, animal, or plant), co-cultures, microbiome samples
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Input Requirement: 50–100 ng total RNA (lower input possible for enriched samples)
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Sequencing Recommendations:
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Total RNA-seq with rRNA depletion or poly-A selection depending on host-pathogen pairing
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40–100 million reads/sample to ensure coverage of both transcriptomes
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Custom genome alignment and separation of host and pathogen reads included
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Please refer to our Shipping Guidelines for project-specific guidance.
Turnaround Time
Typical turnaround is 10-14 business days from sample receipt. Expedited options are available depending on project scope and sequencing depth.
Frequently Asked Questions (FAQs)
Q: Can I use dual RNA-seq for human-microbiome studies?
A: Yes. Dual RNA-seq is commonly applied to microbiome-host research, including studies of gut, skin, and lung microbiota interactions.
Q: Is ribosomal RNA depletion required?
A: Yes, especially for bacterial or fungal pathogens. We use rRNA depletion protocols tailored for both eukaryotic and prokaryotic RNA species.
Q: How are host and pathogen reads separated?
A: Reads are aligned to a merged reference or in parallel, then binned based on unique mapping, ensuring minimal cross-mapping.
Q: What read depth is recommended?
A: 40–100 M paired-end reads per sample to achieve ≥10 M reads on the pathogen transcriptome in low-biomass infections.
Got more questions? Contact our team and get a free consultation anytime. info@augenomics.com
Glossary of Terms
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Dual RNA-seq: Sequencing that captures the transcriptomes of two interacting organisms simultaneously
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Host-Pathogen Interaction: Molecular and cellular interactions between a host and its pathogen
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rRNA Depletion: Removal of abundant ribosomal RNA to improve sequencing depth of informative transcripts
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Co-culture: Lab setup where two or more organisms are grown together to mimic biological interactions
