Dual RNA sequencing is a transcriptomics approach that simultaneously captures and analyzes RNA from two or more interacting organisms, such as a host and its pathogen. Unlike conventional RNA sequencing, which profiles a single species, Dual RNA-seq enables researchers to investigate dynamic gene expression changes in both organisms without physically separating them.

Using total mixed RNA with dual rRNA depletion or poly(A) enrichment, this method reveals coordinated transcriptional responses and uncovers the molecular mechanisms underlying infection, immunity, symbiosis, and other biological interactions.

Advantages of Our Dual RNA-seq Service

• Simultaneous Host–Pathogen Transcriptome Profiling

Analyze gene expression changes in both interacting species within a single sequencing experiment.

• Broad Sample Compatibility

Supports a wide range of biological systems, including:

• - Host–bacteria interactions
• - Host–fungi interactions
• - Host–protozoa interactions
• - Plant–pathogen systems
• - Mammalian infection models
• - Mixed RNA samples and infected tissues or cells

• Low-Input Library Preparation

Optimized protocols and molecular barcode technology enable library construction from limited RNA inputs.

• High-Quality Sequencing & Bioinformatics

Utilizes Illumina sequencing platforms and high-performance computing (HPC) for accurate data generation and efficient analysis.

• Comprehensive Data Analysis

Standard and advanced analyses include:

• - Differential gene expression
• - Functional annotation
• - Pathway enrichment analysis
• - Weighted Gene Co-expression Network Analysis (WGCNA)
• - Virulence factor annotation
• - Protein–protein interaction (PPI) network analysis
• - Host–pathogen interaction analysis

• End-to-End Support

Complete project support from experimental design and library preparation to sequencing, bioinformatics, and data interpretation.

Applications

Dual RNA sequencing is widely used in studies involving:

• • Host–pathogen interactions
• • Infectious disease research
• • Plant disease and resistance mechanisms
• • Host immune response analysis
• • Microbial pathogenesis
• • Symbiosis and mutualistic interactions
• • Parasite–host biology
• • Bacteria–fungi co-culture studies
• • Comparative genomics
• • Evolutionary biology
• • Functional genomics

Dual RNA-seq Workflow

1. Sample Preparation

Collection of infected tissues, cultured cells, or mixed RNA samples followed by RNA extraction and quality assessment.

2. Library Preparation

Dual rRNA depletion or poly(A) enrichment, library construction, indexing, and quality control.

3. High-Throughput Sequencing

Sequencing performed on advanced Illumina platforms to generate high-quality paired-end transcriptome data.

4. Bioinformatics Analysis

Comprehensive downstream analysis including:

• • Raw data quality control
• • Host and pathogen read separation
• • Reference genome alignment
• • Gene expression quantification
• • Differential expression analysis
• • Functional annotation
• • GO and KEGG pathway enrichment
• • WGCNA
• • Virulence factor annotation
• • Protein–protein interaction (PPI) analysis
• • Host–pathogen interaction network analysis

Service Specification

	Sample Requirements: Total RNA ≥ 1 μg, Concentration≥10 ng/µL, OD260/280=1.8-2.0 Cells ≥ 5×106 Tissue ≥ 500 mg, Minimum Quantity: 100 mg
	Sequencing: Illumina platform PE150 Sequencing 12-24Gb
	Data Analysis Transcriptome analysis Weighted Gene Co-expression Network Analysis (WGCNA) Virulence factor annotation Protein-protein interaction network analysis ….and more

Analysis Pipeline

Deliverables

• • The original sequencing data
• • Experimental results
• • Data analysis report
• • Details in Dual RNA-seq for your writing (customization)

1. Are reference genomes required for both species in Dual RNA-seq?

Reference genomes for both interacting species are recommended because they improve read alignment, gene annotation, and expression analysis. If a reference genome is available for only one species, reads can first be mapped to that genome, while the remaining reads may be analyzed using a closely related reference genome or de novo transcriptome assembly. For bacterial pathogens, a reference genome is preferred, although pan-genome approaches may be considered when appropriate.

2. What are the advantages of Dual RNA-seq over conventional RNA-seq?

Unlike conventional RNA sequencing, which profiles a single organism, Dual RNA-seq simultaneously analyzes the transcriptomes of interacting species—such as a host and a pathogen—in a single experiment. This approach:

• • Captures coordinated gene expression changes in both species.

• • Eliminates the need to physically separate interacting organisms.
• • Reduces sample processing bias and information loss.
• • Provides a more comprehensive understanding of host–pathogen interactions.
• • Enables cost-effective analysis using a single sequencing library.

3. What types of RNA sequencing are available?

RNA sequencing can be tailored to different research objectives. Common RNA-seq approaches include:

• • mRNA Sequencing
• • Total RNA Sequencing
• • Small RNA (miRNA) Sequencing
• • Long Non-coding RNA (lncRNA) Sequencing
• • Circular RNA (circRNA) Sequencing
• • Full-Length Transcriptome Sequencing (Iso-Seq)
• • Dual RNA Sequencing
• • Single-Cell RNA Sequencing (scRNA-seq)