ArticleNature protocols2016
A highly multiplexed and sensitive RNA-seq protocol for simultaneous analysis of host and pathogen transcriptomes.
Article in Nature protocols, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Article
- Metatranscriptomic insights into host-microbiome interactions underlying asymptomatic COVID-19 cases.Scientific reports · 2026Article
- RNA polymerase stalling-derived genome instability underlies ribosomal antibiotic efficacy and resistance evolution.Nature communications · 2024Article
- Algal methylated compounds shorten the lag phase of Phaeobacter inhibens bacteria.Nature microbiology · 2024Article
- Untangling Cellular Host-Pathogen Encounters at Infection Bottlenecks.Infection and immunity · 2023Review
- Article
- Resolving the Microalgal Gene Landscape at the Strain Level: a Novel Hybrid Transcriptome ofApplied and environmental microbiology · 2022Article
- Respiratory immune status and microbiome in recovered COVID-19 patients revealed by metatranscriptomic analyses.Frontiers in cellular and infection microbiology · 2022Article
- Targeted RNA-Seq Reveals theBiology · 2021Article
- Article
- Best practices on the differential expression analysis of multi-species RNA-seq.Genome biology · 2021Review
- Clinical Evaluation of a Metagenomics-Based Assay for Pneumonia Management.Frontiers in microbiology · 2021Article
- Evolution of Drug-ResistantFrontiers in microbiology · 2021Review
- Glutamate dehydrogenase (Gdh2)-dependent alkalization is dispensable for escape from macrophages and virulence of Candida albicans.PLoS pathogens · 2020Article
- A Common Genetic Variation in Langerin (CD207) Compromises Cellular Uptake of Staphylococcus aureus.Journal of innate immunity · 2020Article
- Review
- Clinical metagenomics.Nature reviews. Genetics · 2019Review
- Path-seq identifies an essential mycolate remodeling program for mycobacterial host adaptation.Molecular systems biology · 2019Article
- Article
- Bioinformatic analysis of bacteria and host cell dual RNA-sequencing experiments.Briefings in bioinformatics · 2018Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
The ability to simultaneously characterize the bacterial and host expression programs during infection would facilitate a comprehensive understanding of pathogen-host interactions. Although RNA sequencing (RNA-seq) has greatly advanced our ability to study the transcriptomes of prokaryotes and eukaryotes separately, limitations in existing protocols for the generation and analysis of RNA-seq data have hindered simultaneous profiling of host and bacterial pathogen transcripts from the same sample. Here we provide a detailed protocol for simultaneous analysis of host and bacterial transcripts by RNA-seq. Importantly, this protocol details the steps required for efficient host and bacteria lysis, barcoding of samples, technical advances in sample preparation for low-yield sample inputs and a computational pipeline for analysis of both mammalian and microbial reads from mixed host-pathogen RNA-seq data. Sample preparation takes 3 d from cultured cells to pooled libraries. Data analysis takes an additional day. Compared with previous methods, the protocol detailed here provides a sensitive, facile and generalizable approach that is suitable for large-scale studies and will enable the field to obtain in-depth analysis of host-pathogen interactions in infection models.
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Registered trials
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