ArticleBMC genomics2012
How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 146 papers.
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Who cites it
146 citing papers in PubMed, 241 citations in OpenAlex.
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- The Genetic Determinants of Extreme UV Radiation and Desiccation Tolerance in a Bacterium Recovered from the Stratosphere.Microorganisms · 2025Article
- Comparison of transcriptomic profiles between intracellular and extracellular Bartonella henselae.Communications biology · 2025Article
- Improved RNA preparation for RNA-seq of the intracellular bacteriumFrontiers in microbiology · 2025Article
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- CleanUpRNAseq: An R/Bioconductor Package for Detecting and Correcting DNA Contamination in RNA-Seq Data.Biotech (Basel (Switzerland)) · 2024Article
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- An expanded transcriptome atlas for Bacteroides thetaiotaomicron reveals a small RNA that modulates tetracycline sensitivity.Nature microbiology · 2024Article
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- INVADEseq to identify cell-adherent or invasive bacteria and the associated host transcriptome at single-cell-level resolution.Nature protocols · 2023Review
- Transcriptome Analysis ofPathogens (Basel, Switzerland) · 2023Article
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86 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundHigh-throughput sequencing of cDNA libraries (RNA-Seq) has proven to be a highly effective approach for studying bacterial transcriptomes. A central challenge in designing RNA-Seq-based experiments is estimating a priori the number of reads per sample needed to detect and quantify thousands of individual transcripts with a large dynamic range of abundance.
resultsWe have conducted a systematic examination of how changes in the number of RNA-Seq reads per sample influences both profiling of a single bacterial transcriptome and the comparison of gene expression among samples. Our findings suggest that the number of reads typically produced in a single lane of the Illumina HiSeq sequencer far exceeds the number needed to saturate the annotated transcriptomes of diverse bacteria growing in monoculture. Moreover, as sequencing depth increases, so too does the detection of cDNAs that likely correspond to spurious transcripts or genomic DNA contamination. Finally, even when dozens of barcoded individual cDNA libraries are sequenced in a single lane, the vast majority of transcripts in each sample can be detected and numerous genes differentially expressed between samples can be identified.
conclusionsOur analysis provides a guide for the many researchers seeking to determine the appropriate sequencing depth for RNA-Seq-based studies of diverse bacterial species.
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