Evidence map›Paper›PMID 39453698›Full record

ArticleMicrobial genomics2024

Comparison of direct cDNA and PCR-cDNA Nanopore sequencing of RNA from

Gillian Rodger, Samuel Lipworth, Lucinda Barrett, Sarah Oakley, Derrick W Crook, David W Eyre, Nicole Stoesser

Abstract readComparative Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Microbial genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed, 1 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

5 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
  2. Review
  3. Review
  4. Article
  5. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors.

Gillian RodgerNuffield Department of Medicine, University of Oxford, Oxford, UK.
Samuel LipworthNuffield Department of Medicine, University of Oxford, Oxford, UK.
Lucinda BarrettOxford University Hospitals NHS Foundation Trust, Oxford, UK.
Sarah OakleyOxford University Hospitals NHS Foundation Trust, Oxford, UK.
Derrick W CrookNuffield Department of Medicine, University of Oxford, Oxford, UK.
David W EyreNIHR Health Protection Unit in Antimicrobial Resistance and Healthcare-associated Infection, University of Oxford, Oxford, UK.
Nicole StoesserNuffield Department of Medicine, University of Oxford, Oxford, UK.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Whole-transcriptome (long-read) RNA sequencing (Oxford Nanopore Technologies, ONT) holds promise for reference-agnostic analysis of differential gene expression in pathogenic bacteria, including for antimicrobial resistance genes (ARGs). However, direct cDNA ONT sequencing requires large concentrations of polyadenylated mRNA, and amplification protocols may introduce technical bias. Here we evaluated the impact of direct cDNA- and cDNA PCR-based ONT sequencing on transcriptomic analysis of clinical

Indexed as

DNA, ComplementaryEscherichia coliNanopore SequencingEscherichia coli InfectionsGene Expression ProfilingHigh-Throughput Nucleotide SequencingHumansPolymerase Chain ReactionRNA, BacterialSequence Analysis, RNATranscriptomeDNA, ComplementaryRNA, Bacterialantimicrobial resistance gene expressionbacterial transcriptomicsEscherichia colilong-read RNA-Seqnanopore sequencing

Identifiers

PMID39453698
PMCPMC11507042

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.