Evidence map›Paper›PMID 39819888›Full record

ArticleCommunications biology2025

Enhancing single-cell transcriptomics using interposed anchor oligonucleotide sequences.

Jianfeng Sun, Martin Philpott, Danson Loi, Gabriela Hoffman, Jonathan Robson, Neelam Mehta, Eleanor Calcutt, Vicki Gamble, Tom Brown, Tom Brown and 2 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Communications biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–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

4 citing papers in PubMed.

  1. Article
  2. Article
  3. Review
  4. Review
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

12 authors.

Jianfeng SunBotnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0002-1274-5080
Martin PhilpottBotnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, UK.
Danson LoiBotnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, UK.
Gabriela HoffmanATDBio Ltd (now part of Biotage), Oxford, UK.
Jonathan RobsonATDBio Ltd (now part of Biotage), Oxford, UK.
Neelam MehtaBotnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, UK.
Eleanor CalcuttBotnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, UK.
Vicki GambleBotnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, UK.
Tom BrownATDBio Ltd (now part of Biotage), Oxford, UK.
Tom BrownChemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0002-6538-3036
Udo OppermannBotnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, UK.
Adam P CribbsBotnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, UK. adam.cribbs@ndorms.ox.ac.uk.ORCID http://orcid.org/0000-0001-5288-3077

Funding

RCUK | Medical Research Council (MRC) MR/V010182/1
6 · The paper itself

Abstract

Single-cell transcriptomics, which utilises barcodes and unique molecular identifiers (UMIs) for polyA+ mRNA capture, is compromised by oligonucleotide synthesis errors. To address this, we modified the oligonucleotide capture design and integrated an interposed anchor between the barcode and the UMI. This design significantly reduces the need to discard reads due to synthesis inaccuracies. Our results demonstrate that this anchor-enhanced design substantially improves gene expression profiles in droplet-based single-cell sequencing analyses.

Indexed as

Gene Expression ProfilingOligonucleotidesSingle-Cell AnalysisTranscriptomeHumansRNA, MessengerSequence Analysis, RNAOligonucleotidesRNA, Messenger

Identifiers

PMID39819888
PMCPMC11739374

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Registered trials

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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.