Cited by 1,010Genomics and Phylogenetic StudiesSingle-cell and spatial transcriptomicsMolecular Biology Techniques and Applications

Counting absolute numbers of molecules using unique molecular identifiers

Kivioja, Teemu, Vähärautio, Anna, Karlsson, Kasper, Bonke, Martin, Enge, Martin, Linnarsson, Sten, Taipale, Jussi·2012·Nature Methods

Abstract

Counting individual RNA or DNA molecules is difficult because they are hard to copy quantitatively for detection. To overcome this limitation, we applied unique molecular identifiers (UMIs), which make each molecule in a population distinct, to genome-scale human karyotyping and mRNA sequencing in Drosophila melanogaster. Use of this method can improve accuracy of almost any next-generation sequencing method, including chromatin immunoprecipitation-sequencing, genome assembly, diagnostics and manufacturing-process control and monitoring.

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Crossref · 10.1038/nmeth.1778

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37 of 37 references verified0 citation errors · 0 not checkable

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  • Inclusion of added reference transcripts and the use of unique molecule identifiers (UMIs) have been applied to overcome amplification bias and to improve gene quantification.

    “The inclusion of added reference transcripts and the use of unique molecule identifiers (UMIs) have been applied to overcome amplification bias and to improve gene quantification [177, 178].”

    From A survey of best practices for RNA-seq data analysis (2016) · cites this paper as [178]

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Authors
Kivioja, T., Vähärautio, A., Karlsson, K., Bonke, M., Enge, M., Linnarsson, S., & Taipale, J.
Affiliations
  • University of Helsinki (FI)
  • Karolinska Institutet (SE)
  • Science for Life Laboratory (SE)
Corresponding author
  • Linnarsson, Sten
  • Taipale, Jussi
Venue
Nature Methods
Published
2011-11-20
Volume
9
Issue
1
Pages
72-74
ISSN
  • 1548-7091 (ISSN-L)
  • 1548-7105
OpenAlex
W2041677964
Cited by
1,010
References
38
Citations by year
2026: 62 · 2025: 58 · 2024: 59 · 2023: 80 · 2022: 77 · 2021: 104 · 2020: 87 · 2019: 108 · 2018: 96 · 2017: 96 · 2016: 66 · 2015: 41 · 2014: 44 · 2013: 19 · 2012: 12
FWCI
9.73
Type
journal article
Language
en
Open access
closed
Locations
  • Nature Methods (publishedVersion)
  • PubMed (publishedVersion)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Molecular Biology Techniques and Applications
Keywords
unique molecular identifiers, Down syndrome, Drosophila melanogaster, mRNA quantification, single-molecule sequencing, ChIP-seq, genome assembly
MeSH terms
Animals, Down Syndrome, Drosophila melanogaster, Female, Humans, Karyotyping, Male, RNA, Messenger, Gene Library, Sequence Analysis, RNA, Genomics, Chromatin Immunoprecipitation

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