Counting absolute numbers of molecules using unique molecular identifiers
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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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
- Licence
- www.springer.com/tdm (tdm)
- 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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