Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells
Open accessPublished version of a preprint
Abstract
We describe droplet-assisted RNA targeting by single-cell sequencing (DART-seq), a versatile technology that enables multiplexed amplicon sequencing and transcriptome profiling in single cells. We applied DART-seq to simultaneously characterize the non-A-tailed transcripts of a segmented dsRNA virus and the transcriptome of the infected cell. In addition, we used DART-seq to simultaneously determine the natively paired, variable region heavy and light chain amplicons and the transcriptome of B lymphocytes.
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Prior enrichment methods based on multiplexed PCR, custom RT beads, or linear amplification each have constraints on target number, quality, or the need to choose genes beforehand.
“Diverse approaches exist for enriching transcripts using multiplexed PCR34, custom RT beads35, or linear amplification36; however, each of these is limited by number of target genes, quality, and/or a priori gene selection.”
From Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing (2020) · cites this paper as [35]
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References 31 · Cited by 75
- Authors
- Saikia, M., Burnham, P., Keshavjee, S. H., Wang, M. F. Z., Heyang, M., Moral-Lopez, P., Hinchman, M. M., Danko, C. G., Parker, J. S. L., & De Vlaminck, I.
- Affiliations
- Cornell University (US)
- ORCID
- Venue
- Nature Methods
- Published
- 2018-12-17
- Volume
- 16
- Issue
- 1
- Pages
- 59-62
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC6378878
- OpenAlex
- W2949430636
- Cited by
- 75
- References
- 31
- Citations by year
- 2026: 2 · 2025: 6 · 2024: 11 · 2023: 7 · 2022: 9 · 2021: 14 · 2020: 12 · 2019: 13 · 2018: 1
- FWCI
- 4.00
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Methods (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Science Foundation (1144153)
- National Institutes of Health (1dp2ai138242-01, DGE-1144153)
- National Institute of Allergy and Infectious Diseases (DP2 AI138242, R21AI144557)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Physical Sciences › Engineering › Biomedical Engineering › Innovative Microfluidic and Catalytic Techniques Innovation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- DArTseq, single-cell transcriptomics, viral transcriptome, B cells, single-cell RNA sequencing
- MeSH terms
- Animals, B-Lymphocytes, Cell Line, Gene Expression Profiling, Reverse Transcription, Mice, Single-Cell Analysis, Transcriptome, Real-Time Polymerase Chain Reaction
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