Targeting individual cells by barcode in pooled sequence libraries
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Abstract
Transcriptional profiling of thousands of single cells in parallel by RNA-seq is now routine. However, due to reliance on pooled library preparation, targeting analysis to particular cells of interest is difficult. Here, we present a multiplexed PCR method for targeted sequencing of select cells from pooled single-cell sequence libraries. We demonstrated this molecular enrichment method on multiple cell types within pooled single-cell RNA-seq libraries produced from primary human blood cells. We show how molecular enrichment can be combined with FACS to efficiently target ultra-rare cell types, such as the recently identified AXL+SIGLEC6+ dendritic cell (AS DC) subset, in order to reduce the required sequencing effort to profile single cells by 100-fold. Our results demonstrate that DNA barcodes identifying cells within pooled sequencing libraries can be used as targets to enrich for specific molecules of interest, for example reads from a set of target cells.
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Molecular random access has largely relied on PCR, which uses up to ~20-30 heating and cooling cycles with DNA polymerase to selectively amplify specific DNA sequences from a DNA data pool using primers.
“To date, molecular random access has largely relied on conventional polymerase chain reaction (PCR)8,10,12,13, which uses up to ~20–30 heating and cooling cycles with DNA polymerase to selectively amplify specific DNA sequences from a DNA data pool using primers.”
From Random access DNA memory using Boolean search in an archival file storage system (2021) · cites this paper as [13]
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Random access DNA memory using Boolean search in an archival file storage system
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Self-citationRebimbas, R., Glória, I., Chegão, J., Al-Rawi, M., Mousakhani Ganjeh, A., & Saraiva, J. A. (2026) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2026.03.003
- Authors
- Ranu, N., Villani, A.-C., Hacohen, N., & Blainey, P. C.
- Affiliations
- Massachusetts Institute of Technology (US)
- Broad Institute (US)
- Corresponding author
- Blainey, Paul C
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-09-26
- Volume
- 47
- Issue
- 1
- Pages
- e4-e4
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC6326790
- OpenAlex
- W2950355142
- Cited by
- 13
- References
- 33
- Citations by year
- 2026: 1 · 2025: 1 · 2021: 4 · 2020: 4 · 2019: 1 · 2018: 1 · 2016: 1
- FWCI
- 0.89
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
- Funders
- National Institute of Allergy and Infectious Disease (U24AI11866803)
- National Human Genome Research Institute (RM1HG00619307)
- Centers of Excellence in Genomic Science (RM1HG00619307)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Keywords
- single-cell RNA sequencing, DNA barcodes, targeted sequencing, multiplex PCR, FACS cell sorting, blood cells, sequencing cost reduction
- MeSH terms
- Blood Cells, DNA, Humans, Leukocytes, Mononuclear, Cell Lineage, DNA Barcoding, Taxonomic, Single-Cell Analysis, High-Throughput Nucleotide Sequencing, Multiplex Polymerase Chain Reaction
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