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Genome Biol. 2018 Dec 19;19(1):224. doi: 10.1186/s13059-018-1603-1.

Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics.

Author information

1
Technology Innovation Lab, New York Genome Center, New York, NY, USA.
2
NYU Center for Genomics and Systems Biology, New York Genome Center, New York, NY, USA.
3
BioLegend Inc., San Diego, CA, USA.
4
Technology Innovation Lab, New York Genome Center, New York, NY, USA. psmibert@nygenome.org.
5
NYU Center for Genomics and Systems Biology, New York Genome Center, New York, NY, USA. rsatija@nygenome.org.

Abstract

Despite rapid developments in single cell sequencing, sample-specific batch effects, detection of cell multiplets, and experimental costs remain outstanding challenges. Here, we introduce Cell Hashing, where oligo-tagged antibodies against ubiquitously expressed surface proteins uniquely label cells from distinct samples, which can be subsequently pooled. By sequencing these tags alongside the cellular transcriptome, we can assign each cell to its original sample, robustly identify cross-sample multiplets, and "super-load" commercial droplet-based systems for significant cost reduction. We validate our approach using a complementary genetic approach and demonstrate how hashing can generalize the benefits of single cell multiplexing to diverse samples and experimental designs.

PMID:
30567574
PMCID:
PMC6300015
DOI:
10.1186/s13059-018-1603-1
[Indexed for MEDLINE]
Free PMC Article

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