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

Marlon Stoeckius, Shiwei Zheng, Brian Houck-Loomis, Stephanie Hao, Bertrand Z. Yeung, William M. Mauck, Peter Smibert, Rahul Satija

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Article number224
JournalGenome Biology
Volume19
Issue number1
DOIs
StatePublished - Dec 19 2018

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Genomics
antibody
genomics
antibodies
Antibodies
experimental design
droplet
cells
protein
sampling
cost
Costs and Cost Analysis
surface proteins
Transcriptome
transcriptome
droplets
detection
Membrane Proteins
Research Design
cost reduction

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

Cite this

Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics. / Stoeckius, Marlon; Zheng, Shiwei; Houck-Loomis, Brian; Hao, Stephanie; Yeung, Bertrand Z.; Mauck, William M.; Smibert, Peter; Satija, Rahul.

In: Genome Biology, Vol. 19, No. 1, 224, 19.12.2018.

Research output: Contribution to journalArticle

Stoeckius, M, Zheng, S, Houck-Loomis, B, Hao, S, Yeung, BZ, Mauck, WM, Smibert, P & Satija, R 2018, 'Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics', Genome Biology, vol. 19, no. 1, 224. https://doi.org/10.1186/s13059-018-1603-1
Stoeckius, Marlon ; Zheng, Shiwei ; Houck-Loomis, Brian ; Hao, Stephanie ; Yeung, Bertrand Z. ; Mauck, William M. ; Smibert, Peter ; Satija, Rahul. / Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics. In: Genome Biology. 2018 ; Vol. 19, No. 1.
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