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Nuclei multiplexing with barcoded antibodies for single-nucleus genomics

Jellert T. Gaublomme, Bo Li, Cristin McCabe, Abigail Knecht, Eugene Drokhlyansky, Nicholas Van Wittenberghe, Julia Waldman, Danielle Dionne, Lan Nguyen, Phil De Jager, Bertrand Yeung, Xinfang Zhao, Naomi Habib, Orit Rozenblatt-Rosen, Aviv Regev
doi: https://doi.org/10.1101/476036
Jellert T. Gaublomme
1Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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  • For correspondence: jellert@broadinstitute.org orit@broadinstitute.org aregev@broadinstitute.org
Bo Li
1Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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Cristin McCabe
1Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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Abigail Knecht
1Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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Eugene Drokhlyansky
1Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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Nicholas Van Wittenberghe
1Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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Julia Waldman
1Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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Danielle Dionne
1Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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Lan Nguyen
1Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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Phil De Jager
2Center for Translational & Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA.
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Bertrand Yeung
3BioLegend Inc., San Diego, CA, USA
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Xinfang Zhao
3BioLegend Inc., San Diego, CA, USA
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Naomi Habib
1Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
4Edmond and Lily Safra Center for Brain Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
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Orit Rozenblatt-Rosen
1Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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  • For correspondence: jellert@broadinstitute.org orit@broadinstitute.org aregev@broadinstitute.org
Aviv Regev
1Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
5Howard Hughes Medical Institute, Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
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  • For correspondence: jellert@broadinstitute.org orit@broadinstitute.org aregev@broadinstitute.org
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Abstract

Single-nucleus RNA-Seq (snRNA-seq) enables the interrogation of cellular states in complex tissues that are challenging to dissociate, including frozen clinical samples. This opens the way, in principle, to large studies, such as those required for human genetics, clinical trials, or precise cell atlases of large organs. However, such applications are currently limited by batch effects, sequential processing, and costs. To address these challenges, we present an approach for multiplexing snRNA-seq, using sample-barcoded antibodies against the nuclear pore complex to uniquely label nuclei from distinct samples. Comparing human brain cortex samples profiled in multiplex with or without hashing antibodies, we demonstrate that nucleus hashing does not significantly alter the recovered transcriptome profiles. We further developed demuxEM, a novel computational tool that robustly detects inter-sample nucleus multiplets and assigns singlets to their samples of origin by antibody barcodes, and validated its accuracy using gender-specific gene expression, species-mixing and natural genetic variation. Nucleus hashing significantly reduces cost per nucleus, recovering up to about 5 times as many single nuclei per microfluidc channel. Our approach provides a robust technique for diverse studies including tissue atlases of isogenic model organisms or from a single larger human organ, multiple biopsies or longitudinal samples of one donor, and large-scale perturbation screens.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted November 23, 2018.
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Nuclei multiplexing with barcoded antibodies for single-nucleus genomics
Jellert T. Gaublomme, Bo Li, Cristin McCabe, Abigail Knecht, Eugene Drokhlyansky, Nicholas Van Wittenberghe, Julia Waldman, Danielle Dionne, Lan Nguyen, Phil De Jager, Bertrand Yeung, Xinfang Zhao, Naomi Habib, Orit Rozenblatt-Rosen, Aviv Regev
bioRxiv 476036; doi: https://doi.org/10.1101/476036
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Nuclei multiplexing with barcoded antibodies for single-nucleus genomics
Jellert T. Gaublomme, Bo Li, Cristin McCabe, Abigail Knecht, Eugene Drokhlyansky, Nicholas Van Wittenberghe, Julia Waldman, Danielle Dionne, Lan Nguyen, Phil De Jager, Bertrand Yeung, Xinfang Zhao, Naomi Habib, Orit Rozenblatt-Rosen, Aviv Regev
bioRxiv 476036; doi: https://doi.org/10.1101/476036

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