Nuclei multiplexing with barcoded antibodies for single-nucleus genomics

Jellert T. Gaublomme; Bo Li; Cristin McCabe; Abigail Knecht; Yiming Yang; Eugene Drokhlyansky; Nicholas Van Wittenberghe; Julia Waldman; Danielle Dionne; Lan Nguyen; Philip L. De Jager; Bertrand Yeung; Xinfang Zhao; Naomi Habib; Orit Rozenblatt-Rosen; Aviv Regev

doi:10.1038/s41467-019-10756-2

Nuclei multiplexing with barcoded antibodies for single-nucleus genomics

Jellert T. Gaublomme^*, Bo Li, Cristin McCabe, Abigail Knecht, Yiming Yang, Eugene Drokhlyansky, Nicholas Van Wittenberghe, Julia Waldman, Danielle Dionne, Lan Nguyen, Philip L. De Jager, Bertrand Yeung, Xinfang Zhao, Naomi Habib, Orit Rozenblatt-Rosen, Aviv Regev

^*Corresponding author for this work

Edmond & Lily Safra Center for Brain Sciences

Research output: Contribution to journal › Article › peer-review

74 Scopus citations

Abstract

Single-nucleus RNA-seq (snRNA-seq) enables the interrogation of cellular states in complex tissues that are challenging to dissociate or are frozen, and opens the way to human genetics studies, clinical trials, and precise cell atlases of large organs. However, such applications are currently limited by batch effects, processing, and costs. Here, we present an approach for multiplexing snRNA-seq, using sample-barcoded antibodies to uniquely label nuclei from distinct samples. Comparing human brain cortex samples profiled with or without hashing antibodies, we demonstrate that nucleus hashing does not significantly alter recovered profiles. We develop DemuxEM, a computational tool that detects inter-sample multiplets and assigns singlets to their sample of origin, and validate its accuracy using sex-specific gene expression, species-mixing and natural genetic variation. Our approach will facilitate tissue atlases of isogenic model organisms or from multiple biopsies or longitudinal samples of one donor, and large-scale perturbation screens.

Original language	American English
Article number	2907
Journal	Nature Communications
Volume	10
Issue number	1
DOIs	https://doi.org/10.1038/s41467-019-10756-2
State	Published - 1 Dec 2019

Bibliographical note

Funding Information:
This publication is part of the Human Cell Atlas (www.humancellatlas.org/ publications). We thank Dr. David Bennett at RUSH University for the use of samples from the Religious Order Study (ROS) and the Memory and Aging Project (MAP). We thank Chun (Jimmie) Ye for his input on setting appropriate Demuxlet parameters. We thank Jiarui Ding for helpful discussions in appropriate preprocessing of the species-mixing data. We thank Leslie Gaffney, Anna Hupalowska and Jennifer Rood for help with figure and paper preparation. This work was supported by the NIH BRAIN Initiative grant U19MH114821 and the Klarman Cell Observatory. The ROSMAP sample collection and data used in this paper were supported by U01 AG046152, RF1 AG057473, RF1 AG015819, P30 AG10161, and R01 AG17917.

Publisher Copyright:
© 2019, The Author(s).

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Gaublomme, J. T., Li, B., McCabe, C., Knecht, A., Yang, Y., Drokhlyansky, E., Van Wittenberghe, N., Waldman, J., Dionne, D., Nguyen, L., De Jager, P. L., Yeung, B., Zhao, X., Habib, N., Rozenblatt-Rosen, O., & Regev, A. (2019). Nuclei multiplexing with barcoded antibodies for single-nucleus genomics. Nature Communications, 10(1), Article 2907. https://doi.org/10.1038/s41467-019-10756-2

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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 or are frozen, and opens the way to human genetics studies, clinical trials, and precise cell atlases of large organs. However, such applications are currently limited by batch effects, processing, and costs. Here, we present an approach for multiplexing snRNA-seq, using sample-barcoded antibodies to uniquely label nuclei from distinct samples. Comparing human brain cortex samples profiled with or without hashing antibodies, we demonstrate that nucleus hashing does not significantly alter recovered profiles. We develop DemuxEM, a computational tool that detects inter-sample multiplets and assigns singlets to their sample of origin, and validate its accuracy using sex-specific gene expression, species-mixing and natural genetic variation. Our approach will facilitate tissue atlases of isogenic model organisms or from multiple biopsies or longitudinal samples of one donor, and large-scale perturbation screens.",

author = "Gaublomme, {Jellert T.} and Bo Li and Cristin McCabe and Abigail Knecht and Yiming Yang and Eugene Drokhlyansky and {Van Wittenberghe}, Nicholas and Julia Waldman and Danielle Dionne and Lan Nguyen and {De Jager}, {Philip L.} and Bertrand Yeung and Xinfang Zhao and Naomi Habib and Orit Rozenblatt-Rosen and Aviv Regev",

note = "Funding Information: This publication is part of the Human Cell Atlas (www.humancellatlas.org/ publications). We thank Dr. David Bennett at RUSH University for the use of samples from the Religious Order Study (ROS) and the Memory and Aging Project (MAP). We thank Chun (Jimmie) Ye for his input on setting appropriate Demuxlet parameters. We thank Jiarui Ding for helpful discussions in appropriate preprocessing of the species-mixing data. We thank Leslie Gaffney, Anna Hupalowska and Jennifer Rood for help with figure and paper preparation. This work was supported by the NIH BRAIN Initiative grant U19MH114821 and the Klarman Cell Observatory. The ROSMAP sample collection and data used in this paper were supported by U01 AG046152, RF1 AG057473, RF1 AG015819, P30 AG10161, and R01 AG17917. Publisher Copyright: {\textcopyright} 2019, The Author(s).",

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AU - Li, Bo

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AU - Knecht, Abigail

AU - Yang, Yiming

AU - Drokhlyansky, Eugene

AU - Van Wittenberghe, Nicholas

AU - Waldman, Julia

AU - Dionne, Danielle

AU - Nguyen, Lan

AU - De Jager, Philip L.

AU - Yeung, Bertrand

AU - Zhao, Xinfang

AU - Habib, Naomi

AU - Rozenblatt-Rosen, Orit

AU - Regev, Aviv

N1 - Funding Information: This publication is part of the Human Cell Atlas (www.humancellatlas.org/ publications). We thank Dr. David Bennett at RUSH University for the use of samples from the Religious Order Study (ROS) and the Memory and Aging Project (MAP). We thank Chun (Jimmie) Ye for his input on setting appropriate Demuxlet parameters. We thank Jiarui Ding for helpful discussions in appropriate preprocessing of the species-mixing data. We thank Leslie Gaffney, Anna Hupalowska and Jennifer Rood for help with figure and paper preparation. This work was supported by the NIH BRAIN Initiative grant U19MH114821 and the Klarman Cell Observatory. The ROSMAP sample collection and data used in this paper were supported by U01 AG046152, RF1 AG057473, RF1 AG015819, P30 AG10161, and R01 AG17917. Publisher Copyright: © 2019, The Author(s).

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N2 - Single-nucleus RNA-seq (snRNA-seq) enables the interrogation of cellular states in complex tissues that are challenging to dissociate or are frozen, and opens the way to human genetics studies, clinical trials, and precise cell atlases of large organs. However, such applications are currently limited by batch effects, processing, and costs. Here, we present an approach for multiplexing snRNA-seq, using sample-barcoded antibodies to uniquely label nuclei from distinct samples. Comparing human brain cortex samples profiled with or without hashing antibodies, we demonstrate that nucleus hashing does not significantly alter recovered profiles. We develop DemuxEM, a computational tool that detects inter-sample multiplets and assigns singlets to their sample of origin, and validate its accuracy using sex-specific gene expression, species-mixing and natural genetic variation. Our approach will facilitate tissue atlases of isogenic model organisms or from multiple biopsies or longitudinal samples of one donor, and large-scale perturbation screens.

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Nuclei multiplexing with barcoded antibodies for single-nucleus genomics

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