Nuclei multiplexing with barcoded antibodies for single-nucleus genomics
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 limite...
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| Format: | Article |
| Language: | English |
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Springer Science and Business Media LLC
2020
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| Online Access: | https://hdl.handle.net/1721.1/125028 |
| _version_ | 1811090583791337472 |
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| author | Regev, Aviv |
| author2 | Massachusetts Institute of Technology. Department of Biology |
| author_facet | Massachusetts Institute of Technology. Department of Biology Regev, Aviv |
| author_sort | Regev, Aviv |
| collection | MIT |
| description | 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. |
| first_indexed | 2024-09-23T14:48:31Z |
| format | Article |
| id | mit-1721.1/125028 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T14:48:31Z |
| publishDate | 2020 |
| publisher | Springer Science and Business Media LLC |
| record_format | dspace |
| spelling | mit-1721.1/1250282022-10-01T22:37:35Z Nuclei multiplexing with barcoded antibodies for single-nucleus genomics Regev, Aviv Massachusetts Institute of Technology. Department of Biology Koch Institute for Integrative Cancer Research at MIT General Biochemistry, Genetics and Molecular Biology General Physics and Astronomy General Chemistry 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. BRAIN Initiative (Grant U19MH114821) National Institutes of Health (U.S.) (Grant U01 AG046152) National Institutes of Health (U.S.) (Grant RF1 AG057473) National Institutes of Health (U.S.) (Grant RF1 AG015819) National Institutes of Health (U.S.) (Grant P30 AG10161) National Institutes of Health (U.S.) (Grant R01 AG17917) 2020-05-05T19:43:44Z 2020-05-05T19:43:44Z 2019-07-02 2020-01-28T18:34:21Z Article http://purl.org/eprint/type/JournalArticle 2041-1723 https://hdl.handle.net/1721.1/125028 Gaublomme, Jellert T. et al. “Nuclei multiplexing with barcoded antibodies for single-nucleus genomics.” Nature Communications 10 (2019): Article number 2907 © 2019 The Author(s) en 10.1038/s41467-019-10756-2 Nature Communications Creative Commons Attribution 4.0 International license https://creativecommons.org/licenses/by/4.0/ application/pdf Springer Science and Business Media LLC Nature |
| spellingShingle | General Biochemistry, Genetics and Molecular Biology General Physics and Astronomy General Chemistry Regev, Aviv Nuclei multiplexing with barcoded antibodies for single-nucleus genomics |
| title | Nuclei multiplexing with barcoded antibodies for single-nucleus genomics |
| title_full | Nuclei multiplexing with barcoded antibodies for single-nucleus genomics |
| title_fullStr | Nuclei multiplexing with barcoded antibodies for single-nucleus genomics |
| title_full_unstemmed | Nuclei multiplexing with barcoded antibodies for single-nucleus genomics |
| title_short | Nuclei multiplexing with barcoded antibodies for single-nucleus genomics |
| title_sort | nuclei multiplexing with barcoded antibodies for single nucleus genomics |
| topic | General Biochemistry, Genetics and Molecular Biology General Physics and Astronomy General Chemistry |
| url | https://hdl.handle.net/1721.1/125028 |
| work_keys_str_mv | AT regevaviv nucleimultiplexingwithbarcodedantibodiesforsinglenucleusgenomics |