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Equivalent high-resolution identification of neuronal cell types with single-nucleus and single-cell RNA-sequencing

View ORCID ProfileTrygve E. Bakken, Rebecca D. Hodge, Jeremy M. Miller, Zizhen Yao, Thuc N. Nguyen, Brian Aevermann, Eliza Barkan, Darren Bertagnolli, Tamara Casper, Nick Dee, Emma Garren, Jeff Goldy, Lucas T. Gray, Matthew Kroll, Roger S. Lasken, Kanan Lathia, Sheana Parry, Christine Rimorin, Richard H. Scheuermann, Nicholas J. Schork, Soraya I. Shehata, Michael Tieu, John W. Phillips, Amy Bernard, Kimberly A. Smith, Hongkui Zeng, Ed S. Lein, View ORCID ProfileBosiljka Tasic
doi: https://doi.org/10.1101/239749
Trygve E. Bakken
Allen Institute for Brain Science, Seattle, WA, USA
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Rebecca D. Hodge
Allen Institute for Brain Science, Seattle, WA, USA
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Jeremy M. Miller
Allen Institute for Brain Science, Seattle, WA, USA
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Zizhen Yao
Allen Institute for Brain Science, Seattle, WA, USA
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Thuc N. Nguyen
Allen Institute for Brain Science, Seattle, WA, USA
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Brian Aevermann
J. Craig Venter Institute, La Jolla, CA, USA
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Eliza Barkan
Allen Institute for Brain Science, Seattle, WA, USA
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Darren Bertagnolli
Allen Institute for Brain Science, Seattle, WA, USA
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Tamara Casper
Allen Institute for Brain Science, Seattle, WA, USA
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Nick Dee
Allen Institute for Brain Science, Seattle, WA, USA
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Emma Garren
Allen Institute for Brain Science, Seattle, WA, USA
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Jeff Goldy
Allen Institute for Brain Science, Seattle, WA, USA
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Lucas T. Gray
Allen Institute for Brain Science, Seattle, WA, USA
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Matthew Kroll
Allen Institute for Brain Science, Seattle, WA, USA
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Roger S. Lasken
J. Craig Venter Institute, La Jolla, CA, USA
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Kanan Lathia
Allen Institute for Brain Science, Seattle, WA, USA
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Sheana Parry
Allen Institute for Brain Science, Seattle, WA, USA
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Christine Rimorin
Allen Institute for Brain Science, Seattle, WA, USA
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Richard H. Scheuermann
J. Craig Venter Institute, La Jolla, CA, USA
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Nicholas J. Schork
J. Craig Venter Institute, La Jolla, CA, USA
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Soraya I. Shehata
Allen Institute for Brain Science, Seattle, WA, USA
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Michael Tieu
Allen Institute for Brain Science, Seattle, WA, USA
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John W. Phillips
Allen Institute for Brain Science, Seattle, WA, USA
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Amy Bernard
Allen Institute for Brain Science, Seattle, WA, USA
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Kimberly A. Smith
Allen Institute for Brain Science, Seattle, WA, USA
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Hongkui Zeng
Allen Institute for Brain Science, Seattle, WA, USA
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Ed S. Lein
Allen Institute for Brain Science, Seattle, WA, USA
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Bosiljka Tasic
Allen Institute for Brain Science, Seattle, WA, USA
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  • ORCID record for Bosiljka Tasic
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Abstract

Transcriptional profiling of complex tissues by RNA-sequencing of single nuclei presents some advantages over whole cell analysis. It enables unbiased cellular coverage, lack of cell isolation-based transcriptional effects, and application to archived frozen specimens. Using a well-matched pair of single-nucleus RNA-seq (snRNA-seq) and single-cell RNA-seq (scRNA-seq) SMART-Seq v4 datasets from mouse visual cortex, we demonstrate that similarly high-resolution clustering of closely related neuronal types can be achieved with both methods if intronic sequences are included in nuclear RNA-seq analysis. More transcripts are detected in individual whole cells (∼11,000 genes) than nuclei (∼7,000 genes), but the majority of genes have similar detection across cells and nuclei. We estimate that the nuclear proportion of total cellular mRNA varies from 20% to over 50% for large and small pyramidal neurons, respectively. Together, these results illustrate the high information content of nuclear RNA for characterization of cellular diversity in brain tissues.

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Posted January 19, 2018.
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Equivalent high-resolution identification of neuronal cell types with single-nucleus and single-cell RNA-sequencing
Trygve E. Bakken, Rebecca D. Hodge, Jeremy M. Miller, Zizhen Yao, Thuc N. Nguyen, Brian Aevermann, Eliza Barkan, Darren Bertagnolli, Tamara Casper, Nick Dee, Emma Garren, Jeff Goldy, Lucas T. Gray, Matthew Kroll, Roger S. Lasken, Kanan Lathia, Sheana Parry, Christine Rimorin, Richard H. Scheuermann, Nicholas J. Schork, Soraya I. Shehata, Michael Tieu, John W. Phillips, Amy Bernard, Kimberly A. Smith, Hongkui Zeng, Ed S. Lein, Bosiljka Tasic
bioRxiv 239749; doi: https://doi.org/10.1101/239749
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Equivalent high-resolution identification of neuronal cell types with single-nucleus and single-cell RNA-sequencing
Trygve E. Bakken, Rebecca D. Hodge, Jeremy M. Miller, Zizhen Yao, Thuc N. Nguyen, Brian Aevermann, Eliza Barkan, Darren Bertagnolli, Tamara Casper, Nick Dee, Emma Garren, Jeff Goldy, Lucas T. Gray, Matthew Kroll, Roger S. Lasken, Kanan Lathia, Sheana Parry, Christine Rimorin, Richard H. Scheuermann, Nicholas J. Schork, Soraya I. Shehata, Michael Tieu, John W. Phillips, Amy Bernard, Kimberly A. Smith, Hongkui Zeng, Ed S. Lein, Bosiljka Tasic
bioRxiv 239749; doi: https://doi.org/10.1101/239749

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