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Single-nucleus and single-cell transcriptomes capture cortical neuron diversity at similarly high resolution
  • +25
  • 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
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
Eliza Barkan
Allen Institute for Brain Science, Seattle, WA, USA
Darren Bertagnolli
Allen Institute for Brain Science, Seattle, WA, USA
Tamara Casper
Allen Institute for Brain Science, Seattle, WA, USA
Nick Dee
Allen Institute for Brain Science, Seattle, WA, USA
Emma Garren
Allen Institute for Brain Science, Seattle, WA, USA
Jeff Goldy
Allen Institute for Brain Science, Seattle, WA, USA
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
Roger S. Lasken
J. Craig Venter Institute, La Jolla, CA, USA
Kanan Lathia
Allen Institute for Brain Science, Seattle, WA, USA
Sheana Parry
Allen Institute for Brain Science, Seattle, WA, USA
Christine Rimorin
Allen Institute for Brain Science, Seattle, WA, USA
Richard H. Scheuermann
J. Craig Venter Institute, La Jolla, CA, USA
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
Michael Tieu
Allen Institute for Brain Science, Seattle, WA, USA
John W. Phillips
Allen Institute for Brain Science, Seattle, WA, USA
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
Hongkui Zeng
Allen Institute for Brain Science, Seattle, WA, USA
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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Abstract

Transcriptomic profiling of complex tissues by single-nucleus RNA-sequencing (snRNA-seq) presents some advantages over single-cell RNA-sequencing (scRNA-seq). snRNA-seq provides less biased cellular coverage, does not appear to suffer cell isolation-based transcriptional artifacts, and can be applied to archived frozen specimens. We used well-matched snRNA-seq and scRNA-seq datasets from mouse visual cortex to demonstrate that similarly high cell type resolution of closely related neuronal types can be achieved with both methods if intronic sequences are included in snRNA-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.