Single-nucleus and single-cell transcriptomes compared in matched cortical cell types.
Transcriptomic profiling of complex tissues by single-nucleus RNA-sequencing (snRNA-seq) affords 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...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2018-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0209648 |
| _version_ | 1818899729213292544 |
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| author | Trygve E Bakken Rebecca D Hodge Jeremy A Miller Zizhen Yao Thuc Nghi Nguyen Brian Aevermann Eliza Barkan Darren Bertagnolli Tamara Casper Nick Dee Emma Garren Jeff Goldy Lucas T Graybuck 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 |
| author_facet | Trygve E Bakken Rebecca D Hodge Jeremy A Miller Zizhen Yao Thuc Nghi Nguyen Brian Aevermann Eliza Barkan Darren Bertagnolli Tamara Casper Nick Dee Emma Garren Jeff Goldy Lucas T Graybuck 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 |
| author_sort | Trygve E Bakken |
| collection | DOAJ |
| description | Transcriptomic profiling of complex tissues by single-nucleus RNA-sequencing (snRNA-seq) affords 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 compare cell type detection. Although more transcripts are detected in individual whole cells (~11,000 genes) than nuclei (~7,000 genes), we demonstrate that closely related neuronal cell types can be similarly discriminated with both methods if intronic sequences are included in snRNA-seq analysis. 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. |
| first_indexed | 2024-12-19T19:52:35Z |
| format | Article |
| id | doaj.art-a582d6cca35342eaac24aa2cf90cf4a8 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-19T19:52:35Z |
| publishDate | 2018-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-a582d6cca35342eaac24aa2cf90cf4a82022-12-21T20:07:55ZengPublic Library of Science (PLoS)PLoS ONE1932-62032018-01-011312e020964810.1371/journal.pone.0209648Single-nucleus and single-cell transcriptomes compared in matched cortical cell types.Trygve E BakkenRebecca D HodgeJeremy A MillerZizhen YaoThuc Nghi NguyenBrian AevermannEliza BarkanDarren BertagnolliTamara CasperNick DeeEmma GarrenJeff GoldyLucas T GraybuckMatthew KrollRoger S LaskenKanan LathiaSheana ParryChristine RimorinRichard H ScheuermannNicholas J SchorkSoraya I ShehataMichael TieuJohn W PhillipsAmy BernardKimberly A SmithHongkui ZengEd S LeinBosiljka TasicTranscriptomic profiling of complex tissues by single-nucleus RNA-sequencing (snRNA-seq) affords 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 compare cell type detection. Although more transcripts are detected in individual whole cells (~11,000 genes) than nuclei (~7,000 genes), we demonstrate that closely related neuronal cell types can be similarly discriminated with both methods if intronic sequences are included in snRNA-seq analysis. 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.https://doi.org/10.1371/journal.pone.0209648 |
| spellingShingle | Trygve E Bakken Rebecca D Hodge Jeremy A Miller Zizhen Yao Thuc Nghi Nguyen Brian Aevermann Eliza Barkan Darren Bertagnolli Tamara Casper Nick Dee Emma Garren Jeff Goldy Lucas T Graybuck 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 Single-nucleus and single-cell transcriptomes compared in matched cortical cell types. PLoS ONE |
| title | Single-nucleus and single-cell transcriptomes compared in matched cortical cell types. |
| title_full | Single-nucleus and single-cell transcriptomes compared in matched cortical cell types. |
| title_fullStr | Single-nucleus and single-cell transcriptomes compared in matched cortical cell types. |
| title_full_unstemmed | Single-nucleus and single-cell transcriptomes compared in matched cortical cell types. |
| title_short | Single-nucleus and single-cell transcriptomes compared in matched cortical cell types. |
| title_sort | single nucleus and single cell transcriptomes compared in matched cortical cell types |
| url | https://doi.org/10.1371/journal.pone.0209648 |
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