1
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Yao Z, van Velthoven CTJ, Kunst M, Zhang M, McMillen D, Lee C, Jung W, Goldy J, Abdelhak A, Aitken M, Baker K, Baker P, Barkan E, Bertagnolli D, Bhandiwad A, Bielstein C, Bishwakarma P, Campos J, Carey D, Casper T, Chakka AB, Chakrabarty R, Chavan S, Chen M, Clark M, Close J, Crichton K, Daniel S, DiValentin P, Dolbeare T, Ellingwood L, Fiabane E, Fliss T, Gee J, Gerstenberger J, Glandon A, Gloe J, Gould J, Gray J, Guilford N, Guzman J, Hirschstein D, Ho W, Hooper M, Huang M, Hupp M, Jin K, Kroll M, Lathia K, Leon A, Li S, Long B, Madigan Z, Malloy J, Malone J, Maltzer Z, Martin N, McCue R, McGinty R, Mei N, Melchor J, Meyerdierks E, Mollenkopf T, Moonsman S, Nguyen TN, Otto S, Pham T, Rimorin C, Ruiz A, Sanchez R, Sawyer L, Shapovalova N, Shepard N, Slaughterbeck C, Sulc J, Tieu M, Torkelson A, Tung H, Valera Cuevas N, Vance S, Wadhwani K, Ward K, Levi B, Farrell C, Young R, Staats B, Wang MQM, Thompson CL, Mufti S, Pagan CM, Kruse L, Dee N, Sunkin SM, Esposito L, Hawrylycz MJ, Waters J, Ng L, Smith K, Tasic B, Zhuang X, Zeng H. A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain. Nature 2023; 624:317-332. [PMID: 38092916 PMCID: PMC10719114 DOI: 10.1038/s41586-023-06812-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 10/31/2023] [Indexed: 12/17/2023]
Abstract
The mammalian brain consists of millions to billions of cells that are organized into many cell types with specific spatial distribution patterns and structural and functional properties1-3. Here we report a comprehensive and high-resolution transcriptomic and spatial cell-type atlas for the whole adult mouse brain. The cell-type atlas was created by combining a single-cell RNA-sequencing (scRNA-seq) dataset of around 7 million cells profiled (approximately 4.0 million cells passing quality control), and a spatial transcriptomic dataset of approximately 4.3 million cells using multiplexed error-robust fluorescence in situ hybridization (MERFISH). The atlas is hierarchically organized into 4 nested levels of classification: 34 classes, 338 subclasses, 1,201 supertypes and 5,322 clusters. We present an online platform, Allen Brain Cell Atlas, to visualize the mouse whole-brain cell-type atlas along with the single-cell RNA-sequencing and MERFISH datasets. We systematically analysed the neuronal and non-neuronal cell types across the brain and identified a high degree of correspondence between transcriptomic identity and spatial specificity for each cell type. The results reveal unique features of cell-type organization in different brain regions-in particular, a dichotomy between the dorsal and ventral parts of the brain. The dorsal part contains relatively fewer yet highly divergent neuronal types, whereas the ventral part contains more numerous neuronal types that are more closely related to each other. Our study also uncovered extraordinary diversity and heterogeneity in neurotransmitter and neuropeptide expression and co-expression patterns in different cell types. Finally, we found that transcription factors are major determinants of cell-type classification and identified a combinatorial transcription factor code that defines cell types across all parts of the brain. The whole mouse brain transcriptomic and spatial cell-type atlas establishes a benchmark reference atlas and a foundational resource for integrative investigations of cellular and circuit function, development and evolution of the mammalian brain.
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Affiliation(s)
- Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA.
| | | | | | - Meng Zhang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
| | | | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Won Jung
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
| | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Pamela Baker
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Eliza Barkan
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | - Daniel Carey
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Min Chen
- University of Pennsylvania, Philadelphia, PA, USA
| | | | - Jennie Close
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Scott Daniel
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Tim Dolbeare
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - James Gee
- University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Jessica Gloe
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - James Gray
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Windy Ho
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Mike Huang
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Madie Hupp
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Kelly Jin
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Kanan Lathia
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Arielle Leon
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Su Li
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Brian Long
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Zach Madigan
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Zoe Maltzer
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Naomi Martin
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Rachel McCue
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Ryan McGinty
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Nicholas Mei
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Jose Melchor
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Sven Otto
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Lane Sawyer
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Noah Shepard
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Josef Sulc
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Herman Tung
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Shane Vance
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Katelyn Ward
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Boaz Levi
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Rob Young
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Brian Staats
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Shoaib Mufti
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Lauren Kruse
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Jack Waters
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA.
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2
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Dorrity MW, Saunders LM, Duran M, Srivatsan SR, Barkan E, Jackson DL, Sattler SM, Ewing B, Queitsch C, Shendure J, Raible DW, Kimelman D, Trapnell C. Proteostasis governs differential temperature sensitivity across embryonic cell types. Cell 2023; 186:5015-5027.e12. [PMID: 37949057 DOI: 10.1016/j.cell.2023.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 05/29/2023] [Accepted: 10/11/2023] [Indexed: 11/12/2023]
Abstract
Embryonic development is remarkably robust, but temperature stress can degrade its ability to generate animals with invariant anatomy. Phenotypes associated with environmental stress suggest that some cell types are more sensitive to stress than others, but the basis of this sensitivity is unknown. Here, we characterize hundreds of individual zebrafish embryos under temperature stress using whole-animal single-cell RNA sequencing (RNA-seq) to identify cell types and molecular programs driving phenotypic variability. We find that temperature perturbs the normal proportions and gene expression programs of numerous cell types and also introduces asynchrony in developmental timing. The notochord is particularly sensitive to temperature, which we map to a specialized cell type: sheath cells. These cells accumulate misfolded protein at elevated temperature, leading to a cascading structural failure of the notochord and anatomic defects. Our study demonstrates that whole-animal single-cell RNA-seq can identify mechanisms for developmental robustness and pinpoint cell types that constitute key failure points.
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Affiliation(s)
- Michael W Dorrity
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Structural and Computational Biology, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
| | - Lauren M Saunders
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Madeleine Duran
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Sanjay R Srivatsan
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Eliza Barkan
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Dana L Jackson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Sydney M Sattler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Brent Ewing
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - David W Raible
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - David Kimelman
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
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3
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Yao Z, van Velthoven CTJ, Kunst M, Zhang M, McMillen D, Lee C, Jung W, Goldy J, Abdelhak A, Baker P, Barkan E, Bertagnolli D, Campos J, Carey D, Casper T, Chakka AB, Chakrabarty R, Chavan S, Chen M, Clark M, Close J, Crichton K, Daniel S, Dolbeare T, Ellingwood L, Gee J, Glandon A, Gloe J, Gould J, Gray J, Guilford N, Guzman J, Hirschstein D, Ho W, Jin K, Kroll M, Lathia K, Leon A, Long B, Maltzer Z, Martin N, McCue R, Meyerdierks E, Nguyen TN, Pham T, Rimorin C, Ruiz A, Shapovalova N, Slaughterbeck C, Sulc J, Tieu M, Torkelson A, Tung H, Cuevas NV, Wadhwani K, Ward K, Levi B, Farrell C, Thompson CL, Mufti S, Pagan CM, Kruse L, Dee N, Sunkin SM, Esposito L, Hawrylycz MJ, Waters J, Ng L, Smith KA, Tasic B, Zhuang X, Zeng H. A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain. bioRxiv 2023:2023.03.06.531121. [PMID: 37034735 PMCID: PMC10081189 DOI: 10.1101/2023.03.06.531121] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The mammalian brain is composed of millions to billions of cells that are organized into numerous cell types with specific spatial distribution patterns and structural and functional properties. An essential step towards understanding brain function is to obtain a parts list, i.e., a catalog of cell types, of the brain. Here, we report a comprehensive and high-resolution transcriptomic and spatial cell type atlas for the whole adult mouse brain. The cell type atlas was created based on the combination of two single-cell-level, whole-brain-scale datasets: a single-cell RNA-sequencing (scRNA-seq) dataset of ~7 million cells profiled, and a spatially resolved transcriptomic dataset of ~4.3 million cells using MERFISH. The atlas is hierarchically organized into five nested levels of classification: 7 divisions, 32 classes, 306 subclasses, 1,045 supertypes and 5,200 clusters. We systematically analyzed the neuronal, non-neuronal, and immature neuronal cell types across the brain and identified a high degree of correspondence between transcriptomic identity and spatial specificity for each cell type. The results reveal unique features of cell type organization in different brain regions, in particular, a dichotomy between the dorsal and ventral parts of the brain: the dorsal part contains relatively fewer yet highly divergent neuronal types, whereas the ventral part contains more numerous neuronal types that are more closely related to each other. We also systematically characterized cell-type specific expression of neurotransmitters, neuropeptides, and transcription factors. The study uncovered extraordinary diversity and heterogeneity in neurotransmitter and neuropeptide expression and co-expression patterns in different cell types across the brain, suggesting they mediate a myriad of modes of intercellular communications. Finally, we found that transcription factors are major determinants of cell type classification in the adult mouse brain and identified a combinatorial transcription factor code that defines cell types across all parts of the brain. The whole-mouse-brain transcriptomic and spatial cell type atlas establishes a benchmark reference atlas and a foundational resource for deep and integrative investigations of cell type and circuit function, development, and evolution of the mammalian brain.
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Affiliation(s)
- Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Meng Zhang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
| | | | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Won Jung
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
| | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Pamela Baker
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Eliza Barkan
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Daniel Carey
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Min Chen
- University of Pennsylvania, Philadelphia, PA, USA
| | | | - Jennie Close
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Scott Daniel
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Tim Dolbeare
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - James Gee
- University of Pennsylvania, Philadelphia, PA, USA
| | | | - Jessica Gloe
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - James Gray
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Windy Ho
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Kelly Jin
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Kanan Lathia
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Arielle Leon
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Brian Long
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Zoe Maltzer
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Naomi Martin
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Rachel McCue
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | | | | | - Josef Sulc
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Herman Tung
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Katelyn Ward
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Boaz Levi
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Shoaib Mufti
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Lauren Kruse
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Jack Waters
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
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4
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Berg J, Sorensen SA, Ting JT, Miller JA, Chartrand T, Buchin A, Bakken TE, Budzillo A, Dee N, Ding SL, Gouwens NW, Hodge RD, Kalmbach B, Lee C, Lee BR, Alfiler L, Baker K, Barkan E, Beller A, Berry K, Bertagnolli D, Bickley K, Bomben J, Braun T, Brouner K, Casper T, Chong P, Crichton K, Dalley R, de Frates R, Desta T, Lee SD, D'Orazi F, Dotson N, Egdorf T, Enstrom R, Farrell C, Feng D, Fong O, Furdan S, Galakhova AA, Gamlin C, Gary A, Glandon A, Goldy J, Gorham M, Goriounova NA, Gratiy S, Graybuck L, Gu H, Hadley K, Hansen N, Heistek TS, Henry AM, Heyer DB, Hill D, Hill C, Hupp M, Jarsky T, Kebede S, Keene L, Kim L, Kim MH, Kroll M, Latimer C, Levi BP, Link KE, Mallory M, Mann R, Marshall D, Maxwell M, McGraw M, McMillen D, Melief E, Mertens EJ, Mezei L, Mihut N, Mok S, Molnar G, Mukora A, Ng L, Ngo K, Nicovich PR, Nyhus J, Olah G, Oldre A, Omstead V, Ozsvar A, Park D, Peng H, Pham T, Pom CA, Potekhina L, Rajanbabu R, Ransford S, Reid D, Rimorin C, Ruiz A, Sandman D, Sulc J, Sunkin SM, Szafer A, Szemenyei V, Thomsen ER, Tieu M, Torkelson A, Trinh J, Tung H, Wakeman W, Waleboer F, Ward K, Wilbers R, Williams G, Yao Z, Yoon JG, Anastassiou C, Arkhipov A, Barzo P, Bernard A, Cobbs C, de Witt Hamer PC, Ellenbogen RG, Esposito L, Ferreira M, Gwinn RP, Hawrylycz MJ, Hof PR, Idema S, Jones AR, Keene CD, Ko AL, Murphy GJ, Ng L, Ojemann JG, Patel AP, Phillips JW, Silbergeld DL, Smith K, Tasic B, Yuste R, Segev I, de Kock CPJ, Mansvelder HD, Tamas G, Zeng H, Koch C, Lein ES. Author Correction: Human neocortical expansion involves glutamatergic neuron diversification. Nature 2022; 601:E12. [PMID: 34992294 PMCID: PMC8770134 DOI: 10.1038/s41586-021-04322-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jim Berg
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Jonathan T Ting
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | | | | | | | | | | | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Brian Kalmbach
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Brian R Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Eliza Barkan
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Allison Beller
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Kyla Berry
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Kris Bickley
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Peter Chong
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Tsega Desta
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Tom Egdorf
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - David Feng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Olivia Fong
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Szabina Furdan
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Anna A Galakhova
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Clare Gamlin
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Amanda Gary
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Natalia A Goriounova
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | | | | | - Hong Gu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Tim S Heistek
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Alex M Henry
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Djai B Heyer
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - DiJon Hill
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Chris Hill
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Madie Hupp
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Tim Jarsky
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Sara Kebede
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lisa Keene
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Lisa Kim
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Caitlin Latimer
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Boaz P Levi
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Rusty Mann
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Desiree Marshall
- Department of Pathology, University of Washington, Seattle, WA, USA
| | | | - Medea McGraw
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Erica Melief
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Eline J Mertens
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Leona Mezei
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Norbert Mihut
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | | | - Gabor Molnar
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Alice Mukora
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lindsay Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Kiet Ngo
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Julie Nyhus
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Gaspar Olah
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Aaron Oldre
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Attila Ozsvar
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Daniel Park
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | | | - David Reid
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Josef Sulc
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Aaron Szafer
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Viktor Szemenyei
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | | | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Herman Tung
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Femke Waleboer
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Katelyn Ward
- Allen Institute for Brain Science, Seattle, WA, USA
| | - René Wilbers
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | | | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Pal Barzo
- Department of Neurosurgery, University of Szeged, Szeged, Hungary
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Philip C de Witt Hamer
- Cancer Center Amsterdam, Brain Tumor Center, Department of Neurosurgery, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | | | | | - Manuel Ferreira
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | | | - Patrick R Hof
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sander Idema
- Cancer Center Amsterdam, Brain Tumor Center, Department of Neurosurgery, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | | | - C Dirk Keene
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Andrew L Ko
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Gabe J Murphy
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Jeffrey G Ojemann
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Anoop P Patel
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | - Daniel L Silbergeld
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | | | - Rafael Yuste
- NeuroTechnology Center, Columbia University, New York, NY, USA
| | - Idan Segev
- Edmond and Lily Safra Center for Brain Sciences and Department of Neurobiology, The Hebrew University Jerusalem, Jerusalem, Israel
| | - Christiaan P J de Kock
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Huibert D Mansvelder
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Gabor Tamas
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA.
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA.
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5
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Berg J, Sorensen SA, Ting JT, Miller JA, Chartrand T, Buchin A, Bakken TE, Budzillo A, Dee N, Ding SL, Gouwens NW, Hodge RD, Kalmbach B, Lee C, Lee BR, Alfiler L, Baker K, Barkan E, Beller A, Berry K, Bertagnolli D, Bickley K, Bomben J, Braun T, Brouner K, Casper T, Chong P, Crichton K, Dalley R, de Frates R, Desta T, Lee SD, D'Orazi F, Dotson N, Egdorf T, Enstrom R, Farrell C, Feng D, Fong O, Furdan S, Galakhova AA, Gamlin C, Gary A, Glandon A, Goldy J, Gorham M, Goriounova NA, Gratiy S, Graybuck L, Gu H, Hadley K, Hansen N, Heistek TS, Henry AM, Heyer DB, Hill D, Hill C, Hupp M, Jarsky T, Kebede S, Keene L, Kim L, Kim MH, Kroll M, Latimer C, Levi BP, Link KE, Mallory M, Mann R, Marshall D, Maxwell M, McGraw M, McMillen D, Melief E, Mertens EJ, Mezei L, Mihut N, Mok S, Molnar G, Mukora A, Ng L, Ngo K, Nicovich PR, Nyhus J, Olah G, Oldre A, Omstead V, Ozsvar A, Park D, Peng H, Pham T, Pom CA, Potekhina L, Rajanbabu R, Ransford S, Reid D, Rimorin C, Ruiz A, Sandman D, Sulc J, Sunkin SM, Szafer A, Szemenyei V, Thomsen ER, Tieu M, Torkelson A, Trinh J, Tung H, Wakeman W, Waleboer F, Ward K, Wilbers R, Williams G, Yao Z, Yoon JG, Anastassiou C, Arkhipov A, Barzo P, Bernard A, Cobbs C, de Witt Hamer PC, Ellenbogen RG, Esposito L, Ferreira M, Gwinn RP, Hawrylycz MJ, Hof PR, Idema S, Jones AR, Keene CD, Ko AL, Murphy GJ, Ng L, Ojemann JG, Patel AP, Phillips JW, Silbergeld DL, Smith K, Tasic B, Yuste R, Segev I, de Kock CPJ, Mansvelder HD, Tamas G, Zeng H, Koch C, Lein ES. Human neocortical expansion involves glutamatergic neuron diversification. Nature 2021; 598:151-158. [PMID: 34616067 PMCID: PMC8494638 DOI: 10.1038/s41586-021-03813-8] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/07/2021] [Indexed: 11/09/2022]
Abstract
The neocortex is disproportionately expanded in human compared with mouse1,2, both in its total volume relative to subcortical structures and in the proportion occupied by supragranular layers composed of neurons that selectively make connections within the neocortex and with other telencephalic structures. Single-cell transcriptomic analyses of human and mouse neocortex show an increased diversity of glutamatergic neuron types in supragranular layers in human neocortex and pronounced gradients as a function of cortical depth3. Here, to probe the functional and anatomical correlates of this transcriptomic diversity, we developed a robust platform combining patch clamp recording, biocytin staining and single-cell RNA-sequencing (Patch-seq) to examine neurosurgically resected human tissues. We demonstrate a strong correspondence between morphological, physiological and transcriptomic phenotypes of five human glutamatergic supragranular neuron types. These were enriched in but not restricted to layers, with one type varying continuously in all phenotypes across layers 2 and 3. The deep portion of layer 3 contained highly distinctive cell types, two of which express a neurofilament protein that labels long-range projection neurons in primates that are selectively depleted in Alzheimer's disease4,5. Together, these results demonstrate the explanatory power of transcriptomic cell-type classification, provide a structural underpinning for increased complexity of cortical function in humans, and implicate discrete transcriptomic neuron types as selectively vulnerable in disease.
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Affiliation(s)
- Jim Berg
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Jonathan T Ting
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | | | | | | | | | | | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Brian Kalmbach
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Brian R Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Eliza Barkan
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Allison Beller
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Kyla Berry
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Kris Bickley
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Peter Chong
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Tsega Desta
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Tom Egdorf
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - David Feng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Olivia Fong
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Szabina Furdan
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Anna A Galakhova
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Clare Gamlin
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Amanda Gary
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Natalia A Goriounova
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | | | | | - Hong Gu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Tim S Heistek
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Alex M Henry
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Djai B Heyer
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - DiJon Hill
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Chris Hill
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Madie Hupp
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Tim Jarsky
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Sara Kebede
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lisa Keene
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Lisa Kim
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Caitlin Latimer
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Boaz P Levi
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Rusty Mann
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Desiree Marshall
- Department of Pathology, University of Washington, Seattle, WA, USA
| | | | - Medea McGraw
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Erica Melief
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Eline J Mertens
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Leona Mezei
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Norbert Mihut
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | | | - Gabor Molnar
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Alice Mukora
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lindsay Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Kiet Ngo
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Julie Nyhus
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Gaspar Olah
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Aaron Oldre
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Attila Ozsvar
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Daniel Park
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | | | - David Reid
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Josef Sulc
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Aaron Szafer
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Viktor Szemenyei
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | | | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Herman Tung
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Femke Waleboer
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Katelyn Ward
- Allen Institute for Brain Science, Seattle, WA, USA
| | - René Wilbers
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | | | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Pal Barzo
- Department of Neurosurgery, University of Szeged, Szeged, Hungary
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Philip C de Witt Hamer
- Cancer Center Amsterdam, Brain Tumor Center, Department of Neurosurgery, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | | | | | - Manuel Ferreira
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | | | - Patrick R Hof
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sander Idema
- Cancer Center Amsterdam, Brain Tumor Center, Department of Neurosurgery, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | | | - C Dirk Keene
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Andrew L Ko
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Gabe J Murphy
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Jeffrey G Ojemann
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Anoop P Patel
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | - Daniel L Silbergeld
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | | | - Rafael Yuste
- NeuroTechnology Center, Columbia University, New York, NY, USA
| | - Idan Segev
- Edmond and Lily Safra Center for Brain Sciences and Department of Neurobiology, The Hebrew University Jerusalem, Jerusalem, Israel
| | - Christiaan P J de Kock
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Huibert D Mansvelder
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Gabor Tamas
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA.
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA.
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6
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Srivatsan SR, Regier MC, Barkan E, Franks JM, Packer JS, Grosjean P, Duran M, Saxton S, Ladd JJ, Spielmann M, Lois C, Lampe PD, Shendure J, Stevens KR, Trapnell C. Embryo-scale, single-cell spatial transcriptomics. Science 2021; 373:111-117. [PMID: 34210887 DOI: 10.1126/science.abb9536] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 02/13/2021] [Accepted: 05/24/2021] [Indexed: 12/12/2022]
Abstract
Spatial patterns of gene expression manifest at scales ranging from local (e.g., cell-cell interactions) to global (e.g., body axis patterning). However, current spatial transcriptomics methods either average local contexts or are restricted to limited fields of view. Here, we introduce sci-Space, which retains single-cell resolution while resolving spatial heterogeneity at larger scales. Applying sci-Space to developing mouse embryos, we captured approximate spatial coordinates and whole transcriptomes of about 120,000 nuclei. We identify thousands of genes exhibiting anatomically patterned expression, leverage spatial information to annotate cellular subtypes, show that cell types vary substantially in their extent of spatial patterning, and reveal correlations between pseudotime and the migratory patterns of differentiating neurons. Looking forward, we anticipate that sci-Space will facilitate the construction of spatially resolved single-cell atlases of mammalian development.
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Affiliation(s)
- Sanjay R Srivatsan
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Mary C Regier
- Department of Bioengineering. University of Washington, Seattle, WA, USA.,Institute for Stem Cell and Regenerative Medicine, Seattle, WA, USA
| | - Eliza Barkan
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Jennifer M Franks
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Parker Grosjean
- Department of Bioengineering. University of Washington, Seattle, WA, USA
| | - Madeleine Duran
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Sarah Saxton
- Department of Bioengineering. University of Washington, Seattle, WA, USA
| | - Jon J Ladd
- Translational Research Program, Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Malte Spielmann
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany.,Human Molecular Genomics Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Carlos Lois
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Paul D Lampe
- Translational Research Program, Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA. .,Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Kelly R Stevens
- Department of Bioengineering. University of Washington, Seattle, WA, USA. .,Institute for Stem Cell and Regenerative Medicine, Seattle, WA, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA. .,Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
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7
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Bernasconi SM, Daëron M, Bergmann KD, Bonifacie M, Meckler AN, Affek HP, Anderson N, Bajnai D, Barkan E, Beverly E, Blamart D, Burgener L, Calmels D, Chaduteau C, Clog M, Davidheiser‐Kroll B, Davies A, Dux F, Eiler J, Elliott B, Fetrow AC, Fiebig J, Goldberg S, Hermoso M, Huntington KW, Hyland E, Ingalls M, Jaggi M, John CM, Jost AB, Katz S, Kelson J, Kluge T, Kocken IJ, Laskar A, Leutert TJ, Liang D, Lucarelli J, Mackey TJ, Mangenot X, Meinicke N, Modestou SE, Müller IA, Murray S, Neary A, Packard N, Passey BH, Pelletier E, Petersen S, Piasecki A, Schauer A, Snell KE, Swart PK, Tripati A, Upadhyay D, Vennemann T, Winkelstern I, Yarian D, Yoshida N, Zhang N, Ziegler M. InterCarb: A Community Effort to Improve Interlaboratory Standardization of the Carbonate Clumped Isotope Thermometer Using Carbonate Standards. Geochem Geophys Geosyst 2021; 22:e2020GC009588. [PMID: 34220359 PMCID: PMC8244079 DOI: 10.1029/2020gc009588] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 06/12/2023]
Abstract
Increased use and improved methodology of carbonate clumped isotope thermometry has greatly enhanced our ability to interrogate a suite of Earth-system processes. However, interlaboratory discrepancies in quantifying carbonate clumped isotope (Δ47) measurements persist, and their specific sources remain unclear. To address interlaboratory differences, we first provide consensus values from the clumped isotope community for four carbonate standards relative to heated and equilibrated gases with 1,819 individual analyses from 10 laboratories. Then we analyzed the four carbonate standards along with three additional standards, spanning a broad range of δ47 and Δ47 values, for a total of 5,329 analyses on 25 individual mass spectrometers from 22 different laboratories. Treating three of the materials as known standards and the other four as unknowns, we find that the use of carbonate reference materials is a robust method for standardization that yields interlaboratory discrepancies entirely consistent with intralaboratory analytical uncertainties. Carbonate reference materials, along with measurement and data processing practices described herein, provide the carbonate clumped isotope community with a robust approach to achieve interlaboratory agreement as we continue to use and improve this powerful geochemical tool. We propose that carbonate clumped isotope data normalized to the carbonate reference materials described in this publication should be reported as Δ47 (I-CDES) values for Intercarb-Carbon Dioxide Equilibrium Scale.
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Affiliation(s)
| | - M. Daëron
- Laboratoire des Sciences du Climat et de l’EnvironnementLSCE/IPSLCEA‐CNRS‐UVSQUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - K. D. Bergmann
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - M. Bonifacie
- Université de ParisInstitut de Physique du Globe de ParisCNRSParisFrance
| | - A. N. Meckler
- Bjerknes Centre for Climate Research and Department of Earth ScienceUniversity of BergenBergenNorway
| | - H. P. Affek
- Institute of Earth SciencesHebrew University of JerusalemJerusalemIsrael
| | - N. Anderson
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - D. Bajnai
- Institute of GeosciencesGoethe University FrankfurtFrankfurt am MainGermany
| | - E. Barkan
- Institute of Earth SciencesHebrew University of JerusalemJerusalemIsrael
| | - E. Beverly
- Now at Department of Earth and Atmospheric SciencesUniversity of HoustonHoustonTXUSA
- Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMIUSA
| | - D. Blamart
- Laboratoire des Sciences du Climat et de l’EnvironnementLSCE/IPSLCEA‐CNRS‐UVSQUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - L. Burgener
- Department of Marine, Earth and Atmospheric SciencesNorth Carolina State UniversityRaleighNCUSA
| | - D. Calmels
- Université de ParisInstitut de Physique du Globe de ParisCNRSParisFrance
- Now at Geosciences Paris Sud (GEOPS)Université Paris‐SaclayCNRSOrsayFrance
| | - C. Chaduteau
- Université de ParisInstitut de Physique du Globe de ParisCNRSParisFrance
| | - M. Clog
- Scottish Universities Environmental Research Centre (SUERC)ScotlandUK
| | | | - A. Davies
- Now at Stockholm UniversityStockholmSweden
- Imperial CollegeLondonUK
| | - F. Dux
- Now at School of Earth and Life SciencesUniversity of WollongongWollongongAustralia
- School of GeographyUniversity of MelbourneMelbourneAustralia
| | - J. Eiler
- Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCAUSA
| | - B. Elliott
- Department of Earth, Planetary, and Space SciencesUniversity of California Los AngelesLos AngelesCAUSA
| | | | - J. Fiebig
- Institute of GeosciencesGoethe University FrankfurtFrankfurt am MainGermany
| | - S. Goldberg
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - M. Hermoso
- Université de ParisInstitut de Physique du Globe de ParisCNRSParisFrance
- Univ. Littoral Côte d’OpaleUniv. LilleCNRSLaboratoire d’Océanologie et de Géosciences (UMR 8187 LOG)WimereuxFrance
| | | | - E. Hyland
- Department of Marine, Earth and Atmospheric SciencesNorth Carolina State UniversityRaleighNCUSA
| | - M. Ingalls
- Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCAUSA
- Now at Department of GeosciencesThe Pennsylvania State UniversityUniversity ParkPAUSA
| | - M. Jaggi
- Geological InstituteETH ZürichZürichSwitzerland
| | | | - A. B. Jost
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - S. Katz
- Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMIUSA
| | - J. Kelson
- Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMIUSA
| | - T. Kluge
- Imperial CollegeLondonUK
- Now at Karlsruher Institut für Technologie KITKarlsruheGermany
| | - I. J. Kocken
- Department of Earth SciencesUniversity of UtrechtUtrechtThe Netherlands
| | - A. Laskar
- Institute of Earth SciencesAcademia SinicaTaipeiTaiwan
| | - T. J. Leutert
- Bjerknes Centre for Climate Research and Department of Earth ScienceUniversity of BergenBergenNorway
- Now at Max Planck Institute for ChemistryMainzGermany
| | - D. Liang
- Institute of Earth SciencesAcademia SinicaTaipeiTaiwan
| | - J. Lucarelli
- Department of Earth, Planetary, and Space SciencesUniversity of California Los AngelesLos AngelesCAUSA
| | - T. J. Mackey
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
- Now at Department of Earth and Planetary SciencesUniversity of New MexicoAlbuquerqueNMUSA
| | - X. Mangenot
- Université de ParisInstitut de Physique du Globe de ParisCNRSParisFrance
- Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCAUSA
| | - N. Meinicke
- Bjerknes Centre for Climate Research and Department of Earth ScienceUniversity of BergenBergenNorway
| | - S. E. Modestou
- Bjerknes Centre for Climate Research and Department of Earth ScienceUniversity of BergenBergenNorway
| | - I. A. Müller
- Department of Earth SciencesUniversity of UtrechtUtrechtThe Netherlands
| | | | - A. Neary
- Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMIUSA
| | - N. Packard
- Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMIUSA
| | - B. H. Passey
- Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMIUSA
| | - E. Pelletier
- Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMIUSA
| | - S. Petersen
- Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMIUSA
| | - A. Piasecki
- Bjerknes Centre for Climate Research and Department of Earth ScienceUniversity of BergenBergenNorway
- Now at Department of Earth SciencesDartmouth CollegeHanoverNHUSA
| | | | | | - P. K. Swart
- Department of Marine GeosciencesRostiel School of Marine and Atmospheric SciencesUniversity of MiamiMiamiFLUSA
| | - A. Tripati
- Department of Earth, Planetary, and Space SciencesUniversity of California Los AngelesLos AngelesCAUSA
| | - D. Upadhyay
- Department of Earth, Planetary, and Space SciencesUniversity of California Los AngelesLos AngelesCAUSA
| | - T. Vennemann
- Institute of Earth Surface DynamicsUniversity of LausanneLausanneSwitzerland
| | - I. Winkelstern
- Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMIUSA
- Now at Geology DepartmentGrand Valley State UniversityAllendaleMIUSA
| | - D. Yarian
- Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMIUSA
| | - N. Yoshida
- Earth‐Life Science InstituteTokyo Institute of TechnologyTokyoJapan
- National Institute of Information and Communications TechnologyTokyoJapan
| | - N. Zhang
- Earth‐Life Science InstituteTokyo Institute of TechnologyTokyoJapan
| | - M. Ziegler
- Department of Earth SciencesUniversity of UtrechtUtrechtThe Netherlands
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8
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Gouwens NW, Sorensen SA, Baftizadeh F, Budzillo A, Lee BR, Jarsky T, Alfiler L, Baker K, Barkan E, Berry K, Bertagnolli D, Bickley K, Bomben J, Braun T, Brouner K, Casper T, Crichton K, Daigle TL, Dalley R, de Frates RA, Dee N, Desta T, Lee SD, Dotson N, Egdorf T, Ellingwood L, Enstrom R, Esposito L, Farrell C, Feng D, Fong O, Gala R, Gamlin C, Gary A, Glandon A, Goldy J, Gorham M, Graybuck L, Gu H, Hadley K, Hawrylycz MJ, Henry AM, Hill D, Hupp M, Kebede S, Kim TK, Kim L, Kroll M, Lee C, Link KE, Mallory M, Mann R, Maxwell M, McGraw M, McMillen D, Mukora A, Ng L, Ng L, Ngo K, Nicovich PR, Oldre A, Park D, Peng H, Penn O, Pham T, Pom A, Popović Z, Potekhina L, Rajanbabu R, Ransford S, Reid D, Rimorin C, Robertson M, Ronellenfitch K, Ruiz A, Sandman D, Smith K, Sulc J, Sunkin SM, Szafer A, Tieu M, Torkelson A, Trinh J, Tung H, Wakeman W, Ward K, Williams G, Zhou Z, Ting JT, Arkhipov A, Sümbül U, Lein ES, Koch C, Yao Z, Tasic B, Berg J, Murphy GJ, Zeng H. Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells. Cell 2020; 183:935-953.e19. [PMID: 33186530 PMCID: PMC7781065 DOI: 10.1016/j.cell.2020.09.057] [Citation(s) in RCA: 213] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 07/06/2020] [Accepted: 09/22/2020] [Indexed: 12/20/2022]
Abstract
Neurons are frequently classified into distinct types on the basis of structural, physiological, or genetic attributes. To better constrain the definition of neuronal cell types, we characterized the transcriptomes and intrinsic physiological properties of over 4,200 mouse visual cortical GABAergic interneurons and reconstructed the local morphologies of 517 of those neurons. We find that most transcriptomic types (t-types) occupy specific laminar positions within visual cortex, and, for most types, the cells mapping to a t-type exhibit consistent electrophysiological and morphological properties. These properties display both discrete and continuous variation among t-types. Through multimodal integrated analysis, we define 28 met-types that have congruent morphological, electrophysiological, and transcriptomic properties and robust mutual predictability. We identify layer-specific axon innervation pattern as a defining feature distinguishing different met-types. These met-types represent a unified definition of cortical GABAergic interneuron types, providing a systematic framework to capture existing knowledge and bridge future analyses across different modalities.
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Affiliation(s)
| | | | | | - Agata Budzillo
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Brian R Lee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Tim Jarsky
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Lauren Alfiler
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Eliza Barkan
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Kyla Berry
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Kris Bickley
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Jasmine Bomben
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Thomas Braun
- Byte Physics, Schwarzastraße 9, Berlin 12055, Germany
| | - Krissy Brouner
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Tamara Casper
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Tanya L Daigle
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Rachel Dalley
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Tsega Desta
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Tom Egdorf
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Rachel Enstrom
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Luke Esposito
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Colin Farrell
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - David Feng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Olivia Fong
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Rohan Gala
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Clare Gamlin
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Amanda Gary
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Melissa Gorham
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Lucas Graybuck
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Hong Gu
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Kristen Hadley
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Alex M Henry
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - DiJon Hill
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Madie Hupp
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Sara Kebede
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Tae Kyung Kim
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Lisa Kim
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Matthew Kroll
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Rusty Mann
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Medea McGraw
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Alice Mukora
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Lindsay Ng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Kiet Ngo
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Aaron Oldre
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Daniel Park
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Hanchuan Peng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Osnat Penn
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Thanh Pham
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Alice Pom
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Zoran Popović
- Center for Game Science, Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA
| | | | | | - Shea Ransford
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - David Reid
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | | | - Augustin Ruiz
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - David Sandman
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Kimberly Smith
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Josef Sulc
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Susan M Sunkin
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Aaron Szafer
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Amy Torkelson
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Jessica Trinh
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Herman Tung
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Wayne Wakeman
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Katelyn Ward
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Grace Williams
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Zhi Zhou
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Anton Arkhipov
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Uygar Sümbül
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Christof Koch
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Bosiljka Tasic
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Jim Berg
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Gabe J Murphy
- Allen Institute for Brain Science, Seattle, WA 98109, USA.
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
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9
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Miller J, Hodge R, Novotny M, Ting J, Kalmbach B, Bakken T, Aevermann B, Barkan E, Berkowitz-Cerasano M, Cobbs C, Diez-Fuertes F, Ding SL, Mccorrison J, Schork N, Shehata S, Smith K, Sunkin S, Tran D, Venepally P, Yanny AM, Steemers F, Phillips J, Bernard A, Koch C, Lasken R, Scheuermann R, Lein E. Transcriptomic evidence that von Economo neurons are regionally specialized extratelencephalic-projecting excitatory neurons. IBRO Rep 2019. [DOI: 10.1016/j.ibror.2019.07.894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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10
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Gouwens NW, Sorensen SA, Berg J, Lee C, Jarsky T, Ting J, Sunkin SM, Feng D, Anastassiou CA, Barkan E, Bickley K, Blesie N, Braun T, Brouner K, Budzillo A, Caldejon S, Casper T, Castelli D, Chong P, Crichton K, Cuhaciyan C, Daigle TL, Dalley R, Dee N, Desta T, Ding SL, Dingman S, Doperalski A, Dotson N, Egdorf T, Fisher M, de Frates RA, Garren E, Garwood M, Gary A, Gaudreault N, Godfrey K, Gorham M, Gu H, Habel C, Hadley K, Harrington J, Harris JA, Henry A, Hill D, Josephsen S, Kebede S, Kim L, Kroll M, Lee B, Lemon T, Link KE, Liu X, Long B, Mann R, McGraw M, Mihalas S, Mukora A, Murphy GJ, Ng L, Ngo K, Nguyen TN, Nicovich PR, Oldre A, Park D, Parry S, Perkins J, Potekhina L, Reid D, Robertson M, Sandman D, Schroedter M, Slaughterbeck C, Soler-Llavina G, Sulc J, Szafer A, Tasic B, Taskin N, Teeter C, Thatra N, Tung H, Wakeman W, Williams G, Young R, Zhou Z, Farrell C, Peng H, Hawrylycz MJ, Lein E, Ng L, Arkhipov A, Bernard A, Phillips JW, Zeng H, Koch C. Classification of electrophysiological and morphological neuron types in the mouse visual cortex. Nat Neurosci 2019; 22:1182-1195. [PMID: 31209381 PMCID: PMC8078853 DOI: 10.1038/s41593-019-0417-0] [Citation(s) in RCA: 219] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 04/25/2019] [Indexed: 12/21/2022]
Abstract
Understanding the diversity of cell types in the brain has been an enduring challenge and requires detailed characterization of individual neurons in multiple dimensions. To systematically profile morpho-electric properties of mammalian neurons, we established a single-cell characterization pipeline using standardized patch-clamp recordings in brain slices and biocytin-based neuronal reconstructions. We built a publicly accessible online database, the Allen Cell Types Database, to display these datasets. Intrinsic physiological properties were measured from 1,938 neurons from the adult laboratory mouse visual cortex, morphological properties were measured from 461 reconstructed neurons, and 452 neurons had both measurements available. Quantitative features were used to classify neurons into distinct types using unsupervised methods. We established a taxonomy of morphologically and electrophysiologically defined cell types for this region of the cortex, with 17 electrophysiological types, 38 morphological types and 46 morpho-electric types. There was good correspondence with previously defined transcriptomic cell types and subclasses using the same transgenic mouse lines.
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Affiliation(s)
| | | | - Jim Berg
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Tim Jarsky
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Jonathan Ting
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Susan M Sunkin
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - David Feng
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Eliza Barkan
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Kris Bickley
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Nicole Blesie
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Thomas Braun
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Krissy Brouner
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Agata Budzillo
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Tamara Casper
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Dan Castelli
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Peter Chong
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | | | - Tanya L Daigle
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Rachel Dalley
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Tsega Desta
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Song-Lin Ding
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Samuel Dingman
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | | | - Tom Egdorf
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Michael Fisher
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Emma Garren
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Amanda Gary
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Keith Godfrey
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Melissa Gorham
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Hong Gu
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Caroline Habel
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Kristen Hadley
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Julie A Harris
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Alex Henry
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - DiJon Hill
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Sam Josephsen
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Sara Kebede
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Lisa Kim
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Matthew Kroll
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Brian Lee
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Tracy Lemon
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Xiaoxiao Liu
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Brian Long
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Rusty Mann
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Medea McGraw
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Stefan Mihalas
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Alice Mukora
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Gabe J Murphy
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Lindsay Ng
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Kiet Ngo
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | | | - Aaron Oldre
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Daniel Park
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Sheana Parry
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Jed Perkins
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - David Reid
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - David Sandman
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | | | | | - Josef Sulc
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Aaron Szafer
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Bosiljka Tasic
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Naz Taskin
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Corinne Teeter
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Herman Tung
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Wayne Wakeman
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Grace Williams
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Rob Young
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Zhi Zhou
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Colin Farrell
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Hanchuan Peng
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Ed Lein
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Anton Arkhipov
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, Washington, USA.
| | - Christof Koch
- Allen Institute for Brain Science, Seattle, Washington, USA
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11
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Bakken TE, Hodge RD, Miller JA, Yao Z, Nguyen TN, Aevermann B, Barkan E, Bertagnolli D, Casper T, Dee N, Garren E, Goldy J, Graybuck LT, Kroll M, Lasken RS, Lathia K, Parry S, Rimorin C, Scheuermann RH, Schork NJ, Shehata SI, Tieu M, Phillips JW, Bernard A, Smith KA, Zeng H, Lein ES, Tasic B. Single-nucleus and single-cell transcriptomes compared in matched cortical cell types. PLoS One 2018; 13:e0209648. [PMID: 30586455 PMCID: PMC6306246 DOI: 10.1371/journal.pone.0209648] [Citation(s) in RCA: 291] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 12/10/2018] [Indexed: 12/21/2022] Open
Abstract
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.
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Affiliation(s)
- Trygve E. Bakken
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Rebecca D. Hodge
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Jeremy A. Miller
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Thuc Nghi Nguyen
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Brian Aevermann
- J. Craig Venter Institute, La Jolla, CA, United States of America
| | - Eliza Barkan
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Darren Bertagnolli
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Tamara Casper
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Emma Garren
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Lucas T. Graybuck
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Matthew Kroll
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Roger S. Lasken
- J. Craig Venter Institute, La Jolla, CA, United States of America
| | - Kanan Lathia
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Sheana Parry
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Christine Rimorin
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | | | | | - Soraya I. Shehata
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - John W. Phillips
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Kimberly A. Smith
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Ed S. Lein
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Bosiljka Tasic
- Allen Institute for Brain Science, Seattle, WA, United States of America
- * E-mail:
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12
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Tasic B, Yao Z, Graybuck LT, Smith KA, Nguyen TN, Bertagnolli D, Goldy J, Garren E, Economo MN, Viswanathan S, Penn O, Bakken T, Menon V, Miller J, Fong O, Hirokawa KE, Lathia K, Rimorin C, Tieu M, Larsen R, Casper T, Barkan E, Kroll M, Parry S, Shapovalova NV, Hirschstein D, Pendergraft J, Sullivan HA, Kim TK, Szafer A, Dee N, Groblewski P, Wickersham I, Cetin A, Harris JA, Levi BP, Sunkin SM, Madisen L, Daigle TL, Looger L, Bernard A, Phillips J, Lein E, Hawrylycz M, Svoboda K, Jones AR, Koch C, Zeng H. Shared and distinct transcriptomic cell types across neocortical areas. Nature 2018; 563:72-78. [PMID: 30382198 DOI: 10.1038/s41586-018-0654-5] [Citation(s) in RCA: 917] [Impact Index Per Article: 152.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 09/24/2018] [Indexed: 12/11/2022]
Abstract
The neocortex contains a multitude of cell types that are segregated into layers and functionally distinct areas. To investigate the diversity of cell types across the mouse neocortex, here we analysed 23,822 cells from two areas at distant poles of the mouse neocortex: the primary visual cortex and the anterior lateral motor cortex. We define 133 transcriptomic cell types by deep, single-cell RNA sequencing. Nearly all types of GABA (γ-aminobutyric acid)-containing neurons are shared across both areas, whereas most types of glutamatergic neurons were found in one of the two areas. By combining single-cell RNA sequencing and retrograde labelling, we match transcriptomic types of glutamatergic neurons to their long-range projection specificity. Our study establishes a combined transcriptomic and projectional taxonomy of cortical cell types from functionally distinct areas of the adult mouse cortex.
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Affiliation(s)
| | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Emma Garren
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Michael N Economo
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Sarada Viswanathan
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Osnat Penn
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Vilas Menon
- Allen Institute for Brain Science, Seattle, WA, USA.,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | | | - Olivia Fong
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Kanan Lathia
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Eliza Barkan
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Sheana Parry
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | - Aaron Szafer
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Ian Wickersham
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ali Cetin
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Boaz P Levi
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Loren Looger
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Karel Svoboda
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | | | | | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
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13
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Abstract
Plant production in the sea is a primary mechanism of global oxygen formation and carbon fixation. For this reason, and also because the ocean is a major sink for fossil fuel carbon dioxide, much attention has been given to estimating marine primary production. Here, we describe an approach for estimating production of photosynthetic oxygen, based on the isotopic composition of dissolved oxygen of seawater. This method allows the estimation of integrated oceanic productivity on a time scale of weeks.
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Affiliation(s)
- B Luz
- The Institute of Earth Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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14
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15
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Klein A, Barkan E, Barkan A, Hoogervorst-Spalter H, Arie R, Kaufmann H. Liver diseases and cancer associated with lack of lymphocytic cortisol metabolism enhancing factor. Metabolism 1980; 29:780-6. [PMID: 7402079 DOI: 10.1016/0026-0495(80)90204-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Barkan A, Barkan E, Hoogervorst-Spalter H, Kaufman H, Klein A. Effect of tumor removal on the presence of lymphocytic cortisol metabolism-enhancing factor in plasma of cancer patients. J Natl Cancer Inst 1980; 64:1333-5. [PMID: 6929371 DOI: 10.1093/jnci/64.6.1333] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Because lymphocytic cortisol metabolism-enhancing factor (LCMEF) is absent in the plasma of cancer patients (CP), this study was undertaken to determine the influence of tumor removal on this phenomenon. Known concentrations of human lymphocytes were incubated with cortisol in media containing 50% phosphate-buffered saline (PBS) and 50% of one of the following: a) homologic normal plasma (HP),b) plasma from patients with noncancerous diseases (NCD) before surgery, c) plasma from patients with NCD after surgery, d) plasma from CP before tumor removal, e) plasma from CP after tumor removal, f) plasma from long-surviving CP (LSCP), and g) PBS. With the exception of plasma from the LSCP group, all the plasma had the capacity to enhance the lymphocytic cortisol metabolism (LCM) when compared with that of PBS. There was no significant difference between the metabolism obtained with HP and that obtained with plasma from patients with NCD either before or after surgery. The plasma from CP led to a significant reduction in activity, with no significant difference in conversion rates before and after tumor removal. The plasma from LSCP failed to enhance LCM, had a conversion rate similar to that of PBS and significantly lower than that of the plasma from CP, and appeared to contain no LCMEF. These findings, which showed that the lack of LCMEF in CP is not influenced by tumor removal, may indicate 1) that the lack of LCMEF preceded the appearance of cancer or 2) irreversibility of a possible anti-LCMEF synthesis effect was induced by the tumor.
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