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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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Miller JA, Guillozet-Bongaarts A, Gibbons LE, Postupna N, Renz A, Beller AE, Sunkin SM, Ng L, Rose SE, Smith KA, Szafer A, Barber C, Bertagnolli D, Bickley K, Brouner K, Caldejon S, Chapin M, Chua ML, Coleman NM, Cudaback E, Cuhaciyan C, Dalley RA, Dee N, Desta T, Dolbeare TA, Dotson NI, Fisher M, Gaudreault N, Gee G, Gilbert TL, Goldy J, Griffin F, Habel C, Haradon Z, Hejazinia N, Hellstern LL, Horvath S, Howard K, Howard R, Johal J, Jorstad NL, Josephsen SR, Kuan CL, Lai F, Lee E, Lee F, Lemon T, Li X, Marshall DA, Melchor J, Mukherjee S, Nyhus J, Pendergraft J, Potekhina L, Rha EY, Rice S, Rosen D, Sapru A, Schantz A, Shen E, Sherfield E, Shi S, Sodt AJ, Thatra N, Tieu M, Wilson AM, Montine TJ, Larson EB, Bernard A, Crane PK, Ellenbogen RG, Keene CD, Lein E. Neuropathological and transcriptomic characteristics of the aged brain. eLife 2017; 6. [PMID: 29120328 PMCID: PMC5679757 DOI: 10.7554/elife.31126] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 10/22/2017] [Indexed: 12/11/2022] Open
Abstract
As more people live longer, age-related neurodegenerative diseases are an increasingly important societal health issue. Treatments targeting specific pathologies such as amyloid beta in Alzheimer’s disease (AD) have not led to effective treatments, and there is increasing evidence of a disconnect between traditional pathology and cognitive abilities with advancing age, indicative of individual variation in resilience to pathology. Here, we generated a comprehensive neuropathological, molecular, and transcriptomic characterization of hippocampus and two regions cortex in 107 aged donors (median = 90) from the Adult Changes in Thought (ACT) study as a freely-available resource (http://aging.brain-map.org/). We confirm established associations between AD pathology and dementia, albeit with increased, presumably aging-related variability, and identify sets of co-expressed genes correlated with pathological tau and inflammation markers. Finally, we demonstrate a relationship between dementia and RNA quality, and find common gene signatures, highlighting the importance of properly controlling for RNA quality when studying dementia.
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Affiliation(s)
| | | | - Laura E Gibbons
- Department of Medicine, University of Washington, Seattle, United States
| | - Nadia Postupna
- Department of Pathology, University of Washington, Seattle, United States
| | - Anne Renz
- Kaiser Permanente Washington Health Research Institute, Seattle, United States
| | - Allison E Beller
- Department of Pathology, University of Washington, Seattle, United States
| | - Susan M Sunkin
- Allen Institute for Brain Science, Seattle, United States
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, United States
| | - Shannon E Rose
- Department of Pathology, University of Washington, Seattle, United States
| | | | - Aaron Szafer
- Allen Institute for Brain Science, Seattle, United States
| | - Chris Barber
- Allen Institute for Brain Science, Seattle, United States
| | | | | | - Krissy Brouner
- Allen Institute for Brain Science, Seattle, United States
| | | | - Mike Chapin
- Allen Institute for Brain Science, Seattle, United States
| | - Mindy L Chua
- Department of Pathology, University of Washington, Seattle, United States
| | - Natalie M Coleman
- Department of Pathology, University of Washington, Seattle, United States
| | - Eiron Cudaback
- Department of Pathology, University of Washington, Seattle, United States
| | | | | | - Nick Dee
- Allen Institute for Brain Science, Seattle, United States
| | - Tsega Desta
- Allen Institute for Brain Science, Seattle, United States
| | - Tim A Dolbeare
- Allen Institute for Brain Science, Seattle, United States
| | | | - Michael Fisher
- Allen Institute for Brain Science, Seattle, United States
| | | | - Garrett Gee
- Allen Institute for Brain Science, Seattle, United States
| | | | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, United States
| | - Fiona Griffin
- Allen Institute for Brain Science, Seattle, United States
| | - Caroline Habel
- Allen Institute for Brain Science, Seattle, United States
| | - Zeb Haradon
- Allen Institute for Brain Science, Seattle, United States
| | - Nika Hejazinia
- Allen Institute for Brain Science, Seattle, United States
| | - Leanne L Hellstern
- Department of Pathology, University of Washington, Seattle, United States
| | - Steve Horvath
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, United States
| | - Kim Howard
- Department of Pathology, University of Washington, Seattle, United States
| | - Robert Howard
- Allen Institute for Brain Science, Seattle, United States
| | - Justin Johal
- Allen Institute for Brain Science, Seattle, United States
| | - Nikolas L Jorstad
- Department of Pathology, University of Washington, Seattle, United States
| | - Samuel R Josephsen
- Department of Pathology, University of Washington, Seattle, United States
| | | | - Florence Lai
- Allen Institute for Brain Science, Seattle, United States
| | - Eric Lee
- Allen Institute for Brain Science, Seattle, United States
| | - Felix Lee
- Allen Institute for Brain Science, Seattle, United States
| | - Tracy Lemon
- Allen Institute for Brain Science, Seattle, United States
| | - Xianwu Li
- Department of Pathology, University of Washington, Seattle, United States
| | - Desiree A Marshall
- Department of Pathology, University of Washington, Seattle, United States
| | - Jose Melchor
- Allen Institute for Brain Science, Seattle, United States
| | | | - Julie Nyhus
- Allen Institute for Brain Science, Seattle, United States
| | | | | | - Elizabeth Y Rha
- Department of Pathology, University of Washington, Seattle, United States
| | - Samantha Rice
- Department of Pathology, University of Washington, Seattle, United States
| | - David Rosen
- Allen Institute for Brain Science, Seattle, United States
| | - Abharika Sapru
- Department of Pathology, University of Washington, Seattle, United States
| | - Aimee Schantz
- Department of Pathology, University of Washington, Seattle, United States
| | - Elaine Shen
- Allen Institute for Brain Science, Seattle, United States
| | - Emily Sherfield
- Department of Pathology, University of Washington, Seattle, United States
| | - Shu Shi
- Allen Institute for Brain Science, Seattle, United States
| | - Andy J Sodt
- Allen Institute for Brain Science, Seattle, United States
| | | | - Michael Tieu
- Allen Institute for Brain Science, Seattle, United States
| | - Angela M Wilson
- Department of Pathology, University of Washington, Seattle, United States
| | - Thomas J Montine
- Department of Pathology, University of Washington, Seattle, United States
| | - Eric B Larson
- Kaiser Permanente Washington Health Research Institute, Seattle, United States
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, United States
| | - Paul K Crane
- Department of Medicine, University of Washington, Seattle, United States
| | - Richard G Ellenbogen
- Department of Neurological Surgery, University of Washington, Seattle, United States
| | - C Dirk Keene
- Department of Pathology, University of Washington, Seattle, United States
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, United States
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