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Gregor BW, Coston ME, Adams EM, Arakaki J, Borensztejn A, Do TP, Fuqua MA, Haupt A, Hendershott MC, Leung W, Mueller IA, Nath A, Nelson AM, Rafelski SM, Sanchez EE, Swain-Bowden MJ, Tang WJ, Thirstrup DJ, Wiegraebe W, Whitney BP, Yan C, Gunawardane RN, Gaudreault N. Automated human induced pluripotent stem cell culture and sample preparation for 3D live-cell microscopy. Nat Protoc 2024; 19:565-594. [PMID: 38087082 DOI: 10.1038/s41596-023-00912-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 09/08/2023] [Indexed: 02/12/2024]
Abstract
To produce abundant cell culture samples to generate large, standardized image datasets of human induced pluripotent stem (hiPS) cells, we developed an automated workflow on a Hamilton STAR liquid handler system. This was developed specifically for culturing hiPS cell lines expressing fluorescently tagged proteins, which we have used to study the principles by which cells establish and maintain robust dynamic localization of cellular structures. This protocol includes all details for the maintenance, passage and seeding of cells, as well as Matrigel coating of 6-well plastic plates and 96-well optical-grade, glass plates. We also developed an automated image-based hiPS cell colony segmentation and feature extraction pipeline to streamline the process of predicting cell count and selecting wells with consistent morphology for high-resolution three-dimensional (3D) microscopy. The imaging samples produced with this protocol have been used to study the integrated intracellular organization and cell-to-cell variability of hiPS cells to train and develop deep learning-based label-free predictions from transmitted-light microscopy images and to develop deep learning-based generative models of single-cell organization. This protocol requires some experience with robotic equipment. However, we provide details and source code to facilitate implementation by biologists less experienced with robotics. The protocol is completed in less than 10 h with minimal human interaction. Overall, automation of our cell culture procedures increased our imaging samples' standardization, reproducibility, scalability and consistency. It also reduced the need for stringent culturist training and eliminated culturist-to-culturist variability, both of which were previous pain points of our original manual pipeline workflow.
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Affiliation(s)
| | | | | | - Joy Arakaki
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | - Thao P Do
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | - Amanda Haupt
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | - Winnie Leung
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | - Aditya Nath
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | | | | | | | - W Joyce Tang
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | | | | | - Calysta Yan
- Allen Institute for Cell Science, Seattle, WA, USA
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2
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Viana MP, Chen J, Knijnenburg TA, Vasan R, Yan C, Arakaki JE, Bailey M, Berry B, Borensztejn A, Brown EM, Carlson S, Cass JA, Chaudhuri B, Cordes Metzler KR, Coston ME, Crabtree ZJ, Davidson S, DeLizo CM, Dhaka S, Dinh SQ, Do TP, Domingus J, Donovan-Maiye RM, Ferrante AJ, Foster TJ, Frick CL, Fujioka G, Fuqua MA, Gehring JL, Gerbin KA, Grancharova T, Gregor BW, Harrylock LJ, Haupt A, Hendershott MC, Hookway C, Horwitz AR, Hughes HC, Isaac EJ, Johnson GR, Kim B, Leonard AN, Leung WW, Lucas JJ, Ludmann SA, Lyons BM, Malik H, McGregor R, Medrash GE, Meharry SL, Mitcham K, Mueller IA, Murphy-Stevens TL, Nath A, Nelson AM, Oluoch SA, Paleologu L, Popiel TA, Riel-Mehan MM, Roberts B, Schaefbauer LM, Schwarzl M, Sherman J, Slaton S, Sluzewski MF, Smith JE, Sul Y, Swain-Bowden MJ, Tang WJ, Thirstrup DJ, Toloudis DM, Tucker AP, Valencia V, Wiegraebe W, Wijeratna T, Yang R, Zaunbrecher RJ, Labitigan RLD, Sanborn AL, Johnson GT, Gunawardane RN, Gaudreault N, Theriot JA, Rafelski SM. Integrated intracellular organization and its variations in human iPS cells. Nature 2023; 613:345-354. [PMID: 36599983 PMCID: PMC9834050 DOI: 10.1038/s41586-022-05563-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 11/15/2022] [Indexed: 01/06/2023]
Abstract
Understanding how a subset of expressed genes dictates cellular phenotype is a considerable challenge owing to the large numbers of molecules involved, their combinatorics and the plethora of cellular behaviours that they determine1,2. Here we reduced this complexity by focusing on cellular organization-a key readout and driver of cell behaviour3,4-at the level of major cellular structures that represent distinct organelles and functional machines, and generated the WTC-11 hiPSC Single-Cell Image Dataset v1, which contains more than 200,000 live cells in 3D, spanning 25 key cellular structures. The scale and quality of this dataset permitted the creation of a generalizable analysis framework to convert raw image data of cells and their structures into dimensionally reduced, quantitative measurements that can be interpreted by humans, and to facilitate data exploration. This framework embraces the vast cell-to-cell variability that is observed within a normal population, facilitates the integration of cell-by-cell structural data and allows quantitative analyses of distinct, separable aspects of organization within and across different cell populations. We found that the integrated intracellular organization of interphase cells was robust to the wide range of variation in cell shape in the population; that the average locations of some structures became polarized in cells at the edges of colonies while maintaining the 'wiring' of their interactions with other structures; and that, by contrast, changes in the location of structures during early mitotic reorganization were accompanied by changes in their wiring.
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Affiliation(s)
| | - Jianxu Chen
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | - Ritvik Vasan
- Allen Institute for Cell Science, Seattle, WA, USA
| | - Calysta Yan
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | - Matte Bailey
- Allen Institute for Cell Science, Seattle, WA, USA
| | - Ben Berry
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | - Eva M Brown
- Allen Institute for Cell Science, Seattle, WA, USA
| | - Sara Carlson
- Allen Institute for Cell Science, Seattle, WA, USA
| | - Julie A Cass
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | | | | | | | | | | | | | | | - Thao P Do
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | - Amanda Haupt
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | | | | | | | - Eric J Isaac
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | - Brian Kim
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | | | | | | | | | - Haseeb Malik
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | | | | | | | | | | | - Aditya Nath
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | - Youngmee Sul
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | - W Joyce Tang
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | | | | | | | | | | | - Ruian Yang
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | - Ramon Lorenzo D Labitigan
- Department of Biology and Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Adrian L Sanborn
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
| | | | | | | | - Julie A Theriot
- Department of Biology and Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
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3
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Puchalski RB, Shah N, Miller J, Dalley R, Nomura SR, Yoon JG, Smith KA, Lankerovich M, Bertagnolli D, Bickley K, Boe AF, Brouner K, Butler S, Caldejon S, Chapin M, Datta S, Dee N, Desta T, Dolbeare T, Dotson N, Ebbert A, Feng D, Feng X, Fisher M, Gee G, Goldy J, Gourley L, Gregor BW, Gu G, Hejazinia N, Hohmann J, Hothi P, Howard R, Joines K, Kriedberg A, Kuan L, Lau C, Lee F, Lee H, Lemon T, Long F, Mastan N, Mott E, Murthy C, Ngo K, Olson E, Reding M, Riley Z, Rosen D, Sandman D, Shapovalova N, Slaughterbeck CR, Sodt A, Stockdale G, Szafer A, Wakeman W, Wohnoutka PE, White SJ, Marsh D, Rostomily RC, Ng L, Dang C, Jones A, Keogh B, Gittleman HR, Barnholtz-Sloan JS, Cimino PJ, Uppin MS, Keene CD, Farrokhi FR, Lathia JD, Berens ME, Iavarone A, Bernard A, Lein E, Phillips JW, Rostad SW, Cobbs C, Hawrylycz MJ, Foltz GD. An anatomic transcriptional atlas of human glioblastoma. Science 2018; 360:660-663. [PMID: 29748285 DOI: 10.1126/science.aaf2666] [Citation(s) in RCA: 304] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 03/30/2018] [Indexed: 12/20/2022]
Abstract
Glioblastoma is an aggressive brain tumor that carries a poor prognosis. The tumor's molecular and cellular landscapes are complex, and their relationships to histologic features routinely used for diagnosis are unclear. We present the Ivy Glioblastoma Atlas, an anatomically based transcriptional atlas of human glioblastoma that aligns individual histologic features with genomic alterations and gene expression patterns, thus assigning molecular information to the most important morphologic hallmarks of the tumor. The atlas and its clinical and genomic database are freely accessible online data resources that will serve as a valuable platform for future investigations of glioblastoma pathogenesis, diagnosis, and treatment.
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Affiliation(s)
- Ralph B Puchalski
- Allen Institute for Brain Science, Seattle, WA 98109, USA. .,Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Nameeta Shah
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA. .,Mazumdar Shaw Center for Translational Research, Bangalore 560099, India
| | - Jeremy Miller
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Rachel Dalley
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Steve R Nomura
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Jae-Guen Yoon
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | | | - Michael Lankerovich
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | | | - Kris Bickley
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Andrew F Boe
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Krissy Brouner
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Mike Chapin
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Suvro Datta
- 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
| | - Tim Dolbeare
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Amanda Ebbert
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - David Feng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Xu Feng
- Radia Inc., Lynnwood, WA 98036, USA
| | - Michael Fisher
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Garrett Gee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Guangyu Gu
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Nika Hejazinia
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - John Hohmann
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Parvinder Hothi
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Robert Howard
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Kevin Joines
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Ali Kriedberg
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Leonard Kuan
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Chris Lau
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Felix Lee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Hwahyung Lee
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Tracy Lemon
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Fuhui Long
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Naveed Mastan
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Erika Mott
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Chantal Murthy
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Kiet Ngo
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Eric Olson
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Melissa Reding
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Zack Riley
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - David Rosen
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - David Sandman
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Andrew Sodt
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Aaron Szafer
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Wayne Wakeman
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Don Marsh
- White Marsh Forests, Seattle, WA 98119, USA
| | - Robert C Rostomily
- Department of Neurosurgery, Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA.,Department of Neurological Surgery, Houston Methodist Hospital and Research Institute, Houston, TX 77030, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Chinh Dang
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Allan Jones
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Haley R Gittleman
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Jill S Barnholtz-Sloan
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Patrick J Cimino
- Department of Pathology, Division of Neuropathology, University of Washington School of Medicine, Seattle, WA 98104, USA
| | - Megha S Uppin
- Nizam's Institute of Medical Sciences, Punjagutta, Hyderabad 500082, India
| | - C Dirk Keene
- Department of Pathology, Division of Neuropathology, University of Washington School of Medicine, Seattle, WA 98104, USA
| | | | - Justin D Lathia
- Department of Cellular and Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Michael E Berens
- TGen, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Antonio Iavarone
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA.,Department of Neurology, Columbia University, New York, NY 10032, USA.,Department of Pathology, Columbia University, New York, NY 10032, USA
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Charles Cobbs
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | | | - Greg D Foltz
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
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4
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Miller JA, Ding SL, Sunkin SM, Smith KA, Ng L, Szafer A, Ebbert A, Riley ZL, Royall JJ, Aiona K, Arnold JM, Bennet C, Bertagnolli D, Brouner K, Butler S, Caldejon S, Carey A, Cuhaciyan C, Dalley RA, Dee N, Dolbeare TA, Facer BAC, Feng D, Fliss TP, Gee G, Goldy J, Gourley L, Gregor BW, Gu G, Howard RE, Jochim JM, Kuan CL, Lau C, Lee CK, Lee F, Lemon TA, Lesnar P, McMurray B, Mastan N, Mosqueda N, Naluai-Cecchini T, Ngo NK, Nyhus J, Oldre A, Olson E, Parente J, Parker PD, Parry SE, Stevens A, Pletikos M, Reding M, Roll K, Sandman D, Sarreal M, Shapouri S, Shapovalova NV, Shen EH, Sjoquist N, Slaughterbeck CR, Smith M, Sodt AJ, Williams D, Zöllei L, Fischl B, Gerstein MB, Geschwind DH, Glass IA, Hawrylycz MJ, Hevner RF, Huang H, Jones AR, Knowles JA, Levitt P, Phillips JW, Sestan N, Wohnoutka P, Dang C, Bernard A, Hohmann JG, Lein ES. Transcriptional landscape of the prenatal human brain. Nature 2014; 508:199-206. [PMID: 24695229 PMCID: PMC4105188 DOI: 10.1038/nature13185] [Citation(s) in RCA: 820] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 02/26/2014] [Indexed: 12/21/2022]
Abstract
The anatomical and functional architecture of the human brain is largely determined by prenatal transcriptional processes. We describe an anatomically comprehensive atlas of mid-gestational human brain, including de novo reference atlases, in situ hybridization, ultra-high resolution magnetic resonance imaging (MRI) and microarray analysis on highly discrete laser microdissected brain regions. In developing cerebral cortex, transcriptional differences are found between different proliferative and postmitotic layers, wherein laminar signatures reflect cellular composition and developmental processes. Cytoarchitectural differences between human and mouse have molecular correlates, including species differences in gene expression in subplate, although surprisingly we find minimal differences between the inner and human-expanded outer subventricular zones. Both germinal and postmitotic cortical layers exhibit fronto-temporal gradients, with particular enrichment in frontal lobe. Finally, many neurodevelopmental disorder and human evolution-related genes show patterned expression, potentially underlying unique features of human cortical formation. These data provide a rich, freely-accessible resource for understanding human brain development.
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Affiliation(s)
- Jeremy A Miller
- 1] Allen Institute for Brain Science, Seattle, Washington 98103, USA [2]
| | - Song-Lin Ding
- 1] Allen Institute for Brain Science, Seattle, Washington 98103, USA [2]
| | - Susan M Sunkin
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Kimberly A Smith
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Aaron Szafer
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Amanda Ebbert
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Zackery L Riley
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Joshua J Royall
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Kaylynn Aiona
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - James M Arnold
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Crissa Bennet
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | | | - Krissy Brouner
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Stephanie Butler
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Shiella Caldejon
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Anita Carey
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | | | - Rachel A Dalley
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Tim A Dolbeare
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | | | - David Feng
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Tim P Fliss
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Garrett Gee
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Lindsey Gourley
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | | | - Guangyu Gu
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Robert E Howard
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Jayson M Jochim
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Chihchau L Kuan
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Christopher Lau
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Chang-Kyu Lee
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Felix Lee
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Tracy A Lemon
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Phil Lesnar
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Bergen McMurray
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Naveed Mastan
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Nerick Mosqueda
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Theresa Naluai-Cecchini
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, 1959 North East Pacific Street, Box 356320, Seattle, Washington 98195, USA
| | - Nhan-Kiet Ngo
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Julie Nyhus
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Aaron Oldre
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Eric Olson
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Jody Parente
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Patrick D Parker
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Sheana E Parry
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Allison Stevens
- 1] Department of Radiology, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA [2] Computer Science and AI Lab, MIT, Cambridge, Massachusetts 02139, USA
| | - Mihovil Pletikos
- Department of Neurobiology and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, Connecticut 06510, USA
| | - Melissa Reding
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Kate Roll
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - David Sandman
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Melaine Sarreal
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Sheila Shapouri
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | | | - Elaine H Shen
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Nathan Sjoquist
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | | | - Michael Smith
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Andy J Sodt
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Derric Williams
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Lilla Zöllei
- Department of Radiology, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA
| | - Bruce Fischl
- 1] Department of Radiology, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA [2] Computer Science and AI Lab, MIT, Cambridge, Massachusetts 02139, USA
| | - Mark B Gerstein
- 1] Program in Computational Biology and Bioinformatics, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA [2] Department of Computer Science, Yale University, New Haven, Connecticut 06520, USA
| | - Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology and Semel Institute David Geffen School of Medicine, UCLA, Los Angeles, California 90095, USA
| | - Ian A Glass
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, 1959 North East Pacific Street, Box 356320, Seattle, Washington 98195, USA
| | | | - Robert F Hevner
- 1] Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington 98101, USA [2] Department of Neurological Surgery, University of Washington School of Medicine, Seattle, Washington 98105, USA
| | - Hao Huang
- Advanced Imaging Research Center, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Allan R Jones
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - James A Knowles
- Zilkha Neurogenetic Institute, and Department of Psychiatry, University of Southern California, Los Angeles, California 90033, USA
| | - Pat Levitt
- 1] Department of Pediatrics, Children's Hospital, Los Angeles, California 90027, USA [2] Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - John W Phillips
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Nenad Sestan
- Department of Neurobiology and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, Connecticut 06510, USA
| | - Paul Wohnoutka
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Chinh Dang
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - John G Hohmann
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
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5
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Hawrylycz MJ, Lein ES, Guillozet-Bongaarts AL, Shen EH, Ng L, Miller JA, van de Lagemaat LN, Smith KA, Ebbert A, Riley ZL, Abajian C, Beckmann CF, Bernard A, Bertagnolli D, Boe AF, Cartagena PM, Chakravarty MM, Chapin M, Chong J, Dalley RA, David Daly B, Dang C, Datta S, Dee N, Dolbeare TA, Faber V, Feng D, Fowler DR, Goldy J, Gregor BW, Haradon Z, Haynor DR, Hohmann JG, Horvath S, Howard RE, Jeromin A, Jochim JM, Kinnunen M, Lau C, Lazarz ET, Lee C, Lemon TA, Li L, Li Y, Morris JA, Overly CC, Parker PD, Parry SE, Reding M, Royall JJ, Schulkin J, Sequeira PA, Slaughterbeck CR, Smith SC, Sodt AJ, Sunkin SM, Swanson BE, Vawter MP, Williams D, Wohnoutka P, Zielke HR, Geschwind DH, Hof PR, Smith SM, Koch C, Grant SGN, Jones AR. An anatomically comprehensive atlas of the adult human brain transcriptome. Nature 2012; 489:391-399. [PMID: 22996553 DOI: 10.1038/nature11405] [Citation(s) in RCA: 1693] [Impact Index Per Article: 141.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 07/09/2012] [Indexed: 01/07/2023]
Abstract
Neuroanatomically precise, genome-wide maps of transcript distributions are critical resources to complement genomic sequence data and to correlate functional and genetic brain architecture. Here we describe the generation and analysis of a transcriptional atlas of the adult human brain, comprising extensive histological analysis and comprehensive microarray profiling of ∼900 neuroanatomically precise subdivisions in two individuals. Transcriptional regulation varies enormously by anatomical location, with different regions and their constituent cell types displaying robust molecular signatures that are highly conserved between individuals. Analysis of differential gene expression and gene co-expression relationships demonstrates that brain-wide variation strongly reflects the distributions of major cell classes such as neurons, oligodendrocytes, astrocytes and microglia. Local neighbourhood relationships between fine anatomical subdivisions are associated with discrete neuronal subtypes and genes involved with synaptic transmission. The neocortex displays a relatively homogeneous transcriptional pattern, but with distinct features associated selectively with primary sensorimotor cortices and with enriched frontal lobe expression. Notably, the spatial topography of the neocortex is strongly reflected in its molecular topography-the closer two cortical regions, the more similar their transcriptomes. This freely accessible online data resource forms a high-resolution transcriptional baseline for neurogenetic studies of normal and abnormal human brain function.
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Affiliation(s)
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | | | - Elaine H Shen
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Jeremy A Miller
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | | | - Kimberly A Smith
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Amanda Ebbert
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Zackery L Riley
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Chris Abajian
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Christian F Beckmann
- MIRA Institute, University of Twente & Donders Institute, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | | | - Andrew F Boe
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Preston M Cartagena
- Department of Psychiatry & Human Behavior, University of California, Irvine, California 92697, USA
| | - M Mallar Chakravarty
- Allen Institute for Brain Science, Seattle, Washington 98103, USA; Kimel Family Translational Imaging-Genetics Laboratory, Centre for Addiction and Mental Health Toronto, Ontario M5S 2S1, Canada
| | - Mike Chapin
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Jimmy Chong
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Rachel A Dalley
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Barry David Daly
- University of Maryland School of Medicine, Department of Diagnostic Radiology, University of Maryland Medical Center, Baltimore, Maryland 21201, USA
| | - Chinh Dang
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Suvro Datta
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Tim A Dolbeare
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Vance Faber
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - David Feng
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - David R Fowler
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | | | - Zeb Haradon
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - David R Haynor
- Department of Radiology, University of Washington, Seattle, Washington 98195, USA
| | - John G Hohmann
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Steve Horvath
- Department of Human Genetics, Gonda Research Center, David Geffen School of Medicine, Los Angeles, California 90095, USA
| | - Robert E Howard
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | | | - Jayson M Jochim
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Marty Kinnunen
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Christopher Lau
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Evan T Lazarz
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Tracy A Lemon
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Ling Li
- Office of the Chief Medical Examiner, Baltimore, MD, Department of Pediatrics, University of Maryland, Baltimore, Maryland 21201, USA
| | - Yang Li
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - John A Morris
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | | | - Patrick D Parker
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Sheana E Parry
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Melissa Reding
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Joshua J Royall
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Jay Schulkin
- Department of Neuroscience, Georgetown University, School of Medicine, Washington DC 20007, USA
| | - Pedro Adolfo Sequeira
- Functional Genomics Laboratory, Department of Psychiatry & Human Behavior, School of Medicine, University of California, Irvine, California 92697, USA
| | | | | | - Andy J Sodt
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Susan M Sunkin
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Beryl E Swanson
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Marquis P Vawter
- Functional Genomics Laboratory, Department of Psychiatry & Human Behavior, School of Medicine, University of California, Irvine, California 92697, USA
| | - Derric Williams
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Paul Wohnoutka
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - H Ronald Zielke
- The Eunice Kennedy Shriver NICHD Brain and Tissue Bank for Developmental Disorders, University of Maryland, Baltimore, Maryland 21201, USA
| | - Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology and Department of Human Genetics, and Semel Institute, David Geffen School of Medicine-UCLA, Los Angeles, California 90095, USA
| | - Patrick R Hof
- Fishberg Department of Neuroscience and Friedman Brain Institute, Mount Sinai School of Medicine, New York, New York 10029, USA
| | | | - Christof Koch
- Allen Institute for Brain Science, Seattle, Washington 98103, USA; Computation & Neural Systems, California Institute of Technology, Pasadena, California 91125, USA
| | - Seth G N Grant
- Genes to Cognition Programme, Edinburgh University, Edinburgh EH16 4SB, UK
| | - Allan R Jones
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
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