Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

Tal Iram

doi:10.1038/s41586-018-0590-4

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

, , , , Tal Iram

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1391 Citations (Scopus)

Abstract

Here we present a compendium of single-cell transcriptomic data from the model organism Mus musculus that comprises more than 100,000 cells from 20 organs and tissues. These data represent a new resource for cell biology, reveal gene expression in poorly characterized cell populations and enable the direct and controlled comparison of gene expression in cell types that are shared between tissues, such as T lymphocytes and endothelial cells from different anatomical locations. Two distinct technical approaches were used for most organs: one approach, microfluidic droplet-based 3′-end counting, enabled the survey of thousands of cells at relatively low coverage, whereas the other, full-length transcript analysis based on fluorescence-activated cell sorting, enabled the characterization of cell types with high sensitivity and coverage. The cumulative data provide the foundation for an atlas of transcriptomic cell biology.

Original language	English
Pages (from-to)	367-372
Number of pages	6
Journal	Nature
Volume	562
Issue number	7727
DOIs	https://doi.org/10.1038/s41586-018-0590-4
Publication status	Published - 18 Oct 2018
Externally published	Yes

Bibliographical note

Funding Information:
Acknowledgements We thank Sony Biotechnology for making an SH800S instrument available for this project. Some of the cell sorting/flow cytometry analysis for this project was performed using a Sony SH800S instrument in the Stanford Shared FACS Facility. Some FACS experiments used instruments in the VA Flow Cytometry Core, which is supported by the US Department of Veterans Affairs, Palo Alto Veterans Institute for Research and the National Institutes of Health. This work was supported by the Chan Zuckerberg Biohub, NIH Grant DP1 AG053015 and the NOMIS Foundation (T.W.-C.) as well as partly by the Stanford Islet Research Core in the Stanford Diabetes Research Center (P30 DK116074). We thank A. McGeever for contributions to the design of the Tabula Muris web portal.

Publisher Copyright:
© 2018, Springer Nature Limited.

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10.1038/s41586-018-0590-4

Cite this

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title = "Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris",

abstract = "Here we present a compendium of single-cell transcriptomic data from the model organism Mus musculus that comprises more than 100,000 cells from 20 organs and tissues. These data represent a new resource for cell biology, reveal gene expression in poorly characterized cell populations and enable the direct and controlled comparison of gene expression in cell types that are shared between tissues, such as T lymphocytes and endothelial cells from different anatomical locations. Two distinct technical approaches were used for most organs: one approach, microfluidic droplet-based 3′-end counting, enabled the survey of thousands of cells at relatively low coverage, whereas the other, full-length transcript analysis based on fluorescence-activated cell sorting, enabled the characterization of cell types with high sensitivity and coverage. The cumulative data provide the foundation for an atlas of transcriptomic cell biology.",

author = "Nicholas Schaum and Jim Karkanias and Neff, {Norma F.} and May, {Andrew P.} and Quake, {Stephen R.} and Tony Wyss-Coray and Spyros Darmanis and Joshua Batson and Olga Botvinnik and Chen, {Michelle B.} and Steven Chen and Foad Green and Jones, {Robert C.} and Ashley Maynard and Lolita Penland and Pisco, {Angela Oliveira} and Sit, {Rene V.} and Stanley, {Geoffrey M.} and Webber, {James T.} and Fabio Zanini and Tal Iram",

note = "Funding Information: Acknowledgements We thank Sony Biotechnology for making an SH800S instrument available for this project. Some of the cell sorting/flow cytometry analysis for this project was performed using a Sony SH800S instrument in the Stanford Shared FACS Facility. Some FACS experiments used instruments in the VA Flow Cytometry Core, which is supported by the US Department of Veterans Affairs, Palo Alto Veterans Institute for Research and the National Institutes of Health. This work was supported by the Chan Zuckerberg Biohub, NIH Grant DP1 AG053015 and the NOMIS Foundation (T.W.-C.) as well as partly by the Stanford Islet Research Core in the Stanford Diabetes Research Center (P30 DK116074). We thank A. McGeever for contributions to the design of the Tabula Muris web portal. Publisher Copyright: {\textcopyright} 2018, Springer Nature Limited.",

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AU - Karkanias, Jim

AU - Neff, Norma F.

AU - May, Andrew P.

AU - Quake, Stephen R.

AU - Wyss-Coray, Tony

AU - Darmanis, Spyros

AU - Batson, Joshua

AU - Botvinnik, Olga

AU - Chen, Michelle B.

AU - Chen, Steven

AU - Green, Foad

AU - Jones, Robert C.

AU - Maynard, Ashley

AU - Penland, Lolita

AU - Pisco, Angela Oliveira

AU - Sit, Rene V.

AU - Stanley, Geoffrey M.

AU - Webber, James T.

AU - Zanini, Fabio

AU - Iram, Tal

N1 - Funding Information: Acknowledgements We thank Sony Biotechnology for making an SH800S instrument available for this project. Some of the cell sorting/flow cytometry analysis for this project was performed using a Sony SH800S instrument in the Stanford Shared FACS Facility. Some FACS experiments used instruments in the VA Flow Cytometry Core, which is supported by the US Department of Veterans Affairs, Palo Alto Veterans Institute for Research and the National Institutes of Health. This work was supported by the Chan Zuckerberg Biohub, NIH Grant DP1 AG053015 and the NOMIS Foundation (T.W.-C.) as well as partly by the Stanford Islet Research Core in the Stanford Diabetes Research Center (P30 DK116074). We thank A. McGeever for contributions to the design of the Tabula Muris web portal. Publisher Copyright: © 2018, Springer Nature Limited.

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N2 - Here we present a compendium of single-cell transcriptomic data from the model organism Mus musculus that comprises more than 100,000 cells from 20 organs and tissues. These data represent a new resource for cell biology, reveal gene expression in poorly characterized cell populations and enable the direct and controlled comparison of gene expression in cell types that are shared between tissues, such as T lymphocytes and endothelial cells from different anatomical locations. Two distinct technical approaches were used for most organs: one approach, microfluidic droplet-based 3′-end counting, enabled the survey of thousands of cells at relatively low coverage, whereas the other, full-length transcript analysis based on fluorescence-activated cell sorting, enabled the characterization of cell types with high sensitivity and coverage. The cumulative data provide the foundation for an atlas of transcriptomic cell biology.

AB - Here we present a compendium of single-cell transcriptomic data from the model organism Mus musculus that comprises more than 100,000 cells from 20 organs and tissues. These data represent a new resource for cell biology, reveal gene expression in poorly characterized cell populations and enable the direct and controlled comparison of gene expression in cell types that are shared between tissues, such as T lymphocytes and endothelial cells from different anatomical locations. Two distinct technical approaches were used for most organs: one approach, microfluidic droplet-based 3′-end counting, enabled the survey of thousands of cells at relatively low coverage, whereas the other, full-length transcript analysis based on fluorescence-activated cell sorting, enabled the characterization of cell types with high sensitivity and coverage. The cumulative data provide the foundation for an atlas of transcriptomic cell biology.

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JO - Nature

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ER -

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

Abstract

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