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

A ‘mouse atlas’, comprising single-cell transcriptomic data from more than 100,000 cells from 20 organs and tissues, has been created as a resource for cell biology.

Nicholas Schaum
Jim Karkanias
Tony Wyss-Coray
Research03 Oct 2018
Nature

Volume: 562, P: 367-372
Overloading And unpacKing (OAK) - droplet-based combinatorial indexing for ultra-high throughput single-cell multiomic profiling

Single-cell sequencing approaches need to balance sensitivity, throughput and experimental complexity. Here the authors combine droplet-based microfluidics and combinatorial indexing to develop OAK, a versatile method for ultra-high throughput single-cell multiomic profiling.

Bing Wu
Hayley M. Bennett
Spyros Darmanis
ResearchOpen Access23 Oct 2024
Nature Communications

Volume: 15, P: 1-12
Correction: Corrigendum: Solid-phase proximity ligation assays for individual or parallel protein analyses with readout via real-time PCR or sequencing

Rachel Yuan Nong
Di Wu
Spyros Darmanis
Amendments and Corrections26 Mar 2015
Nature Protocols

Volume: 10, P: 644
Molecular hallmarks of heterochronic parabiosis at single-cell resolution

A transcriptomics study demonstrates cell-type-specific responses to differentially aged blood and shows young blood to have restorative and rejuvenating effects that may be invoked through enhanced mitochondrial function.

Róbert Pálovics
Andreas Keller
Tony Wyss-Coray
Research02 Mar 2022
Nature

Volume: 603, P: 309-314
Ageing hallmarks exhibit organ-specific temporal signatures

Bulk RNA sequencing of organs and plasma proteomics at different ages across the mouse lifespan is integrated with data from the Tabula Muris Senis, a transcriptomic atlas of ageing mouse tissues, to describe organ-specific changes in gene expression during ageing.

Nicholas Schaum
Benoit Lehallier
Tony Wyss-Coray
Research15 Jul 2020
Nature

Volume: 583, P: 596-602
Detection of brain neovascularization induced by focal ischemia

YoneJung Yoon
Georgios Voloudakis
Anastasios Georgakopoulos
Research15 Sept 2021
Molecular Psychiatry

Volume: 26, P: 1719
ERα dysfunction caused by ESR1 mutations and therapeutic pressure promotes lineage plasticity in ER⁺ breast cancer

Liang et al. study the impact of ERα antagonist/degraders against different Esr1 mutations in murine models and find that inhibition of mutant ERα induces lineage plasticity, which is also observed in Esr1-wild-type mice with long-term estrogen deprivation.

Jackson Liang
Xiaosai Yao
Ciara Metcalfe
Research13 Jan 2025
Nature Cancer

Volume: 6, P: 357-371
Induction of a distinct macrophage population and protection from lung injury and fibrosis by Notch2 blockade

Macrophages are pleiotropic and can have different functions and phenotypes. Here the authors show that a population of macrophages, previously described as pro-fibrotic, can be induced through Notch2 blockade and that in a mouse lung injury and fibrosis model this macrophage population does not promote inflammation or fibrosis.

Mayra Cruz Tleugabulova
Sandra P. Melo
Maximilian Nitschké
ResearchOpen Access06 Nov 2024
Nature Communications

Volume: 15, P: 1-18
Coordinated wound responses in a regenerative animal-algal holobiont

The term ‘holobiont’ refers to a multicellular organism and its microbial symbionts. Whether and how symbionts react to host injury and how cellular responses are integrated across species remain unexplored. Here, the authors report a deeply conserved animal regeneration regulatory program that links molecular networks across species in an animal-algal holobiont.

Dania Nanes Sarfati
Yuan Xue
Bo Wang
ResearchOpen Access13 May 2024
Nature Communications

Volume: 15, P: 1-16
Leveraging the Cell Ontology to classify unseen cell types

Classifying cells into unseen cell types remains challenging in scRNA-seq analysis. Here we show that Cell Ontology enables an accurate classification of unseen cell types through considering the cell type relationships in the Cell Ontology graph.

Sheng Wang
Angela Oliveira Pisco
Russ B. Altman
ResearchOpen Access21 Sept 2021
Nature Communications

Volume: 12, P: 1-11
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse

A single-cell transcriptomic atlas across the lifespan of the mouse, denoted Tabula Muris Senis, provides molecular information about the hallmarks of ageing in a range of tissues and cell types.

Nicole Almanzar
Jane Antony
James Zou
Research15 Jul 2020
Nature

Volume: 583, P: 590-595
In situ tumour arrays reveal early environmental control of cancer immunity

Skin tumour array by microporation (STAMP) captures the dynamic relationships of spatial, cellular and molecular components of tumour rejection and has the potential to translate therapeutic concepts into successful clinical strategies.

Guadalupe Ortiz-Muñoz
Markus Brown
Christine Moussion
ResearchOpen Access31 May 2023
Nature

Volume: 618, P: 827-833
MARS: discovering novel cell types across heterogeneous single-cell experiments

MARS uses a meta-learning strategy for annotating known cell types and identifying novel ones across single-cell RNA-seq datasets.

Maria Brbić
Marinka Zitnik
Jure Leskovec
Research19 Oct 2020
Nature Methods

Volume: 17, P: 1200-1206
Single cell analysis of human foetal liver captures the transcriptional profile of hepatobiliary hybrid progenitors

The liver parenchyma consists of several cell types, but the origin of this tissue in humans is unclear. Here, the authors perform single cell RNA sequencing of human fetal and adult liver to identify a hepatobiliary hybrid progenitor population of cells, which have a similar gene signature to mouse oval cells.

Joe M. Segal
Deniz Kent
S. Tamir Rashid
ResearchOpen Access26 Jul 2019
Nature Communications

Volume: 10, P: 1-14
A molecular cell atlas of mouse lemur, an emerging model primate

Together with a companion paper, the generation of a transcriptomic atlas for the mouse lemur and analyses of example cell types establish this animal as a molecularly tractable primate model organism.

Antoine de Morree
Iwijn De Vlaminck
Mark A. Krasnow
ResearchOpen Access30 Jul 2025
Nature

Volume: 644, P: 173-184
Mouse lemur cell atlas informs primate genes, physiology and disease

Together with an accompanying paper presenting a transcriptomic atlas of the mouse lemur, interrogation of the atlas provides a rich body of data to support the use of the organism as a model for primate biology and health.

Camille Ezran
Shixuan Liu
Mark A. Krasnow
ResearchOpen Access30 Jul 2025
Nature

Volume: 644, P: 185-196
Human melanocyte development and melanoma dedifferentiation at single-cell resolution

Constructing a single-cell transcriptional map of primary human epidermal melanocytes, Belote et al. uncover distinct subpopulations of melanocytes, characterize dedifferentiation patterns associated with melanoma prognosis and uncover the unique cellular origins of acral melanoma.

Rachel L. Belote
Daniel Le
Robert L. Judson-Torres
Research02 Sept 2021
Nature Cell Biology

Volume: 23, P: 1035-1047
Single-cell proteomics enabled by next-generation sequencing or mass spectrometry

This Review covers the state of the art in applying mass spectrometry- or next-generation sequencing-based techniques for single-cell proteomics analysis, offering suggestions for maximizing the advantages of both approaches.

Hayley M. Bennett
William Stephenson
Spyros Darmanis
Reviews02 Mar 2023
Nature Methods

Volume: 20, P: 363-374
Systemic cytokines drive conserved severity-associated myeloid responses across bacterial and viral infections

Multi-cohort analysis of single cell and bulk transcriptional data combined with in vitro and in vivo experiments highlight the role of IL1R2+ myeloid cells on tissue injury during severe infection.

Kimberly Kajihara
Donghong Yan
Miguel Reyes
ResearchOpen Access23 Jul 2025
Communications Biology

Volume: 8, P: 1-11
An organism-wide atlas of hormonal signaling based on the mouse lemur single-cell transcriptome

Endocrinologists have traditionally focused on studying one hormone or organ system at a time. Here the authors use transcriptomic data from the mouse lemur to globally characterize primate hormonal signaling, describing hormone sources and targets, identifying conserved and primate specific regulation, and elucidating principles of the network.

Shixuan Liu
Camille Ezran
James E. Ferrell Jr.
ResearchOpen Access11 Mar 2024
Nature Communications

Volume: 15, P: 1-27
Tracheal aspirate RNA sequencing identifies distinct immunological features of COVID-19 ARDS

Here, the authors perform transcriptional profiling on tracheal aspirates of adults requiring mechanical ventilation for SARS-CoV2-induced acute respiratory distress syndrome (ARDS) and identify a dysregulated host response predicted to predicted to be potentially modulated by dexamethasone.

Aartik Sarma
Stephanie A. Christenson
Charles R. Langelier
ResearchOpen Access26 Aug 2021
Nature Communications

Volume: 12, P: 1-10
Adversarial domain translation networks for integrating large-scale atlas-level single-cell datasets

An adversarial domain translation framework is presented for scalable integration of single-cell atlases across samples, technical platforms, data modalities and species.

Jia Zhao
Gefei Wang
Can Yang
Research30 May 2022
Nature Computational Science

Volume: 2, P: 317-330
PS1 FAD mutants decrease ephrinB2-regulated angiogenic functions, ischemia-induced brain neovascularization and neuronal survival

YoneJung Yoon
Georgios Voloudakis
Anastasios Georgakopoulos
Research15 Jun 2020
Molecular Psychiatry

Volume: 26, P: 1996-2012
Persistent features of intermittent transcription

Michael Wilkinson
Spyros Darmanis
Greg Huber
ResearchOpen Access21 Feb 2020
Scientific Reports

Volume: 10, P: 1-10
Solid-phase proximity ligation assays for individual or parallel protein analyses with readout via real-time PCR or sequencing

Rachel Yuan Nong
Di Wu
Spyros Darmanis
Protocols30 May 2013
Nature Protocols

Volume: 8, P: 1234-1248

Search

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

Overloading And unpacKing (OAK) - droplet-based combinatorial indexing for ultra-high throughput single-cell multiomic profiling

Correction: Corrigendum: Solid-phase proximity ligation assays for individual or parallel protein analyses with readout via real-time PCR or sequencing

Molecular hallmarks of heterochronic parabiosis at single-cell resolution

Ageing hallmarks exhibit organ-specific temporal signatures

Detection of brain neovascularization induced by focal ischemia

ERα dysfunction caused by ESR1 mutations and therapeutic pressure promotes lineage plasticity in ER⁺ breast cancer

Induction of a distinct macrophage population and protection from lung injury and fibrosis by Notch2 blockade

Coordinated wound responses in a regenerative animal-algal holobiont

Leveraging the Cell Ontology to classify unseen cell types

A single-cell transcriptomic atlas characterizes ageing tissues in the mouse

In situ tumour arrays reveal early environmental control of cancer immunity

MARS: discovering novel cell types across heterogeneous single-cell experiments

Single cell analysis of human foetal liver captures the transcriptional profile of hepatobiliary hybrid progenitors

A molecular cell atlas of mouse lemur, an emerging model primate

Mouse lemur cell atlas informs primate genes, physiology and disease

Human melanocyte development and melanoma dedifferentiation at single-cell resolution

Single-cell proteomics enabled by next-generation sequencing or mass spectrometry

Systemic cytokines drive conserved severity-associated myeloid responses across bacterial and viral infections

An organism-wide atlas of hormonal signaling based on the mouse lemur single-cell transcriptome

Tracheal aspirate RNA sequencing identifies distinct immunological features of COVID-19 ARDS

Adversarial domain translation networks for integrating large-scale atlas-level single-cell datasets

PS1 FAD mutants decrease ephrinB2-regulated angiogenic functions, ischemia-induced brain neovascularization and neuronal survival

Persistent features of intermittent transcription

Solid-phase proximity ligation assays for individual or parallel protein analyses with readout via real-time PCR or sequencing

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