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

By N. Schaum, Jim Karkanias, N. Neff, A. May, Stephen R. Quake, T. Wyss‐Coray, S. Darmanis, Joshua Batson, O. Botvinnik, Michelle B. Chen and 108 more. 2018

2,436 citations recorded by the source corpus.

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. 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.

Subfields: Biophysics, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Biophysics

In Molecular Biology

Citations in the corpus

Giotto: a toolbox for integrative analysis and visualization of spatial expression data (2021, background): “However, recent studies have also shown that identical cell types may have tissue-specific expression patterns [1, 2], indicating that the tissue environment plays an important role in mediating cell states.”
The integrated stress response: From mechanism to disease (2020, background): “Although HRI was long thought to have a specialized role in erythroid cells dedicated to hemoglobin synthesis (40), it is now recognized that HRI is widely expressed in several cell types and organs (41) and responds to multiple other forms of cellular cell stress, such as oxidative and mitochondria”
A human cell atlas of fetal gene expression (2020, background): “We emphasize that our process for annotating cell types benefited tremendously from the myriad single-cell atlases of specific human organs or other mammals that have been generated to date (8, 9, 11, 16, 28, 50, 108, 139).”
The UCSC Genome Browser database: 2023 update (2022, positive): “There are also two aggregate tracks: Tabula Sapiens (19), which contains data from the Tabula Sapiens Consortium providing an atlas of nearly 500 000 cells from 24 organs of 15 normal humans, and a Merged Cells track, which is an aggregate track created by the Genome Browser containing data from 12 ”