The Single-cell Transcriptional Landscape of Mammalian Organogenesis

Overview

Journal Nature

Specialty Science

Date 2019 Feb 22

PMID 30787437

Citations 1617

Authors

Junyue Cao

Malte Spielmann

Xiaojie Qiu

Xingfan Huang

Daniel M Ibrahim

Andrew J Hill

Fan Zhang

Stefan Mundlos

Lena Christiansen

Frank J Steemers

Cole Trapnell

Jay Shendure

Affiliations

Soon will be listed here.

Abstract

Mammalian organogenesis is a remarkable process. Within a short timeframe, the cells of the three germ layers transform into an embryo that includes most of the major internal and external organs. Here we investigate the transcriptional dynamics of mouse organogenesis at single-cell resolution. Using single-cell combinatorial indexing, we profiled the transcriptomes of around 2 million cells derived from 61 embryos staged between 9.5 and 13.5 days of gestation, in a single experiment. The resulting 'mouse organogenesis cell atlas' (MOCA) provides a global view of developmental processes during this critical window. We use Monocle 3 to identify hundreds of cell types and 56 trajectories, many of which are detected only because of the depth of cellular coverage, and collectively define thousands of corresponding marker genes. We explore the dynamics of gene expression within cell types and trajectories over time, including focused analyses of the apical ectodermal ridge, limb mesenchyme and skeletal muscle.

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