The single-cell transcriptional landscape of mammalian organogenesis.

Nature
Junyue CaoJay Shendure

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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Citations

Jul 25, 2019·Journal of Bone and Mineral Research : the Official Journal of the American Society for Bone and Mineral Research·Matthew B GreenblattSarfaraz Lalani
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Methods Mentioned

BETA
scRNA-seq
RNA-seq
fluorescence-activated cell sorting
PCR
electrophoresis
PCA

Software Mentioned

sci
EnrichR
igraph
deML
scrublet
SimplePPT
kmeans
seq
learnGraph
seq3

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