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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 20, 2019 |
| Title |
The dynamic transcriptional landscape of mammalian organogenesis at single cell resolution |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
During mammalian organogenesis, the cells of the three germ layers transform into an embryo that includes most major internal and external organs. The key regulators of developmental defects can be studied during this crucial period, but conventional approaches lack the throughput and resolution to obtain a global view of the molecular states and trajectories of a rapidly diversifying and expanding number of cell types. Here we set out to investigate the transcriptional dynamics of mouse development during organogenesis at single cell resolution. With an improved single cell combinatorial indexing-based protocol (‘sci-RNA-seq3’), we profiled over 2 million cells derived from 61 mouse embryos staged between 9.5 and 13.5 days of gestation (E9.5 to E13.5; 10 to 15 replicates per timepoint). We identify hundreds of expanding, contracting and transient cell types, many of which are only detected because of the depth of cellular coverage obtained here, and define the corresponding sets of cell type-specific marker genes, several of which we validate by whole mount in situ hybridization. We explore the dynamics of proliferation and gene expression within cell types over time, including focused analyses of the apical ectodermal ridge, limb mesenchyme and skeletal muscle. With a new algorithm (Monocle 3), we identify the major single cell developmental trajectories of mouse organogenesis, and within these discover examples of distinct paths to the same endpoint, i.e. branching and convergence. These data comprise a foundational resource for mammalian developmental biology, and are made available in a way that will facilitate their ongoing annotation by the research community.
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| Overall design |
2 million cells derived from 61 mouse embryos staged between 9.5 and 13.5 days of gestation (E9.5 to E13.5; 10 to 15 replicates per timepoint)
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| Contributor(s) |
Cao J, Spielmann M, Qiu X, Ibrahim DM, Huang X, Hill AJ, Zhang F, Mundlos S, Christiansen L, Steemers FJ, Trapnell C, Shendure J |
| Citation(s) |
30787437 |
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| Submission date |
Sep 13, 2018 |
| Last update date |
Mar 08, 2019 |
| Contact name |
Junyue Cao |
| E-mail(s) |
[email protected]
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| Organization name |
University of Washington
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| Department |
Department of Genome Sciences
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| Lab |
Shendure lab
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| Street address |
Foege Building S-210, 3720 15th Ave NE
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195-5065 |
| Country |
USA |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (760)
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| Relations |
| BioProject |
PRJNA490754 |
| SRA |
SRP161714 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE119945_cell_annotate.csv.gz |
101.4 Mb |
(ftp)(http) |
CSV |
| GSE119945_gene_annotate.csv.gz |
244.5 Kb |
(ftp)(http) |
CSV |
| GSE119945_gene_count.txt.gz |
3.7 Gb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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