GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE119945 Query DataSets for GSE119945
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
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.
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)
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
Submission date Sep 13, 2018
Last update date Mar 08, 2019
Contact name Junyue Cao
Organization name University of Washington
Department Department of Genome Sciences
Lab Shendure lab
Street address Foege Building S-210, 3720 15th Ave NE
City Seattle
State/province WA
ZIP/Postal code 98195-5065
Country USA
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (760)
GSM3388476 sci3-me-001
GSM3388477 sci3-me-002
GSM3388478 sci3-me-003
BioProject PRJNA490754
SRA SRP161714

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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 SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap