Search Tips
Description
Summary from GEO:

"To comprehensively delineate the ontogeny of an organ system, we generated 112,217 single- cell transcriptomes representing all endoderm populations within the mouse embryo until midgestation. We employed graph-based approaches to model differentiating cells for spatio- temporal characterization of developmental trajectories. Our analysis reveals the detailed architecture of the emergence of the first (primitive or extra-embryonic) endodermal population and pluripotent epiblast. We uncover an unappreciated relationship between descendants of these lineages, before the onset of gastrulation, suggesting that mixing of extra-embryonic and embryonic endoderm cells occurs more than once during mammalian development. We map the trajectories of endoderm cells as they acquire embryonic versus extra-embryonic fates, and their spatial convergence within the gut endoderm; revealing them to be globally similar but retaining aspects of their lineage history. We observe the regionalized localization of cells along the forming gut tube, reflecting their extra-embryonic or embryonic origin, and their coordinate patterning into organ-specific territories along the anterior-posterior axis."

Overall design from GEO:

"Cells were isolated from sequentially-staged wild-type mouse embryos between E3.5 and E8.75. Whole embryos were used for single-cell isolations for stages E3.5-E5.5. Endodermal tissue layers were isolated from E6.5-E8.75 stages. Gut tube of E8.75 were sorted based on GFP expression and another dataset was generated using anterior - posterior positioning. Each sample was measured in replicate with E5.5 and E7.5 measured in triplicates."
Subject of Study
Mus musculus
Subject(s)
Cell Differentiation
Endoderm
Single-Cell Analysis
Transcriptome
Access via GEO


Accession #: GSE123046

Access via BioProject


Accession #: PRJNA507408

Access via SRA


Accession #: SRP171031

Access Restrictions
Free to All
Access Instructions
The NCBI Gene Expression Omnibus. BioProject, and SRA databases provide open access to these files.
Associated Publications
Nowotschin S, Setty M, Kuo Y, Liu V, Garg V, Sharma R, Simon C, Saiz N, Gardner R, Boutet S, Church D, Hoodless P, Hadjantonakis A, Pe'er D. The emergent landscape of the mouse gut endoderm at single-cell resolution. Nature. 2019; 569(7756):361-367.
Equipment Used
Illumina NovaSeq 6000
Dataset Format(s)
CSV, TAR
Dataset Size
720.4 MB
Data Catalog Record Updated
2023-11-14