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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:

"Total RNA was extracted from bulk tissue and dissociated cells of 13ss (~E8.75) gut tubes, from bulk tissue from anterior, anterior-midgut, midgut-posterior and posterior sections of 13ss gut tubes, as well as from extra-embryonic visceral endoderm and embryonic visceral endoderm of E7.5 embryos (see also table in section: Bulk RNA processing). The Trizol method (Invitrogen) was used for RNA extraction."
Subject of Study
Mus musculus
Subject(s)
Endoderm
RNA-Seq
Single-Cell Analysis
Transcriptome
Access via GEO


Accession #: GSE123124

Access via BioProject


Accession #: PRJNA507604

Access via SRA


Accession #: SRP171152

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 HiSeq 4000

High throughput gene sequencing system

Invitrogen TRIzol™ Reagent

a complete, ready-to-use reagent for the isolation of high-quality total RNA or the simultaneous isolation of RNA, DNA, and protein from a variety of biological samples.

Dataset Format(s)
CSV, TAR
Dataset Size
2.1 MB
Data Catalog Record Updated
2023-11-14