HCA Data Explorer

The emergent landscape of the mouse gut endoderm at single-cell resolution

Updated October 20, 2021

To delineate the ontogeny of the mammalian endoderm, we generated 112,217 single-cell transcriptomes representing all endoderm populations within the mouse embryo until midgestation. By employing graph-based approaches, we modelled differentiating cells for spatio-temporal characterization of developmental trajectories and defined the transcriptional architecture that accompanies the emergence of the first (primitive or extra-embryonic) endodermal population and its sister pluripotent (embryonic) epiblast lineage. We uncovered a relationship between descendants of these two lineages, whereby epiblast cells differentiate into endoderm at two distinct time-points, before and during gastrulation. Trajectories of endoderm cells were mapped as they acquired embryonic versus extra-embryonic fates, and as they spatially converged within the nascent gut endoderm; revealing them to be globally similar but retaining aspects of their lineage history. We observed the regionalized identity of cells along the anterior-posterior axis of the emergent gut tube, reflecting their embryonic or extra-embryonic origin, and their coordinate patterning into organ-specific territories.

Manu SettySloan Kettering Institute, Memorial Sloan Kettering Cancer Centersettym@mskcc.org
Anna-Katerina HadjantonakisSloan Kettering Institute, Memorial Sloan Kettering Cancer Centerhadj@mskcc.org
Dana Pe'erSloan Kettering Institute, Memorial Sloan Kettering Cancer Centerpeerd@mskcc.org
Sonja Nowotschin (Experimental Scientist)1
Manu Setty (Computational Scientist)1
Ying-Yi Kuo (Experimental Scientist)1
Vincent Liu (Computational Scientist)1
Vidur Garg (Experimental Scientist)1
Roshan Sharma (Computational Scientist)1
Claire S Simon (Experimental Scientist)1
Nestor Saiz (Experimental Scientist)1
Rui Gardner (Experimental Scientist)1
Stephane C Boutet (Experimental Scientist)2
Deanna M Church (Investigator)2
Pamela A Hoodless (Investigator)3
Anna-Katerina Hadjantonakis (Principal Investigator)1
Dana Pe'er (Principal Investigator)1
1Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center
210X Genomics
3Terry Fox Laboratory, BC Cancer Agency
Parisa Nejad
William Sullivan

To reference this project, please use the following link:

https://explore.data.humancellatlas.org/projects/4e6f083b-5b9a-4393-9890-2a83da8188f1

Supplementary links are provided by contributors and represent items such as additional data which can’t be hosted here; code that was used to analyze this data; or tools and visualizations associated with this specific dataset.

1.https://github.com/dpeerlab/Harmony
INSDC Project Accessions:
SRP171031, SRP171152
GEO Series Accessions:INSDC Study Accessions:

For information regarding data sharing and data use, please see our Data Access Policy.

Analysis Portals

None

Project Label

Mouse Endoderm Project

Species

Mus musculus

Sample Type

specimens

Anatomical Entity

3 anatomical entities

Organ Part

4 organ parts

Selected Cell Types

endodermal cell

Disease Status (Specimen)

normal

Disease Status (Donor)

normal

Development Stage

adult

Library Construction Method

10x 3' v2

Nucleic Acid Source

single cell

Paired End

true

File Format

4 file formats

Cell Count Estimate

112.2k

Donor Count

6
bam21 file(s)fastq.gz568 file(s)h5ad1 file(s)loom23 file(s)