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| Status |
Public on Apr 10, 2019 |
| Title |
The emergent landscape of the mouse gut endoderm at single-cell resolution |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
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.
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| Contributor(s) |
Nowotschin S, Kuo Y, Lui V, Garg V, Sharma R, Simon CS, Saiz N, Gardner R, Boutet SC, Church DM, Hoodless PA, Hadjantonakis A, Pe'er D, Setty M |
| Citation(s) |
30959515 |
| Submission date |
Nov 28, 2018 |
| Last update date |
Mar 26, 2020 |
| Contact name |
Manu Setty |
| E-mail(s) |
manu.talanki@gmail.com
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| Organization name |
Memorial Sloan-Kettering Cancer Center
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| Department |
Computational Biology
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| Lab |
Dana Pe'er
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| Street address |
415-417 East 68th Street - 11th Floor (Z-1131)
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (29)
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| This SubSeries is part of SuperSeries: |
| GSE123135 |
The emergent landscape of the mouse gut endoderm at single-cell resolution |
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| Relations |
| BioProject |
PRJNA507408 |
| SRA |
SRP171031 |
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