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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 |
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.
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| Contributor(s) |
Nowotschin S, Setty M, 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 |
| Citation(s) |
30959515 |
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| Submission date |
Nov 29, 2018 |
| Last update date |
May 26, 2019 |
| Contact name |
Manu Setty |
| E-mail(s) |
[email protected]
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| Organization name |
Fred Hutchinson Cancer Center
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| Department |
Basic Sciences Division
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| Street address |
1100 Fairview Ave N
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
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| Platforms (1) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
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| Samples (16)
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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 |
PRJNA507604 |
| SRA |
SRP171152 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE123124_RAW.tar |
2.1 Mb |
(http)(custom) |
TAR (of CSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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