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Series GSE123046 Query DataSets for GSE123046
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
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.
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.
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
Organization name Memorial Sloan-Kettering Cancer Center
Department Computational Biology
Lab Dana Pe'er
Street address 415-417 East 68th Street - 11th Floor (Z-1131)
City New York
State/province NY
ZIP/Postal code 10065
Country USA
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (29)
GSM3494334 E3.5_Rep1
GSM3494335 E3.5_Rep2
GSM3494336 E4.5_Rep1
This SubSeries is part of SuperSeries:
GSE123135 The emergent landscape of the mouse gut endoderm at single-cell resolution
BioProject PRJNA507408
SRA SRP171031

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE123046_RAW.tar 720.4 Mb (http)(custom) TAR (of CSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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