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Series GSE213336 Query DataSets for GSE213336
Status Public on Mar 06, 2024
Title Basal cell extrusion primes pluripotent cells for differentiation
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary The blueprint of the mammalian body plan is laid out during gastrulation, when a trilaminar embryo is formed. This process entails a burst of embryonic cell proliferation, the ingression of pluripotent epithelial cells at the primitive streak, and their priming towards primitive streak fates. How these different events are coordinated remains unknown. Here, we developed a 3D culture of self-renewing pluripotent and epithelial cells that recapitulates the transcriptional and architectural features of the gastrulating mouse embryo. Using this system in combination with microfabrication and in vivo experiments, we found that proliferation triggers basal extrusion in cells that express high levels of the apical polarity protein aPKC. Upon extrusion, cells are more sensitive to Bmp, Wnt, and Nodal signaling, and upregulate the expression of primitive streak markers. This mechanistic coupling between cell position and gene expression ensures that the right cell types become specified at the right place during embryonic development.
Overall design scRNA-Seq, RNA-Seq, BS-Seq
Contributor(s) Satoh N, Rosa VS, Makhlouf A, Kretzmer H, Kumar AS, Grosswendt S, Mattei A, Courbot O, Wolf S, McDole K, Langevin F, Wiacek M, Karpinski D, Elosegui-Artola A, Meissner A, Zernicka-Goetz M, Shahbazi M
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Submission date Sep 14, 2022
Last update date Mar 07, 2024
Contact name Helene Kretzmer
Organization name Max Planck Institute for Molecular Genetics
Department Genome Regulation
Lab Meissner Lab
Street address Ihnestra├če 63
City Berlin
ZIP/Postal code 14195
Country Germany
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (35)
GSM6579114 scRNA_Embryo
GSM6579115 scRNA_ESC
GSM6579116 Embryo3D_rep1
BioProject PRJNA880552

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

Supplementary file Size Download File type/resource
GSE213336_RAW.tar 679.5 Mb (http)(custom) TAR (of BW, TAR)
GSE213336_RNA_TPM.tsv.gz 3.9 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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