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Series GSE229028 Query DataSets for GSE229028
Status Public on May 21, 2024
Title Deciphering lineage specification during early embryogenesis in mouse gastruloids using integrative multi-layered proteomics [scRNA-seq]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Gastrulation is a critical stage of embryonic development during which the three germ layers are established. Deciphering the molecular mechanisms underlying this proces from a protein perspective remains a significant challenge. To address this, we employed a multilayered mass spectrometry-based proteomics approach to investigate the global dynamics of (phospho)protein expression during differentiation of ESCs towards gastruloids – an in vitro model of gastrulation-stage embryogenesis. Our findings revealed that many proteins exhibited temporal expression with unique expression profiles corresponding to the three germ layers. Additionally, we profiled enhancer interaction landscapes in ESCs and gastruloids using p300 proximity labeling, which revealed numerous gastruloid-specific transcription factors and chromatin remodelers. Subsequent degron based perturbations combined with scRNA-seq revealed a critical role for Zeb2 in regulating mouse and human somitogenesis. Overall, this study provides a rich resource for developmental and synthetic biology communities endeavoring to understand mammalian embryogenesis.
 
Overall design Somitic gastruloids were generated as previously described (Protoc. Exch. https://doi.org/10.1038/protex.2018.094, van den Brink et al., Nature 2020). Somitic gastruloids expressing Zeb2-degron tag were treated with 100nM dTAG-13 or DMSO at 72 and 96h during gastruloid formation.
 
Contributor(s) Stelloo S, Vermeulen M
Citation(s) 38754429
Submission date Apr 05, 2023
Last update date May 22, 2024
Contact name Suzan Stelloo
E-mail(s) Stelloo@science.ru.nl
Organization name Radboud University
Department Molecular Biology
Street address Geert Grooteplein Zuid 28
City Nijmegen
ZIP/Postal code 6525 GA
Country Netherlands
 
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (2)
GSM7147997 scRNA_somitic_gastruloids_Zeb2_untreated
GSM7147998 scRNA_somitic_gastruloids_Zeb2_dTAG13
This SubSeries is part of SuperSeries:
GSE229029 Deciphering lineage specification during early embryogenesis in mouse gastruloids using integrative multi-layered proteomics
Relations
BioProject PRJNA952609

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
GSE229028_RAW.tar 239.4 Mb (http)(custom) TAR (of MTX, TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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