<<< Full experiment listing

PXD048347-1

PXD048347 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleDeciphering lineage specification during early embryogenesis using multi-layered proteomics
DescriptionGastrulation is a critical stage in embryonic development during which the germ layers are established. The advances and increasing availability of sequencing technologies led to the identification of gene regulatory programs that control the emergence of the germ layers and its derivatives. However, proteome-based studies of early mammalian development are scarce. To overcome this, we utilized gastruloids and a multilayered mass spectrometry-based proteomics approach to investigate the global dynamics of (phospho)protein expression during gastruloid differentiation. Our findings revealed that many proteins exhibit temporal expression with unique expression profiles corresponding to the three germ layers, which we also validated using single-cell proteomics technology. Notably, detected temporal protein expression dynamics in gastruloids aligns with equivalent mouse embryo stages. Additionally, we profiled enhancer interaction landscapes using P300 proximity labeling, which revealed numerous gastruloid-specific transcription factors and chromatin remodelers. Subsequent degron-based perturbations combined with scRNA-seq identified 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.
HostingRepositoryPRIDE
AnnounceDate2024-09-05
AnnouncementXMLSubmission_2024-09-05_04:58:54.159.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterHarmjan Vos
SpeciesList scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationListNo PTMs are included in the dataset
InstrumentOrbitrap Eclipse
Dataset History
RevisionDatetimeStatusChangeLog Entry
02024-01-09 06:02:08ID requested
12024-09-05 04:58:54announced
22024-10-22 06:57:44announced2024-10-22: Updated project metadata.
Publication List
10.1016/J.STEM.2024.04.017;
Keyword List
submitter keyword: proteomics, dTAG system, interaction proteomics, enhancers, Zeb2, transcription factors, somitoids,Gastruloids, developmental biology
Contact List
Michiel Vermeulen
contact affiliationDepartment of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands
contact emailmichiel.vermeulen@science.ru.nl
lab head
Harmjan Vos
contact affiliationUniversity Medical Center Utrecht Dept. Molecular Cancer Research
contact emailh.r.vos-3@umcutrecht.nl
dataset submitter
Full Dataset Link List
Dataset FTP location
NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/09/PXD048347
PRIDE project URI
Repository Record List
[ + ]