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PXD041328

PXD041328 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleDeciphering lineage specification during early embryogenesis using multi-layered proteomics
DescriptionGastrulation is a critical stage of embryonic development during which the three germ layers are established. Deciphering the molecular mechanisms underlying this process 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 during gastrulation with unique expression profiles corresponding to the three germ layers, which we also validated using an ultra sensitive single cell proteomics approachtechnology. 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.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_06:57:42.852.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
02023-04-04 06:30:50ID requested
12024-09-05 05:32:28announced
22024-10-22 06:57:43announced2024-10-22: 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 affiliationRadboud Universiteit Nijmegen NL
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
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PRIDE project URI
Repository Record List
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