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PXD009700

PXD009700 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleIntegrative multi-omics analysis of intestinal organoid differentiation
DescriptionIntestinal organoids accurately recapitulate epithelial homeostasis in vivo, thereby representing a powerful in vitro system to investigate lineage specification and cellular differentiation. Here, we applied a multi-omics framework on stem cell enriched and -depleted mouse intestinal organoids to obtain a holistic view of the molecular mechanisms that drive differential gene expression during adult intestinal stem cell differentiation. Our data revealed a global rewiring of the transcriptome and proteome between intestinal stem cells and enterocytes, with the majority of dynamic protein expression being transcription-driven. Integrating absolute mRNA and protein copy numbers revealed post-transcriptional regulation of gene expression. Probing the epigenetic landscape identified a large number of cell-type specific regulatory elements, which revealed Hnf4g as a major driver of enterocyte differentiation. In summary, by applying an integrative systems biology approach we uncovered multiple layers of gene expression regulation, which contribute to lineage specification and plasticity of the mouse small intestinal epithelium.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_04:45:29.520.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterRik Lindeboom
SpeciesList scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationListS-carboxamidomethyl-L-cysteine; mono N-acetylated residue; monohydroxylated residue
InstrumentLTQ Orbitrap XL; Orbitrap Fusion; Q Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02018-05-07 06:12:43ID requested
12018-06-25 04:38:02announced
22019-04-03 03:12:51announcedUpdated publication reference for PubMed record(s): 29945941.
32024-10-22 04:45:38announced2024-10-22: Updated project metadata.
Publication List
Lindeboom RG, van Voorthuijsen L, Oost KC, Rodr, í, guez-Colman MJ, Luna-Velez MV, Furlan C, Baraille F, Jansen PW, Ribeiro A, Burgering BM, Snippert HJ, Vermeulen M, Integrative multi-omics analysis of intestinal organoid differentiation. Mol Syst Biol, 14(6):e8227(2018) [pubmed]
10.15252/msb.20188227;
Keyword List
submitter keyword: adult intestinal stem cells,organoids, Hnf4g, enterocytes, systems biology
Contact List
Michiel Vermeulen
contact affiliationRadboud Institute for Molecular Life Sciences, Radboud University, Nijmegen - the Netherlands
contact emailMichiel.Vermeulen@science.ru.nl
lab head
Rik Lindeboom
contact affiliationRadboud Institute for Molecular Life Sciences
contact emailr.lindeboom@science.ru.nl
dataset submitter
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Dataset FTP location
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PRIDE project URI
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