PXD009700 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Integrative multi-omics analysis of intestinal organoid differentiation |
Description | Intestinal 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. |
HostingRepository | PRIDE |
AnnounceDate | 2024-10-22 |
AnnouncementXML | Submission_2024-10-22_04:45:29.520.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Rik Lindeboom |
SpeciesList | scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; |
ModificationList | S-carboxamidomethyl-L-cysteine; mono N-acetylated residue; monohydroxylated residue |
Instrument | LTQ Orbitrap XL; Orbitrap Fusion; Q Exactive |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2018-05-07 06:12:43 | ID requested | |
1 | 2018-06-25 04:38:02 | announced | |
2 | 2019-04-03 03:12:51 | announced | Updated publication reference for PubMed record(s): 29945941. |
⏵ 3 | 2024-10-22 04:45:38 | announced | 2024-10-22: 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 affiliation | Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen - the Netherlands |
contact email | Michiel.Vermeulen@science.ru.nl |
lab head | |
Rik Lindeboom |
contact affiliation | Radboud Institute for Molecular Life Sciences |
contact email | r.lindeboom@science.ru.nl |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD009700
- Label: PRIDE project
- Name: Integrative multi-omics analysis of intestinal organoid differentiation