PXD009700

PXD009700 is an original dataset announced via ProteomeXchange.

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

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.

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;

submitter keyword: adult intestinal stem cells,organoids, Hnf4g, enterocytes, systems biology

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

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/2018/06/PXD009700

PRIDE project URI

• PRIDE
  1. PXD009700
     1. Label: PRIDE project
     2. Name: Integrative multi-omics analysis of intestinal organoid differentiation