PXD010621-1

PXD010621 is an original dataset announced via ProteomeXchange.

Title	A Molecular Roadmap of the Phased Progression of Pluripotency
Description	Pluripotency is highly dynamic and progresses through a continuum of pluripotent stem cell states. The two states that bookend the pluripotency continuum, naïve and primed, are well characterized, but our understanding of the intermediate states and the transitions between them remain incomplete. To address this gap in knowledge, we generated comprehensive maps of the proteome, phosphoproteome, transcriptome, and epigenome of mouse embryonic stem cells transitioning from naïve to primed pluripotency. Through integrative analysis, we find that distinct waves of proteome-resetting mark pluripotent state transitions. Rapid, acute, and widespread changes to the phosphoproteome precede ordered changes to the epigenome, transcriptome, and proteome. Reconstruction of kinase-substrate networks allowed us to uncover signaling dynamics and previously unidentified substrates. Flow cytometry analysis unearthed cell surface markers that track pluripotent state transitions. Collectively, our data provide a comprehensive molecular description of the phased progression of pluripotency and a foundation for investigating mechanisms that regulate pluripotent state transitions.
HostingRepository	PRIDE
AnnounceDate	2019-05-07
AnnouncementXML	Submission_2019-05-07_08:38:34.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mario Oroshi
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	phosphorylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-07-30 07:53:00	ID requested
⏵ 1	2019-05-07 08:38:35	announced
2	2019-05-10 02:53:49	announced	Updated project metadata.
3	2019-06-03 01:31:07	announced	Updated project metadata.

Dataset with its publication pending

curator keyword: Biological

submitter keyword: mass spectrometry, proteomics, phosphoproteomics, phosphorylation, signal transduction, post-translational modification, EasyPhos, stem cell, differentiation, mESC, EpiLC, embryonic, pluripotency, dynamic

Matthias Mann
contact affiliation	Department of Proteomics and Signal Transduction Max Planck Institute of Biochemistry
contact email	mmann@biochem.mpg.de
lab head
Mario Oroshi
contact affiliation	Proteomics
contact email	oroshi@biochem.mpg.de
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/2019/05/PXD010621

PRIDE project URI

• PRIDE
  1. PXD010621
     1. Label: PRIDE project
     2. Name: A Molecular Roadmap of the Phased Progression of Pluripotency