PXD001901

PXD001901 is an original dataset announced via ProteomeXchange.

Title	Dynamic proteomic profiling of extra-embryonic endoderm differentiation in mouse embryonic stem cells
Description	During mammalian pre-implantation development, the cells of the blastocyst’s inner cell mass differentiate into the epiblast and primitive endoderm lineages, which give rise to the fetus and extra-embryonic tissues, respectively. Extra-embryonic endoderm differentiation can be modeled in vitro by induced expression of GATA transcription factors in mouse embryonic stem cells. Here we use this GATA-inducible system to quantitatively monitor the dynamics of global proteomic changes during the early stages of this differentiation event and also investigate the fully differentiated phenotype, as represented by embryo-derived extra-embryonic endoderm (XEN) cells. Using mass spectrometry-based quantitative proteomic profiling with multivariate data analysis tools, we reproducibly quantified 2,336 proteins across three biological replicates and have identified clusters of proteins characterized by distinct, dynamic temporal abundance profiles. We first used this approach to highlight novel marker candidates of the pluripotent state and extra-embryonic endoderm differentiation. Through functional annotation enrichment analysis, we have shown that the downregulation of chromatin-modifying enzymes, the re-organization of membrane trafficking machinery and the breakdown of cell-cell adhesion are successive steps of the extra-embryonic differentiation process. Thus, applying a range of sophisticated clustering approaches to a time-resolved proteomic dataset has allowed the elucidation of complex biological processes which characterize stem cell differentiation and could establish a general paradigm for the investigation of these processes.
HostingRepository	PRIDE
AnnounceDate	2015-06-13
AnnouncementXML	Submission_2015-06-13_03:44:50.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD001901
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Laurent Gatto
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue; TMT6plex-126 reporter+balance reagent acylated residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2015-03-11 02:31:07	ID requested
⏵ 1	2015-06-13 03:44:51	announced

Mulvey CM, Schr, ö, ter C, Gatto L, Dikicioglu D, Fidaner IB, Christoforou A, Deery MJ, Cho LT, Niakan KK, Martinez-Arias A, Lilley KS, Dynamic Proteomic Profiling of Extra-Embryonic Endoderm Differentiation in Mouse Embryonic Stem Cells. Stem Cells, 33(9):2712-25(2015) [pubmed]

curator keyword: Biomedical, Biological

submitter keyword: Differentiation, Extra-embryonic Endoderm (XEN) stem cells, Pluripotency, Quantitative Proteomics, Tandem Mass Tags (TMT)

Kathryn Lilley
contact affiliation	Cambridge Centre for Proteomics Cambridge System Biology Centre Wellcome Trust Stem Cell building University of Cambridge Department of Biochemistry Tennis Court Road Cambridge CB2 1QR
contact email	k.s.lilley@bioc.cam.ac.uk
lab head
Laurent Gatto
contact affiliation	Department of Biochemistry, University of Cambridge
contact email	lg390@cam.ac.uk
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/2015/06/PXD001901

PRIDE project URI

• PRIDE
  1. PXD001901
     1. Label: PRIDE project
     2. Name: Dynamic proteomic profiling of extra-embryonic endoderm differentiation in mouse embryonic stem cells