PXD009217

PXD009217 is an original dataset announced via ProteomeXchange.

Title	Quantitative subcellular proteomics using SILAC reveals enhanced metabolic buffering in ground state pluripotency
Description	The ground state of pluripotency is defined as a minimal unrestricted state as present in the Inner Cell Mass (ICM). Mouse embryonic stem cells (ESCs) grown in a defined serum-free medium with two kinase inhibitors (‘2i’) reflect this state, whereas ESCs grown in the presence of serum (‘serum’) share more similarities with post implantation epiblast cells. Pluripotency results from an intricate interplay between cytoplasmic, nuclear and chromatin-associated proteins. Therefore, quantitative information on the (sub)cellular proteome is essential to gain insight in the molecular mechanisms driving different pluripotent states. Here, we describe a full SILAC workflow and quality controls for proteomic comparison of 2i and serum ESCs. We demonstrate that this workflow is applicable for subcellular proteomics of the cytoplasm, nuclear and chromatin. The obtained quantitative information revealed increased levels of naïve pluripotency factors on the chromatin of 2i ESCs. Further, we demonstrate that these pluripotent states are supported by distinct metabolic programs, which include upregulation of free radical buffering by the glutathione pathway in 2i ESCs. Through induction of intracellular radicals, we show that the altered metabolic environment renders 2i ESCs less sensitive to oxidative stress. Altogether, this work provides novel insights into the proteome landscape underlying ground state pluripotency.
HostingRepository	PRIDE
AnnounceDate	2018-11-07
AnnouncementXML	Submission_2018-11-07_01:36:45.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Guido van Mierlo
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-03-15 07:05:08	ID requested
⏵ 1	2018-11-07 01:36:46	announced

van Mierlo G, Wester RA, Marks H, Quantitative subcellular proteomics using SILAC reveals enhanced metabolic buffering in the pluripotent ground state. Stem Cell Res, 33():135-145(2018) [pubmed]

curator keyword: Biological

submitter keyword: embryonic stem cells,metabolism,naïve pluripotency,SILAC

Hendrik Marks
contact affiliation	Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Nijmegen, the Netherlands
contact email	H.Marks@ncmls.ru.nl
lab head
Guido van Mierlo
contact affiliation	Radboud University
contact email	guidovanmierlo@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD009217
     1. Label: PRIDE project
     2. Name: Quantitative subcellular proteomics using SILAC reveals enhanced metabolic buffering in ground state pluripotency