PXD009217 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2018-03-15 07:05:08 | ID requested | |
⏵ 1 | 2018-11-07 01:36:46 | announced | |
Publication List
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] |
Keyword List
curator keyword: Biological |
submitter keyword: embryonic stem cells,metabolism,naïve pluripotency,SILAC |
Contact List
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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
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[ - ]
- PRIDE
- PXD009217
- Label: PRIDE project
- Name: Quantitative subcellular proteomics using SILAC reveals enhanced metabolic buffering in ground state pluripotency