PXD034448-2

PXD034448 is an original dataset announced via ProteomeXchange.

Title	Comprehensive chromatin proteomics resolves functional phases of pluripotency and identifies changes in regulatory components
Description	The establishment of cellular identity is driven by transcriptional and epigenetic regulators of the chromatin proteome - the chromatome. Comprehensive analyses of the chromatome composition and dynamics can therefore greatly improve our understanding of gene regulatory mechanisms. Here, we developed an accurate mass spectrometry (MS)-based proteomic method called Chromatin Aggregation Capture (ChAC) followed by Data-Independent Acquisition (DIA) and analyzed chromatome reorganizations during major phases of pluripotency. This enabled us to generate a comprehensive atlas of proteomes, chromatomes, and chromatin affinities for the ground, formative and primed pluripotency states, and to pinpoint the specific binding and rearrangement of regulatory components. These comprehensive datasets combined with extensive analyses identified phase-specific factors like QSER1 and JADE1/2/3 and provide a detailed foundation for an in-depth understanding of mechanisms that govern the phased progression of pluripotency. The technical advances reported here can be readily applied to other models in development and disease.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:56:50.453.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Enes Ugur
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2022-06-09 15:28:43	ID requested
1	2023-02-27 06:13:57	announced
⏵ 2	2023-11-14 08:56:50	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: naive, DIA, pluripotency, mass spectrometry, stem cells, formative,Chromatin proteomics, primed

Heinrich Leonhardt
contact affiliation	Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich, 81377, Germany
contact email	h.leonhardt@lmu.de
lab head
Enes Ugur
contact affiliation	Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, LMU Munich & Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry
contact email	ugur@bio.lmu.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/2023/02/PXD034448

PRIDE project URI

• PRIDE
  1. PXD034448
     1. Label: PRIDE project
     2. Name: Comprehensive chromatin proteomics resolves functional phases of pluripotency and identifies changes in regulatory components