PXD061650

PXD061650 is an original dataset announced via ProteomeXchange.

Title	Optimizing PSC culture for generating neural organoids
Description	Cerebral organoids generated according to unguided protocols produce neural tissue with exceptional cell diversity and fidelity to in vivo. However, with only minimal extrinsic intervention, the importance of high quality starting material becomes paramount. Better understanding of what constitutes a high quality stem cell line and how to maintain those properties throughout prolonged culture is therefore a crucial foundation for successful organoid differentiation. In this study, we investigate the proteome and phospho-proteome of human pluripotent stem cells to uncover the mechanisms that drive neural organoid competence. We identify aberrant cell-extracellular matrix interaction and increased oxidative metabolism as hallmarks of poor neural differentiators. Drawing on the proteomic data and published literature, we optimise culturing conditions by using improved coating matrix, sustained supply of the key growth factor FGF2 and reducing oxidative stress. These adjustments improve brain organoid generation across all tested cell lines, though with varying degrees of efficiency. This work highlights the importance of optimal culture conditions to best support stem cells, ultimately enhancing the quality of brain organoids produced.
HostingRepository	PRIDE
AnnounceDate	2025-10-27
AnnouncementXML	Submission_2025-10-27_04:44:43.209.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Pia Jensen
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	phosphorylated residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2025-03-10 07:19:00	ID requested
⏵ 1	2025-10-27 04:44:43	announced

Dataset with its publication pending

submitter keyword: LC-MSMS, proteomics, phospho,Pluripotent stem cells

Martin Røssel Larsen
contact affiliation	Department of biochemistry and molecular biology, BioMS section, University of Southern Denmark
contact email	mrl@bmb.sdu.dk
lab head
Pia Jensen
contact affiliation	University of Southern Denmark
contact email	pjensen@bmb.sdu.dk
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/2025/10/PXD061650

PRIDE project URI

• PRIDE
  1. PXD061650
     1. Label: PRIDE project
     2. Name: Optimizing PSC culture for generating neural organoids