PXD078823-1

PXD078823 is an original dataset announced via ProteomeXchange.

Title	Multi omics reveals mesodermal fate bias and enables predictive cell state control in human pluripotent stem cell biomanufacturing
Description	Despite accelerating interest in using human induced pluripotent stem cell (hiPSC)–derived products for disease modeling and therapeutic development, there is substantial evidence that conventional culture approaches do not fully recapitulate natural embryonic nor lineage committed states. It remains poorly understood how in vitro environmental conditions cause divergence from natural developmental trajectories, and current strategies emphasize restricted characterization of phenotype without appreciating the complexity of biology in maintaining pluripotency and driving differentiation. To address this knowledge gap, we examined hiPSC cell state during short term culture in stirred suspension bioprocesses under varying oxygen and agitation conditions. We profiled intracellular metabolic, transcriptional, and proteomic changes to characterize cellular responses to engineered environments and implications for cell phenotype. Using a random forest framework, we modeled population dynamics over time across metabolic and transcriptional programs and mapped those predictions onto hallmark biological signatures. This integrative approach captures and identifies environmentally reinforced programs, offering a framework to guide optimization of pluripotent cell state maintenance and differentiation.
HostingRepository	PRIDE
AnnounceDate	2026-05-25
AnnouncementXML	Submission_2026-05-25_14:51:16.347.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Daniel Young
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: NEWT:10090;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2026-05-25 13:58:09	ID requested
⏵ 1	2026-05-25 14:51:16	announced

Dataset with its publication pending

submitter keyword: biomanufacturing,iPSC

Antoine Dufour
contact affiliation	Department of Biomedical Engineering, Schulich School of Engineering, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada. Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 1N4, Canada. Snyder Institute for Chronic Diseases, University of Calgary, 3330 Hospital Dr. NW, Calgary, AB, T2N 4N1, Canada.
contact email	Antoine.dufour@ucalgary.ca
lab head
Daniel Young
contact affiliation	University of Calgary
contact email	daniel.young1@ucalgary.ca
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/2026/05/PXD078823

PRIDE project URI

• PRIDE
  1. PXD078823
     1. Label: PRIDE project
     2. Name: Multi omics reveals mesodermal fate bias and enables predictive cell state control in human pluripotent stem cell biomanufacturing