PXD047423

PXD047423 is an original dataset announced via ProteomeXchange.

Title	Trans-omic Profiling Uncovers Molecular Controls of the Early Human Cerebral Organoid Formation
Description	Defining molecular controls that orchestrate human brain development is essential for uncovering the complexity behind neurodevelopment and the pathogenesis of neurological disorders. Due to the difficulties in accessing embryonic and fetal brain tissues, the differentiation of human pluripotent stem cell (hPSC)-derived three-dimensional neural organoids has made it possible to recapitulate this developmental process in vitro and provide a unique opportunity to investigate human brain development and disease. To elucidate the molecular programs that drive this highly dynamic process, here, we generate a comprehensive trans-omic map of the phosphoproteome, proteome, and transcriptome of the initial stages of pluripotency and neural differentiation towards the formation of cerebral organoids. Our integrative analysis uncovers key phospho-signalling events underlying neural lineage differentiation, and their convergence on transcriptional (co-)factors and chromatin remodellers that govern downstream gene regulatory networks (GRNs). Comparative analysis with developing human and mouse embryos using these GRNs demonstrates the fidelity of our early cerebral organoids in modelling embryonic brain development. Finally, we demonstrate biochemical modulation of the AKT signalling as a key molecular switch for controlling human cerebral organoid formation. Our data provides a comprehensive resource to gain insight into the molecular controls in human embryonic brain development and also provide a guide for future development of protocols for human cerebral organoid differentiation.
HostingRepository	PRIDE
AnnounceDate	2024-04-23
AnnouncementXML	Submission_2024-04-22_20:20:00.964.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD047423
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Mark Graham
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2023-11-30 16:42:21	ID requested
⏵ 1	2024-04-22 20:20:01	announced

10.6019/PXD047423;

submitter keyword: organoids, neurodevelopment,proteomics, TMT, homo sapiens, differentiation, phosphoproteomics, quantitative proteomics, biological, LC-MS/MS

Pengyi Yang
contact affiliation	Children's Medical Research Insitute, The University of Sydney
contact email	yangpy7@gmail.com
lab head
Mark Graham
contact affiliation	Children's Medical Research Institute
contact email	mgraham@cmri.org.au
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/2024/04/PXD047423

PRIDE project URI

• PRIDE
  1. PXD047423
     1. Label: PRIDE project
     2. Name: Trans-omic Profiling Uncovers Molecular Controls of the Early Human Cerebral Organoid Formation