PXD040652-2

PXD040652 is an original dataset announced via ProteomeXchange.

Title	Proteomic Analysis of Neural Stem Cell to Oligodendrocyte Precursor Cell Differentiation Reveals Phosphorylation-Dependent Dclk1 Processing
Description	The differentiation from neural stem cells (NSCs) to oligodendrocyte precursor cells (OPCs) is only incompletely understood. In the current study, we used the so-called neurosphere assay to study this process. We performed in vitro differentiation from neurospheres (which predominantly consist of NSCs) to oligospheres (consisting mainly of OPCs) and investigated their proteome by 6plex TMT-labeling and their phosphoproteome by 3plex dimethyl labeling. Among others, we identified a continuous upregulation of double cortin like kinase 1 (Dclk1) as well as its phosphorylation sites in the so-called SP-rich region. Using western blotting and qPCR, we show that two different Dclk1 isoforms (long and short) are present in NSCs and OPCs which gradually interchange during the investigated differentiation process. We further demonstrate that Dclk1 long is proteolytically processed into Dclk1 short and that this process is regulated via phosphorylation in the SP-rich region. Finally, we generated different BioID constructs fused to individual Dclk1 domains and investigate their interactome as well as potential substrates of Dclk1.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_07:06:26.037.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Robert Hardt
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; S-carboxamidoethyl-L-cysteine; biotinylated residue; phosphorylated residue; monohydroxylated residue
Instrument	Orbitrap Fusion Lumos; LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2023-03-07 03:32:53	ID requested
1	2023-08-18 15:52:57	announced
⏵ 2	2023-11-14 07:06:26	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: Phosphoproteomics, neural stem cells, dimethyl, TMT, Dclk1, neural development, proximity biotinylation, oligodendrocyte precursor cells, SILAC, differentiation,Isobaric labeling, PurA

Dominic Winter
contact affiliation	Institute for Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn
contact email	dominic.winter@uni-bonn.de
lab head
Robert Hardt
contact affiliation	Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, 53115 Bonn, Germany
contact email	rhardt@uni-bonn.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/2023/08/PXD040652

PRIDE project URI

• PRIDE
  1. PXD040652
     1. Label: PRIDE project
     2. Name: Proteomic Analysis of Neural Stem Cell to Oligodendrocyte Precursor Cell Differentiation Reveals Phosphorylation-Dependent Dclk1 Processing