PXD046765-1

PXD046765 is an original dataset announced via ProteomeXchange.

Title	Deep proteomic analysis of human microglia and model systems reveal fundamental biological differences of in vitro and ex vivo cells - in-depth human data
Description	Using high resolution quantitative mass spectrometry, we have generated the most comprehensive human and mouse microglia proteomic datasets to date, consisting of over 11,000 proteins across all six microglia groups. Microglia from different sources share a core protein signature of over 5600 proteins, yet fundamental differences are observed between species and culture conditions, indicating limitations for human disease modelling in mouse or in in vitro cultures of microglia. Mouse ex vivo microglia show important differences at the proteome level such as differential expression of inflammation and Alzheimer’s Disease associated proteins. We identify a tenfold difference in protein content of ex vivo and in vitro cells and significant proteome differences associated with protein synthesis, metabolism, microglia marker expression and environmental sensors. Culturing microglia induces rapidly increased growth, protein content and inflammatory protein expression. These changes can be restored by engrafting in vitro cells into the brain, with xenografted hESC-derived microglia closely resembling microglia from human brain. This data provides an important resource for the field and highlights important considerations needed when using model systems to study human physiology and pathology of microglia.
HostingRepository	PRIDE
AnnounceDate	2024-10-23
AnnouncementXML	Submission_2024-10-23_07:45:51.797.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Andrew Howden
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2023-11-07 22:48:59	ID requested
⏵ 1	2024-10-23 07:45:52	announced

Dataset with its publication pending

submitter keyword: proteomics, human,microglia

Dr Andy
contact affiliation	Division of Cell Signalling and Immunology, University of Dundee, Dundee, UK.
contact email	a.howden@dundee.ac.uk
lab head
Andrew Howden
contact affiliation	University of Dundee
contact email	a.howden@dundee.ac.uk
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/2024/10/PXD046765

PRIDE project URI

• PRIDE
  1. PXD046765
     1. Label: PRIDE project
     2. Name: Deep proteomic analysis of human microglia and model systems reveal fundamental biological differences of in vitro and ex vivo cells - in-depth human data