PXD053515-2

PXD053515 is an original dataset announced via ProteomeXchange.

Title	FANS unfixed: isolation and proteomic analysis of mouse cell type-specific brain nuclei
Description	Epigenetic-mediated gene regulation orchestrates brain cell-type gene expression programmes, and epigenetic dysregulation is a major driver of aging and disease-associated changes. Proteins that mediate gene regulation are mostly localised to the nucleus, however, nuclear-localised proteins are often under-represented in gene expression studies and have been understudied in the context of the brain. To address this challenge, we have optimised an approach for nuclei isolation that is compatible with proteomic analysis. This was coupled to a mass spectrometry protocol for detecting proteins in low-concentration samples. We have generated nuclear proteomes for neurons, microglia, and oligodendrocytes from the mouse brain cortex and identified cell-type nuclear proteins associated with chromatin structure and organisation, chromatin modifiers such as transcription factors, and RNA-binding proteins, among others. Our nuclear proteomics platform paves the way for assessing brain cell type changes in the nuclear proteome across health and disease, such as neurodevelopmental, aging, neurodegenerative, and neuroinflammatory conditions.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:53:43.619.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Harry Whitwell
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monomethylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Synapt MS

Revision	Datetime	Status	ChangeLog Entry
0	2024-06-29 16:24:56	ID requested
1	2024-08-09 04:11:41	announced
⏵ 2	2024-10-22 06:53:49	announced	2024-10-22: Updated project metadata.

10.1021/acs.jproteome.4c00161;

Bedwell L, Mavrotas M, Demchenko N, Yaa RM, Willis B, Demianova Z, Syed N, Whitwell HJ, Nott A, FANS Unfixed: Isolation and Proteomic Analysis of Mouse Cell Type-Specific Brain Nuclei. J Proteome Res, 23(9):3847-3857(2024) [pubmed]

submitter keyword: cell-type specific, proteomics, neurons, FANS, microglia,epigenetics, oligodendrocytes

Harry Whitwell
contact affiliation	Division of Systems Medicine, Imperial College London
contact email	h.whitwell@imperial.ac.uk
lab head
Harry Whitwell
contact affiliation	Imperial College London
contact email	h.whitwell@imperial.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/2024/08/PXD053515

PRIDE project URI

• PRIDE
  1. PXD053515
     1. Label: PRIDE project
     2. Name: FANS unfixed: isolation and proteomic analysis of mouse cell type-specific brain nuclei