PXD022335

PXD022335 is an original dataset announced via ProteomeXchange.

Title	Cell-type and subcellular compartment-specific APEX2 proximity labeling reveals activity-dependent nuclear proteome dynamics in the striatum
Description	The vertebrate brain consists of diverse neuronal types, classified by distinct anatomy and function, along with divergent transcriptomes and proteomes. Defining the cell-type specific neuroproteome is important for understanding the development and functional organization of neural circuits. This task remains challenging in complex tissue, due to suboptimal protein isolation techniques that often result in loss of cell-type specific information and incomplete capture of subcellular compartments. Here, we develop a genetically targeted proximity labeling approach to identify cell-type specific subcellular proteome in the mouse brain, confirmed by imaging, electron microscopy, and mass spectrometry. We express subcellular-localized APEX2 to map the proteome of direct and indirect pathway spiny projection neurons in the striatum. The workflow provides sufficient depth to uncover changes in the proteome of striatal neurons following activation of Gαq-coupled signaling cascades. This method enables flexible, cell-type specific quantitative profiling of subcellular proteome snapshots in the mouse brain.
HostingRepository	PRIDE
AnnounceDate	2021-07-10
AnnouncementXML	Submission_2021-08-26_06:12:49.394.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Vasin Dumrongprechachan
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; biotinylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2020-11-04 01:38:34	ID requested
1	2021-07-10 07:07:57	announced
⏵ 2	2021-08-26 06:12:50	announced	2021-08-26: Updated publication reference for PubMed record(s): 34381044.

Dumrongprechachan V, Salisbury RB, Soto G, Kumar M, MacDonald ML, Kozorovitskiy Y, Cell-type and subcellular compartment-specific APEX2 proximity labeling reveals activity-dependent nuclear proteome dynamics in the striatum. Nat Commun, 12(1):4855(2021) [pubmed]

submitter keyword: APEX2, proximity labeling, neurproteomics, striatum

Yevgenia Kozorovitskiy
contact affiliation	Department of Neurobiology, Northwestern University.
contact email	yevgenia.kozorovitskiy@northwestern.edu
lab head
Vasin Dumrongprechachan
contact affiliation	Northwestern University
contact email	vasindumrongprechachan2015@u.northwestern.edu
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/2021/07/PXD022335

PRIDE project URI

• PRIDE
  1. PXD022335
     1. Label: PRIDE project
     2. Name: Cell-type and subcellular compartment-specific APEX2 proximity labeling reveals activity-dependent nuclear proteome dynamics in the striatum