PXD073954-1

PXD073954 is an original dataset announced via ProteomeXchange.

Title	Simultaneous profiling of native-state proteomes and transcriptomes of brain cell types using proximity labeling
Description	Deep molecular phenotyping of cells at transcriptomic and proteomic levels is an essential first step to understanding cellular contributions to development, aging, injury, and disease. Since proteome and transcriptome level abundances only modestly correlate with each other, complementary profiling of both levels of abundances are needed. We report a novel method to capture the cell type-specific transcriptome and proteome simultaneously from both in vitro and in vivo experimental model systems. This method leverages the ability of biotin ligase, TurboID, to biotinylate cytosolic proteins including ribosomal and RNA-binding proteins, which allows enrichment of biotinylated proteins for proteomics as well as protein-associated mRNA for transcriptomics. We validated this approach first using well-controlled in vitro systems to verify that the proteomes and transcriptomes obtained reflect the ground truth, bulk proteomes and transcriptomes. We also show that the effect of a biological stimuli (e.g., neuroinflammatory activation by LPS) can be faithfully captured. We also applied this approach to obtain native-state proteomes and transcriptomes from two key brain cell types (Aldh1l1-expressing astrocytes and Camk2a-expressing neurons), thereby validating the in vivo application of this approach. We also used these data to interrogate protein mRNA concordance and discordance across two brain cell types, providing insights into shared and unique molecular processes such as cytoskeletal and mitochondrial-related functions.
HostingRepository	PRIDE
AnnounceDate	2026-02-16
AnnouncementXML	Submission_2026-02-16_11:29:39.610.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christina Ramelow
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; scientific name: Mus musculus (Mouse); NCBI TaxID: NEWT:10090;
ModificationList	deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2026-02-02 18:22:52	ID requested
⏵ 1	2026-02-16 11:29:40	announced

Dataset with its publication pending

submitter keyword: Proximity labeling

transcriptomics

proteomics

microglia

astrocytes

neurons

mRNA-protein concordance

Srikant Rangaraju
contact affiliation	Associate Professor, Department of Neurology, Yale University School of Medicine
contact email	srikant.rangaraju@yale.edu
lab head
Christina Ramelow
contact affiliation	Emory University
contact email	christinaramelow12@gmail.com
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/2026/02/PXD073954

PRIDE project URI

• PRIDE
  1. PXD073954
     1. Label: PRIDE project
     2. Name: Simultaneous profiling of native-state proteomes and transcriptomes of brain cell types using proximity labeling