PXD054879

PXD054879 is an original dataset announced via ProteomeXchange.

Title	An integrated transcriptomic and proteomic map of the mouse hippocampus at synaptic resolution
Description	Understanding the brain’s molecular diversity requires spatially resolved maps of transcripts and proteins across regions and compartments. Here, we performed deep spatial molecular profiling of the mouse hippocampus, combining microdissection of 3 subregions and 4 strata with fluorescence-activated synaptosome sorting, transcriptomics, and proteomics. This approach revealed thousands of locally enriched molecules spanning diverse receptor, channel, metabolic, and adhesion families. Integration of transcriptome and proteome data highlighted proteins tightly linked to or decoupled from mRNA availability, in part due to protein half-life differences. Incorporation of translatome data identified roles for protein trafficking versus local translation in establishing compartmental organization of pyramidal neurons, with distal dendrites showing increased reliance on local protein synthesis. Classification of CA1 synapses revealed contributions from kinases, cytoskeletal elements, and adhesion molecules in defining synaptic specificity. Together, this study provides a molecular atlas of the hippocampus and its synapses (syndive.org), and offers insights into spatial transcript-protein relationships.
HostingRepository	PRIDE
AnnounceDate	2025-08-28
AnnouncementXML	Submission_2025-08-28_12:30:52.649.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Julian Langer
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-14 03:37:35	ID requested
⏵ 1	2025-08-28 12:30:53	announced

10.1038/s41467-025-63119-5;

Kaulich E, Waselenchuk Q, F, ü, rst N, Desch K, Mosbacher J, Ciirdaeva E, Juengling M, Ray R, Nassim-Assir B, Tushev G, Langer JD, Schuman EM, An integrated transcriptomic and proteomic map of the mouse hippocampus at synaptic resolution. Nat Commun, 16(1):7942(2025) [pubmed]

submitter keyword: proteomics, hippocampus, DIA, synaptosome,brain, CA1, transcriptomics

Julian Langer
contact affiliation	Max Planck Institute for Brain Research Max Planck Institute of Biophysics
contact email	julian.langer@biophys.mpg.de
lab head
Julian Langer
contact affiliation	MPIs for Biophysics and Brain Research
contact email	julian.langer@biophys.mpg.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/2025/08/PXD054879

PRIDE project URI

• PRIDE
  1. PXD054879
     1. Label: PRIDE project
     2. Name: An integrated transcriptomic and proteomic map of the mouse hippocampus at synaptic resolution