PXD053952-1

PXD053952 is an original dataset announced via ProteomeXchange.

Title	A multiomics framework for high-throughput lncRNA characterization uncovers major immune regulators
Description	Long noncoding RNAs (lncRNAs) play crucial roles in eukaryotic biology, yet their functions in the immune system are not fully understood. This study presents a comprehensive resource on the regulation, pathway dependencies, subcellular localizations, and protein interactomes of lncRNAs in immune cells exposed to pathogens. We developed GRADR, a methodology combining gradient profiling and RNA-bound proteome analysis, to map interactomes for all expressed RNAs in a single experiment. Using GRADR and targeted CRISPR multiomics, we identified a network of lncRNAs, including LINC01215, AC022816, and LINC01268 (ROCKI), that influence immunity, mainly through interactions with splicing factors. Our data are compiled into SMyLR, a web interface providing access to our lncRNA regulation and interactome atlas. This resource is expected to significantly advance research into RNA regulation in immunity.
HostingRepository	PRIDE
AnnounceDate	2025-10-06
AnnouncementXML	Submission_2025-10-06_12:20:44.316.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Uwe Linne
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2024-07-15 07:37:41	ID requested
⏵ 1	2025-10-06 12:20:45	announced

10.1038/s41467-025-60084-x;

Schmerer N, Janga H, Aillaud M, Hoffmann J, Aznaourova M, Wende S, Steding H, Halder LD, Uhl M, Boldt F, Stiewe T, Nist A, Jerrentrup L, Kirschbaum A, Ruppert C, Rossbach O, Ntini E, Marsico A, Valasarajan C, Backofen R, Linne U, Pullamsetti SS, Schmeck B, Schulte LN, A searchable atlas of pathogen-sensitive lncRNA networks in human macrophages. Nat Commun, 16(1):4733(2025) [pubmed]

submitter keyword: macrophage,lncRNA, AC022816, inflammation, SMyLR, lung, ROCKI, LINC01215, immunity, GRADR

Uwe Linne
contact affiliation	Philipps-University Marburg Faculty of Chemistry Mass spectrometry facility Hans-Meerwein-Str. 4 Germany
contact email	linneu@staff.uni-marburg.de
lab head
Uwe Linne
contact affiliation	Head of Core Facility Mass Spectrometry, Faculty of Chemistry, Philipps-University Marburg
contact email	linneu@staff.uni-marburg.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/2025/10/PXD053952

PRIDE project URI

• PRIDE
  1. PXD053952
     1. Label: PRIDE project
     2. Name: A multiomics framework for high-throughput lncRNA characterization uncovers major immune regulators