PXD070121

PXD070121 is an original dataset announced via ProteomeXchange.

Title	Design and evaluation of universal control antisense oligonucleotides across cellular models
Description	Antisense oligonucleotides (ASOs) are emerging as a promising therapeutic approach for many disorders. Currently, fourteen ASOs have been FDA/EMA-approved, with many more in preclinical development. An important requirement for preclinical studies is the inclusion of negative controls to properly assess the efficacy of candidate ASOs. As commonly used scrambled or sense ASOs may elicit unwanted off-target effects that could influence downstream data analysis, there is a need for the inclusion of additional negative control ASOs that are well-characterized and well-tolerated. In this study, we designed and evaluated generic control ASOs (cASOs) across four different human cell lines and one murine fibroblast cell line. Characterization at the RNA and protein level revealed potential ASO toxicity mechanisms and species-specific responses as well as cell-type specific effects. In total, three cASOs with a distinct GC content were identified that do not exert off-target effects across different cell lines. To conclude, we report a set of cASOs that are potentially applicable in a broad variety of experiments using ASOs with similar physicochemical properties and across different cellular models.
HostingRepository	PRIDE
AnnounceDate	2026-09-02
AnnouncementXML	Submission_2026-09-01_18:45:54.673.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	An Staes
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	iodoacetamide derivatized residue
Instrument	timsTOF Ultra

Revision	Datetime	Status	ChangeLog Entry
0	2025-10-30 16:42:21	ID requested
⏵ 1	2026-09-01 18:45:55	announced

10.1016/J.OMTN.2026.103051;

submitter keyword: Antisense oligonucleotides,oligonucleotides

Frauke Coppieters
contact affiliation	1)Department of Biomolecular Medicine, Ghent University, Ghent, Belgium 2)Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium 4)Department of Pharmaceutics, Ghent University, Ghent, Belgium
contact email	Frauke.Coppieters@UGent.be
lab head
An Staes
contact affiliation	Medical Protein Chemistry
contact email	an.staes@vib-ugent.be
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/2026/09/PXD070121

PRIDE project URI

• PRIDE
  1. PXD070121
     1. Label: PRIDE project
     2. Name: Design and evaluation of universal control antisense oligonucleotides across cellular models