PXD042545-2

PXD042545 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	SNORA33 Knockdown in chondrocytes
Description	Background: In the experiment where we exposed chondrocytes of 4 healthy donors to OA-SF for 14 days we found several 2’O-methylation and pseudouridylation sites to be differentially modified in OA-SF condition compared to control (regular medium condition). We linked these PTMs to box C/D and H/ACA snoRNAs and selected 7 sites for validation. We did a CRISR/Cas9 mediated knock-down (KD) (not a complete knock-out (KO), as we didn’t pick clones) of these seven selected snoRNAs. Out of these seven snoRNAs, snoRNA33 knock-down stood out as the pseudouridylation at the corresposing site basically disappeared. We also saw differences in translation initiation and fidelity in snoRNA33 depleted cells. Therefore we decided to explore whether the ribosome composition (core and associated ribosomal proteins) is different in cells lacking snoRNA33 = RiboProteome samples (RP) and whether the proteome of these cells is different = Proteome samples (P). In both cases we used a GFP targeting CRISPR/Cas9 cell line as a control.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:10:34.485.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD042545
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Mandy Peffers
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2023-05-30 09:33:51	ID requested
1	2023-10-24 13:04:32	announced
⏵ 2	2023-11-14 09:10:42	announced	2023-11-14: Updated project metadata.
3	2024-10-22 06:10:19	announced	2024-10-22: Updated project metadata.

Publication List

Chabronova A, van den Akker G, Housmans BAC, Caron MMJ, Cremers A, Surtel DAM, Peffers MJ, van Rhijn LW, Marchand V, Motorin Y, Welting TJM, of 28S-U4966 and Affects the Ribosome Translational Apparatus. Int J Mol Sci, 24(16):(2023) [pubmed]
10.6019/PXD042545;

Chabronova A, van den Akker G, Housmans BAC, Caron MMJ, Cremers A, Surtel DAM, Peffers MJ, van Rhijn LW, Marchand V, Motorin Y, Welting TJM, of 28S-U4966 and Affects the Ribosome Translational Apparatus. Int J Mol Sci, 24(16):(2023) [pubmed]

10.6019/PXD042545;

Keyword List

submitter keyword: Human, SNORA33, ribosome

submitter keyword: Human, SNORA33, ribosome

Contact List

Mandy Jayne Peffers
contact affiliation	University of Liverpool
contact email	peffs@liv.ac.uk
lab head
Mandy Peffers
contact affiliation	University of Liverpool
contact email	peffs@liv.ac.uk
dataset submitter

Full Dataset Link List

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/2023/10/PXD042545
PRIDE project URI

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/2023/10/PXD042545

PRIDE project URI

Repository Record List

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