PXD006673

PXD006673 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Hip Osteoarthritis Functional Genomics
Description	The aim of this work is to apply an integrated systems approach to understand the biological underpinnings of hip osteoarthritis that culminates in the need for total joint replacement (TJR). This study is a feasibility pilot that integrates functional genomics data from diseased and non-diseased tissues of OA patients who have undergone TJR. For each tissue, we characterised epigenetic marks (methylation), gene transcription (RNASeq) and expression (quantitative proteomics). We also generated genotype data on the HumanCoreExome array for each individual. This data is part of a pre-publication release.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:37:58.454.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	James Wright
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	Orbitrap Fusion

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2017-06-08 01:16:29	ID requested
1	2018-05-14 03:53:48	announced
⏵ 2	2024-10-22 04:38:06	announced	2024-10-22: Updated project metadata.

Publication List

10.1093/rheumatology/key101;
Steinberg J, Brooks RA, Southam L, Bhatnagar S, Roumeliotis TI, Hatzikotoulas K, Zengini E, Wilkinson JM, Choudhary JS, McCaskie AW, Zeggini E, Widespread epigenomic, transcriptomic and proteomic differences between hip osteophytic and articular chondrocytes in osteoarthritis. Rheumatology (Oxford), 57(8):1481-1489(2018) [pubmed]

10.1093/rheumatology/key101;

Steinberg J, Brooks RA, Southam L, Bhatnagar S, Roumeliotis TI, Hatzikotoulas K, Zengini E, Wilkinson JM, Choudhary JS, McCaskie AW, Zeggini E, Widespread epigenomic, transcriptomic and proteomic differences between hip osteophytic and articular chondrocytes in osteoarthritis. Rheumatology (Oxford), 57(8):1481-1489(2018) [pubmed]

Keyword List

curator keyword: Biomedical
submitter keyword: Hip, Human, Proteogenomics,Osteoarthritis, LC-MS/MS

curator keyword: Biomedical

submitter keyword: Hip, Human, Proteogenomics,Osteoarthritis, LC-MS/MS

Contact List

Jyoti Choudhary
contact affiliation	Wellcome Trust Sanger Institute
contact email	jc4@sanger.ac.uk
lab head
James Wright
contact affiliation	Functional Proteomics, Institute Cancer Research & Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute
contact email	jw13@sanger.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/2018/05/PXD006673
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/2018/05/PXD006673

PRIDE project URI

Repository Record List

[ + ]