PXD002014

PXD002014 is an original dataset announced via ProteomeXchange.

Title	Integrated molecular phenotyping in chondrocytes identifies genes and pathways disrupted in osteoarthritis
Description	Osteoarthritis (OA) is a degenerative joint disease with a substantial health economic burden. There is no current treatment; instead, disease management targets the main symptoms (pain and stiffness) and culminates in joint replacement surgery. OA is a disease of cartilage degeneration, but the molecular changes leading to the development of OA are still poorly understood. In this study we compare methylation, gene transcription and protein abundance at the genome-wide level in individually-matched samples of chondrocytes extracted from affected and relatively healthy articular cartilage across 12 OA patients undergoing total knee replacement. Integration analysis highlights genes that are consistently affected at multiple levels, including AQP1, CLEC3B and COL1A1, and also relevant biological pathways such as extracellular matrix organization, collagen catabolism and proteolysis. Collectively these results provide a first view of the comprehensive molecular landscape underpinning OA development and point to potential therapeutic avenues.
HostingRepository	PRIDE
AnnounceDate	2018-10-24
AnnouncementXML	Submission_2018-10-24_07:53:31.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	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos; Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2015-04-02 08:19:15	ID requested
⏵ 1	2018-10-24 07:53:33	announced

Steinberg J, Ritchie GRS, Roumeliotis TI, Jayasuriya RL, Clark MJ, Brooks RA, Binch ALA, Shah KM, Coyle R, Pardo M, Le Maitre CL, Ramos YFM, Nelissen RGHH, Meulenbelt I, McCaskie AW, Choudhary JS, Wilkinson JM, Zeggini E, Integrative epigenomics, transcriptomics and proteomics of patient chondrocytes reveal genes and pathways involved in osteoarthritis. Sci Rep, 7(1):8935(2017) [pubmed]

curator keyword: Biomedical

submitter keyword: Human, Chondrocytes, TMT, Osteoarthritis, Label Free

Jyoti Choudhary
contact affiliation	Wellcome Trust Sanger Institute
contact email	jc4@sanger.ac.uk
lab head
James Wright
contact affiliation	Proteomic Mass Spectrometry
contact email	jw13@sanger.ac.uk
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/2018/10/PXD002014

PRIDE project URI

• PRIDE
  1. PXD002014
     1. Label: PRIDE project
     2. Name: Integrated molecular phenotyping in chondrocytes identifies genes and pathways disrupted in osteoarthritis