PXD028272

PXD028272 is an original dataset announced via ProteomeXchange.

Title	Isolation and identification of extracellular matrix proteins from oil-based CASPERized mouse brains for matrisomal analysis
Description	The extracellular matrix (ECM) components present within all tissues and organs help to maintain the cytoskeletal architecture and tissue morphology. Although the ECM plays a role in cellular events and signaling pathways, it has not been well studied due its insolubility and complexity. Brain tissue has a higher cell density and weaker mechanical strength than other tissues in the human body. When removing cells using a general decellularization method to produce scaffolds and obtain ECM proteins, various problems must be considered because tissues are easily damaged. To retain the brain shape and ECM components, we performed decellularization in combination with polymerization. We immersed mouse brains in oil for polymerization and decellularization via O-CASPER (Oil-Based Clinically and Experimentally Applicable Acellular Tissue Scaffold Production for Tissue Engineering and Regenerative Medicine) and then isolated ECM components using sequential matrisome preparation reagents (SMPRs), namely, RIPA, PNGase F, and concanavalin A. Adult mouse brains were preserved with our decellularization method. Western blot and LC-MS/MS analyses revealed that ECM components, including collagen and laminin, were isolated more efficiently from decellularized adult mouse brains than from embryonic and neonatal mouse brains using SMPRs. Our method will be useful to obtain matrisomal data and perform functional studies using adult mouse brains and other tissues.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:45:56.178.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD028272
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Byung-gyu kim
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-09-09 08:09:24	ID requested
1	2023-05-10 09:07:40	announced
⏵ 2	2023-11-14 08:45:56	announced	2023-11-14: Updated project metadata.

10.6019/PXD028272;

Ha BG, Jang YJ, Lee E, Kim BG, Myung K, Sun W, Jeong SJ, Isolation and identification of extracellular matrix proteins from oil-based CASPERized mouse brains for matrisomal analysis. Heliyon, 9(4):e14777(2023) [pubmed]

submitter keyword: ECM,Brain, O-CASPER, profiling, decellularization

Sung-Jin Jeong
contact affiliation	Research Group of Developmental Disorders and Rare Diseases, Korea Brain Research Institute (KBRI), Daegu 41062, Republic of Korea
contact email	sjjeong@kbri.re.kr
lab head
Byung-gyu kim
contact affiliation	Center for genomic integrity (CGI), Institute of basic science (IBS), UNIST, Ulsan, 44919, Republic of Korea
contact email	goldenlion@ibs.re.kr
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/2023/05/PXD028272

PRIDE project URI

• PRIDE
  1. PXD028272
     1. Label: PRIDE project
     2. Name: Isolation and identification of extracellular matrix proteins from oil-based CASPERized mouse brains for matrisomal analysis