PXD028272 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 | 2023-05-10 |
AnnouncementXML | Submission_2023-05-10_09:07:39.189.xml |
DigitalObjectIdentifier | https://dx.doi.org/10.6019/PXD028272 |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Supported dataset by repository |
PrimarySubmitter | Byung-gyukim |
SpeciesList | scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; |
ModificationList | No PTMs are included in the dataset |
Instrument | Orbitrap Fusion Lumos |
Dataset History
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. |
Publication List
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] |
Keyword List
submitter keyword: ECM,Brain, O-CASPER, profiling, decellularization |
Contact List
Sung-JinJeong |
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-gyukim |
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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD028272
- Label: PRIDE project
- Name: Isolation and identification of extracellular matrix proteins from oil-based CASPERized mouse brains for matrisomal analysis