PXD010046

PXD010046 is an original dataset announced via ProteomeXchange.

Title	Formaldehyde-crosslinking enables comprehensive profiling of in vivo RNA-interactome in UV-impermeable samples
Description	Development of UV-crosslinking based RNA-interactome capture protocol have expanded the repertoire of RBPs. Apparent limitations of UV-crosslinking, however, have made the RBP profiling to be incomplete and inapplicable to many of the biological samples in physiological contexts. Here we developed formaldehyde-crosslinking based RNA binding protein profiling (FAX-RBP) method and quantitatively compared to UV-crosslinking based RBP profiling (UVX-RBP) in HeLa and Xenopus laevis oocyte/embryo. Quantitative comparison of FAX-RBP with UVX-RBP in HeLa cell demonstrated that FAX-RBP has greatly enhanced efficiency for profiling hundreds of RBPs in vivo. FAX-RBP was then applied to X. laevis oocyte and stage 8 embryo and profiled the dynamics of mRNP complex for over 500 RBPs. FAX-RBP thus provide the most comprehensive and unbiased RBP profile in vivo, demonstrating its potential to expand mRNP profiling into numerous physiological contexts.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:15:39.749.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yongwoo Na
SpeciesList	scientific name: Xenopus laevis (African clawed frog); NCBI TaxID: 8355; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2018-06-06 07:18:21	ID requested
1	2020-11-24 23:05:44	announced
⏵ 2	2024-10-22 05:15:40	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

curator keyword: Technical, Biological

submitter keyword: RBP formaldehyde

Jong-Seo Kim
contact affiliation	Center for RNA Research, Institute for Basic Science, Seoul National University
contact email	jongseokim@snu.ac.kr
lab head
Yongwoo Na
contact affiliation	Seoul National University
contact email	nyw1412@gmail.com
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/2020/11/PXD010046

PRIDE project URI

• PRIDE
  1. PXD010046
     1. Label: PRIDE project
     2. Name: Formaldehyde-crosslinking enables comprehensive profiling of in vivo RNA-interactome in UV-impermeable samples