PXD009571

PXD009571 is an original dataset announced via ProteomeXchange.

Title	Purification of Cross-linked RNA-Protein Complexes by Phenol-Toluol Extraction
Description	Recent methodological advances allowed the identification of an increasing number of RNAbinding proteins (RBPs) and their RNA-binding sites. RNA interactome capture is, however, limited to proteins interacting with polyadenylated RNAs while RBPs associating with nonadenylate RNA classes cannot be purified. Moreover, the vast majority of species that lack poly-A tails in their mRNAs (including all archea and bacteria) are not amenable to RNA interactome capture studies. To overcome these limitations, we have developed a novel protocol, Phenol Toluol extraction (PTex), that does not rely on a specific RNA sequence or motif for isolation of cross-linked ribonucleoproteins (RNPs), but rather purifies them based entirely on their physicochemical properties. PTex captures RBPs that bind to poly-A RNA, but also proteins associating with non-adenylate RNA species (rRNA, tRNA) as short as 30nt. PTex can be used to simplify complex work ows such as PAR-CLIP and reliably recovers RBPs from tissues and bacteria thus significantly expanding the experimental toolbox to species that could previously not be assessed experimentally.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:53:06.859.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Carlos Henrique Vieira e Vieira
SpeciesList	scientific name: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344; NCBI TaxID: 216597; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-04-23 02:12:46	ID requested
1	2019-03-12 08:54:29	announced
⏵ 2	2024-10-22 04:53:14	announced	2024-10-22: Updated project metadata.

Urdaneta EC, Vieira-Vieira CH, Hick T, Wessels HH, Figini D, Moschall R, Medenbach J, Ohler U, Granneman S, Selbach M, Beckmann BM, Purification of cross-linked RNA-protein complexes by phenol-toluol extraction. Nat Commun, 10(1):990(2019) [pubmed]

10.1038/s41467-019-08942-3;

curator keyword: Technical

submitter keyword: Human, LC-MSMS, shotgun, Salmonella, RNA-binding proteins, PTex

Matthias Selbach
contact affiliation	Max-Delbrueck-Centre for Molecular Medicine (MDC), Berlin, Germany.
contact email	matthias.selbach@mdc-berlin.de
lab head
Carlos Henrique Vieira e Vieira
contact affiliation	Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtz-Gemeinschaft
contact email	carlos.vieira@mdc-berlin.de
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/2019/03/PXD009571

PRIDE project URI

• PRIDE
  1. PXD009571
     1. Label: PRIDE project
     2. Name: Purification of Cross-linked RNA-Protein Complexes by Phenol-Toluol Extraction