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PXD009571

PXD009571 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitlePurification of Cross-linked RNA-Protein Complexes by Phenol-Toluol Extraction
DescriptionRecent 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.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_04:53:06.859.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterCarlos 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;
ModificationListiodoacetamide derivatized residue
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02018-04-23 02:12:46ID requested
12019-03-12 08:54:29announced
22024-10-22 04:53:14announced2024-10-22: Updated project metadata.
Publication List
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;
Keyword List
curator keyword: Technical
submitter keyword: Human, LC-MSMS, shotgun, Salmonella, RNA-binding proteins, PTex
Contact List
Matthias Selbach
contact affiliationMax-Delbrueck-Centre for Molecular Medicine (MDC), Berlin, Germany.
contact emailmatthias.selbach@mdc-berlin.de
lab head
Carlos Henrique Vieira e Vieira
contact affiliationMax-Delbrück-Centrum für Molekulare Medizin in der Helmholtz-Gemeinschaft
contact emailcarlos.vieira@mdc-berlin.de
dataset submitter
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Dataset FTP location
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