PXD011071

PXD011071 is an original dataset announced via ProteomeXchange.

Title	Defining the RNA Interactome by Total RNA-Associated Protein Purification
Description	UV crosslinking can be used to identify precise RNA targets for individual proteins, transcriptome-wide. We sought to develop a technique to generate reciprocal data, identifying precise sites of RNA-binding proteome-wide. The resulting technique, total RNA-associated protein purification (TRAPP), relies on SILAC labelling to quantify RNA-associated protein recovery in the presence and absence of irradiation. We utilised TRAPP to study alterations in RNA-protein interactions upon exposure to weak acid stress in yeast. In addition, as UV irradiation induces short distance crosslinks between proteins and nucleic acids, the identity of crosslinked amino acids reveals the exact protein-RNA interacting interface. Precise sites of crosslinking at the level of individual amino acids (iTRAPP) were identified following phospho-peptide enrichment combined with a bioinformatic pipeline (Xi).
HostingRepository	PRIDE
AnnounceDate	2019-03-26
AnnouncementXML	Submission_2019-05-14_07:17:47.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Vadim Shchepachev
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	phosphorylated residue; acetylated residue
Instrument	Orbitrap Fusion Lumos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-09-12 03:47:18	ID requested
1	2019-03-26 09:37:35	announced
⏵ 2	2019-05-14 07:17:48	announced	Updated publication reference for PubMed record(s): 30962360.

Shchepachev V, Bresson S, Spanos C, Petfalski E, Fischer L, Rappsilber J, Tollervey D, Defining the RNA interactome by total RNA-associated protein purification. Mol Syst Biol, 15(4):e8689(2019) [pubmed]

curator keyword: Technical, Biological

submitter keyword: TRAPP RNA-Protein UV

David Tollervey
contact affiliation	Wellcome Centre for Cell Biology, University of Edinburgh, Scotland
contact email	david.tollervey@ed.ac.uk
lab head
Vadim Shchepachev
contact affiliation	Edinburgh University
contact email	vadimvs@yandex.ru
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/PXD011071

PRIDE project URI

• PRIDE
  1. PXD011071
     1. Label: PRIDE project
     2. Name: Defining the RNA Interactome by Total RNA-Associated Protein Purification