PXD000883-1

PXD000883 is an original dataset announced via ProteomeXchange.

Title	RBDmap
Description	The RNA interactomes of HeLa and HEK293 cells jointly comprise 1106 RNA-binding proteins (RBPs), with almost half of these lacking well-defined RNA-binding domains (RBDs), suggesting the existence of numerous unknown RNA-binding architectures. Here, we report on “RBDmap”, a new method built on interactome capture, to comprehensively identify the RBDs of native RBPs in HeLa cells. Making use of in vivo UV-crosslinking of RBPs to polyadenylated RNAs, capture on oligo(dT) magnetic beads, sequential proteolytic digestion and LC-MS/MS combined with a sophisticated scoring algorithm, RBDmap “re-discoveres” many known RNA-binding sites (e.g. RRM, KH) of numerous well characterized RBPs and suggests novel RBDs.
HostingRepository	PRIDE
AnnounceDate	2016-08-09
AnnouncementXML	Submission_2016-08-09_07:12:10.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christian Frese
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2014-04-09 00:47:40	ID requested
⏵ 1	2016-08-09 07:12:11	announced
2	2016-08-11 00:32:07	announced	Updated project metadata.
3	2024-10-22 04:31:12	announced	2024-10-22: Updated project metadata.

Castello A, Fischer B, Frese CK, Horos R, Alleaume AM, Foehr S, Curk T, Krijgsveld J, Hentze MW, Comprehensive Identification of RNA-Binding Domains in Human Cells. Mol Cell, 63(4):696-710(2016) [pubmed]

submitter keyword: RNA-binding proteins, RNA binding domain

Jeroen Krijgsveld
contact affiliation	European Molecular Biology Laboratory, Genome Biology Unit Meyerhofstr. 1 69117 Heidelberg Germany
contact email	krijgsveld@embl.de
lab head
Christian Frese
contact affiliation	EMBL
contact email	frese@embl.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/2016/08/PXD000883

PRIDE project URI

• PRIDE
  1. PXD000883
     1. Label: PRIDE project
     2. Name: RBDmap