PXD009668-2

PXD009668 is an original dataset announced via ProteomeXchange.

Title	Orthogonal Organic Phase Separation protocol (2018)
Description	Identification of RNA–protein interactions currently requires a quantity and quality of sample that precludes their widespread application, especially for dynamic biological systems or precious samples. Here, we present Orthogonal Organic Phase Separation (OOPS), a new approach to enrich RNA Binding Proteins (RBPs) which is compatible with downstream proteomics and RNA sequencing. The flexibility of OOPS enables recovery of RBPs and free protein, or protein-bound RNA and free RNA, from a single sample in an unbiased manner. We have applied OOPS to both eukaryotic and previously inaccessible prokaryotic models, demonstrating its wide applicability, efficacy and consistency. We observe that the proteins identified include the majority of previously known RBPs, as well as novel groups of RBPs, including membrane proteins. Furthermore, applying OOPS to a cell-cycle arrest model, we can determine dynamic changes in RNA–protein interaction. Taken together, OOPS opens new model-independent, easy-to-implement opportunities to characterize RNA–protein interactions and their dynamic behaviour.
HostingRepository	PRIDE
AnnounceDate	2018-12-17
AnnouncementXML	Submission_2019-01-07_03:28:34.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Rayner Queiroz
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	deaminated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-05-04 01:18:07	ID requested
1	2018-12-17 05:15:32	announced
⏵ 2	2019-01-07 03:28:36	announced	Updated publication reference for PubMed record(s): 30607034.

Queiroz RML, Smith T, Villanueva E, Marti-Solano M, Monti M, Pizzinga M, Mirea DM, Ramakrishna M, Harvey RF, Dezi V, Thomas GH, Willis AE, Lilley KS, Comprehensive identification of RNA-protein interactions in any organism using orthogonal organic phase separation (OOPS). Nat Biotechnol, 37(2):169-178(2019) [pubmed]

submitter keyword: OOPS, RNA-binding, Human, E.coli, proteome, RBPome

Prof. Kathryn Lilley
contact affiliation	Biochemistry Dept, University of Cambridge, UK
contact email	ksl23@cam.ac.uk
lab head
Rayner Queiroz
contact affiliation	University of Cambridge
contact email	rq214@cam.ac.uk
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/2018/12/PXD009668

PRIDE project URI

• PRIDE
  1. PXD009668
     1. Label: PRIDE project
     2. Name: Orthogonal Organic Phase Separation protocol (2018)