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PXD009668

PXD009668 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleOrthogonal Organic Phase Separation protocol (2018)
DescriptionIdentification 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.
HostingRepositoryPRIDE
AnnounceDate2018-12-17
AnnouncementXMLSubmission_2019-01-07_03:28:34.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterRayner Queiroz
SpeciesList scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListdeaminated residue; monohydroxylated residue; iodoacetamide derivatized residue
InstrumentOrbitrap Fusion Lumos; Q Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02018-05-04 01:18:07ID requested
12018-12-17 05:15:32announced
22019-01-07 03:28:36announcedUpdated publication reference for PubMed record(s): 30607034.
Publication List
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]
Keyword List
submitter keyword: OOPS, RNA-binding, Human, E.coli, proteome, RBPome
Contact List
Prof. Kathryn Lilley
contact affiliationBiochemistry Dept, University of Cambridge, UK
contact emailksl23@cam.ac.uk
lab head
Rayner Queiroz
contact affiliationUniversity of Cambridge
contact emailrq214@cam.ac.uk
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
Repository Record List
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