PXD023408

PXD023408 is an original dataset announced via ProteomeXchange.

Title	Global mapping of RNA-binding proteins in multi-drug resistant Staphylococcus aureus using 2C_3
Description	S. aureus strain JKD6009 RNase III-HTF and USA300 RNase III-HTF were used in our study to capture the RNA-binding proteome in Staphylococcus aureus. Both strains were inoculated in TSB (Tryptone soya broth, Oxioid CM0129) and overnight cultured in 37°C, 200 rpm shaker. Strain JKD6009 RNase III-HTF was sub-cultured into 190 ml LPM (Coombes et al., 2004) (Low phosphate, low magnesium medium, 5 mM KCl, 7.5 mM (NH4)2SO4, 0.5 mM K2SO4, 8 µM MgCl2, 1 M KH2PO4, 16 mM Tris-HCl, 0.1% casamino acids, 0.3% Glycerol) and grew from OD600 0.01 to 1. Overnight cultures of USA300 RNase III-HTF was re-inoculated to 65 ml fresh TSB to OD600 0.05 and left to grow to an OD600 of ~3. Cells were then filtered through 0.45 µm filters using a vacuum filtration device (UVO3; (McKellar et al., JoVe 2020; Van Nues et al., Nature Communications 2017)) shifted to same volume of LPM medium for 15 min at 37ºC and UV irradiated in LPM in the Vari-X-linker (λ =254 nm) (https://www.vari-x-link.com; (McKellar et al., 2020; Van Nues et al., 2017)) with an energy dose of 2J/cm2. In total, 6 replicates were collected (three technical and two biological replicates) for each experiment.
HostingRepository	PRIDE
AnnounceDate	2022-05-31
AnnouncementXML	Submission_2022-05-31_01:54:26.009.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Liangcui Chu
SpeciesList	scientific name: Staphylococcus aureus; NCBI TaxID: 1280;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-01-04 08:26:02	ID requested
⏵ 1	2022-05-31 01:54:26	announced

Chu LC, Arede P, Li W, Urdaneta EC, Ivanova I, McKellar SW, Wills JC, Fr, ö, hlich T, von Kriegsheim A, Beckmann BM, Granneman S, The RNA-bound proteome of MRSA reveals post-transcriptional roles for helix-turn-helix DNA-binding and Rossmann-fold proteins. Nat Commun, 13(1):2883(2022) [pubmed]

submitter keyword: Staphylococcus aureus, RNA-binding proteins, protein-RNA interactions, UV cross-linking, RBPome, RBDome, silica purification

Sander Granneman
contact affiliation	Medical Research Council Senior Research Fellow Associate Professor in RNA Biochemistry and Research Group Leader Centre for Synthetic and Systems Biology (SynthSys) University of Edinburgh Max Born Crescent CH Waddington Building, room 3.06 EH9 3BF Edinburgh UK
contact email	Sander.Granneman@ed.ac.uk
lab head
Liangcui Chu
contact affiliation	Edinburgh University
contact email	chuliangcui@gmail.com
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/2022/05/PXD023408

PRIDE project URI

• PRIDE
  1. PXD023408
     1. Label: PRIDE project
     2. Name: Global mapping of RNA-binding proteins in multi-drug resistant Staphylococcus aureus using 2C_3