PXD020577-1

PXD020577 is an original dataset announced via ProteomeXchange.

Title	Shewanella oneidensis outer membrane and outer membrane vesicles
Description	This project compares the outer membrane proteome to the proteome of outer membrane vesicles of the bacterium Shewanella onedensis. S. oneidensis outer membrane was purified via the sarkosyl method described in (Brown, 2010). A 50 mL overnight culture of cells were harvested by centrifugation at 10,000× g for 10 min. cell pellet suspended in 20 mL of 20 mM ice-cold sodium phosphate (pH 7.5) and passed four times through a French Press (12000 lb/in2). The lysate was centrifuged at 5,000× g for 30 min to remove unbroken cells. The remaining supernatant was centrifuged at 45,000 × g for 1 h to pellet membranes. Crude membranes were suspended in 20 mL 0.5% Sarkosyl in 20 mM sodium phosphate and shaken horizontally at 200 rpm for 30 min at room temperature. The crude membrane sample was centrifuged at 45,000 × g for 1 h to pellet the OM. The pellet of OM was washed in ice-cold sodium phosphate and recentrifuged. The cells were pelleted by centrifugation at 5000 x g for 20 min at 4°C, and the supernatant was filtered through 0.45 μm pore size filters to remove remaining bacterial cells. Vesicles were obtained by centrifugation at 38,400 x g for 1 h at 4°C in an Avanti J-20XP centrifuge (Beckman Coulter, Inc). Pelleted vesicles were resuspended in 25 ml of 50 mM HEPES (pH 6.8) and filtered through 0.45 μm pore size filters. Vesicles were again pelleted as described above and finally resuspended in 50 mM HEPES, pH 6.8. Extracellular DNA, flagella, and pili can all be co-purified. Protocol was adapted from (Perez-Cruz, 2013).
HostingRepository	PRIDE
AnnounceDate	2021-11-10
AnnouncementXML	Submission_2021-11-10_15:48:29.942.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Lori Zacharoff
SpeciesList	scientific name: Shewanella oneidensis MR-1; NCBI TaxID: 211586;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-07-26 23:40:24	ID requested
⏵ 1	2021-11-10 15:48:30	announced
2	2024-10-22 05:30:16	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: Shewanella oneidensis, bacterial outer membrane vesicles, BdpA, multiheme cytochromes

Mohamed El-Naggar
contact affiliation	University of Southern California
contact email	mnaggar@usc.edu
lab head
Lori Zacharoff
contact affiliation	University of Southern California
contact email	zacharof@usc.edu
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/2021/11/PXD020577

PRIDE project URI

• PRIDE
  1. PXD020577
     1. Label: PRIDE project
     2. Name: Shewanella oneidensis outer membrane and outer membrane vesicles