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PXD005579

DataSet Summary

  • HostingRepository: PRIDE
  • AnnounceDate: 2017-08-09
  • AnnouncementXML: Submission_2017-09-11_00:50:29.xml
  • DigitalObjectIdentifier: http://dx.doi.org/10.6019/PXD005579
  • ReviewLevel: Peer-reviewed dataset
  • DatasetOrigin: Original data
  • RepositorySupport: Supported dataset by repository
  • PrimarySubmitter: Petra Van Damme
  • Title: A Unique Ribosome Signature Reveals bacterium Translation Initiation Sites
  • Description: Overnight stationary cultures of wild type S. Typhimurium (Salmonella enterica serovar Thyphimurium - strain SL1344) grown in LB media at 37°C with agitation (200 rpm) were diluted at 1:200 in LB and grown until they reached and OD600 of 0.5 (i.e., logarithmic (Log) phase grown cells). Bacterial cells were collected by centrifugation (6000 × g, 5 min) at 4°C, flash frozen in liquid nitrogen and cryogenically pulverized using liquid nitrogen cooled pestle and mortar. The frozen pellet of a 50 ml culture was re-suspended and thawed in 1 ml ice-cold lysis buffer (50 mm NH4HCO3 (pH 7.9) supplemented with a complete protease inhibitor cocktail tablet (Roche Diagnostics GmbH, Mannheim, Germany) and subjected to mechanical disruption by two repetitive freeze-thaw and sonication cycles (i.e. 2 minutes of sonication on ice for 20-s bursts at output level 4 with a 40% duty cycle (Branson Sonifier 250; Ultrasonic Convertor)). The lysate was cleared by centrifugation for 15 min at 16,000 × g and the protein concentration measured using the protein assay kit (Bio-Rad) according to the manufacturer's instructions. The lysate was added Gu.HCl (4M f.c.) and subjected to N-terminal COFRADIC analysis. Free amines were blocked at the protein level making use of an N-hydroxysuccinimide ester of (stable isotopic encoded) acetate (i.e. NHS esters of 13C2D3 acetate), which allows distinguishing in vivo and in vitro blocked N-terminal peptides. The modified protein sample was digested overnight with sequencing-grade modified trypsin (1/100 (w/w trypsin /substrate)) at 37°C and subsequent steps of the N-terminal COFRADIC procedure were performed.
  • SpeciesList: scientific name: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344; NCBI TaxID: 216597;
  • ModificationList: Oxidation
  • Instrument: LTQ Orbitrap Velos

Dataset History

VersionDatetimeStatusChangeLog Entry
02016-12-16 01:27:35ID requested
12017-08-09 01:40:55announced
22017-09-11 00:50:30announcedUpdated publication reference for PubMed record(s): 28854918.

Publication List

  1. Giess A, Jonckheere V, Ndah E, Chyżyńska K, Van Damme P, Valen E, Ribosome signatures aid bacterial translation initiation site identification. BMC Biol, 15(1):76(2017) [pubmed]

Keyword List

  1. curator keyword: Biological
  2. submitter keyword: N-terminal COFRADIC, Salmonella T. str SL1344, LTQ Orbitrap Velos, Ribosome profiling

Contact List

    Petra Van Damme
    • contact affiliation: Department of Biochemistry, Ghent University, Belgium
    • contact email: petra.vandamme@ugent.be
    • lab head:
    Petra Van Damme
    • contact affiliation: University of Ghent
    • contact email: petra.vandamme@ugent.be
    • dataset submitter:

Full Dataset Link List

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  2. PRIDE project URI
Repository Record List
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