PXD005844

PXD005844 is an original dataset announced via ProteomeXchange.

Title	REPARATION: Ribosome Profiling Assisted (Re-) Annotation of Bacterial genomes
Description	Prokaryotic genome annotation is highly dependent on automated methods, as manual curation cannot keep up with the exponential growth of sequenced genomes. Current automated techniques depend heavily on sequence context and often underestimate the complexity of the proteome. We developed REPARATION (RibosomeE Profiling Assisted (Re-)AnnotaTION), a de novo algorithm that takes advantage of experimental evidence from ribosome profiling (Ribo-seq) to delineate translated open reading frames (ORFs) in bacteria, independent of genome annotation. Ribo-seq next generation sequencing technique that provides a genome-wide snapshot of the position translating ribosome along an mRNA at the time of the experiment. REPARATION evaluates all possible ORFs in the genome and estimates minimum thresholds to screen for spurious ORFs based on a growth curve model. We applied REPARATION to three annotated bacterial species to obtain a more comprehensive mapping of their translation landscape in support of experimental data. In all cases, we identified hundreds of novel ORFs including variants of previously annotated and novel small ORFs (<71 codons). Our predictions were supported by matching mass spectrometry (MS) proteomics data and sequence conservation analysis. REPARATION is unique in that it makes use of experimental Ribo-seq data to perform de novo ORF delineation in bacterial genomes, and thus can identify putative coding ORFs irrespective of the sequence context of the reading frame.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:35:22.203.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD005844
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Petra Van Damme
SpeciesList	scientific name: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344; NCBI TaxID: 216597;
ModificationList	Oxidation
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-02-04 02:14:23	ID requested
1	2017-08-08 23:58:42	announced
2	2017-11-08 05:01:56	announced	Updated publication reference for PubMed record(s): 28977509.
⏵ 3	2024-10-22 04:35:30	announced	2024-10-22: Updated project metadata.

10.1093/nar/gkx758;

10.6019/PXD005844;

Ndah E, Jonckheere V, Giess A, Valen E, Menschaert G, Van Damme P, REPARATION: ribosome profiling assisted (re-)annotation of bacterial genomes. Nucleic Acids Res, 45(20):e168(2017) [pubmed]

curator keyword: Biological

submitter keyword: shotgun, bacteria,Salmonella Typhimurium SL1344

Petra Van Damme
contact affiliation	VIB Midical Biotechnology Center, University of Gent, 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

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/2017/08/PXD005844

PRIDE project URI

• PRIDE
  1. PXD005844
     1. Label: PRIDE project
     2. Name: REPARATION: Ribosome Profiling Assisted (Re-) Annotation of Bacterial genomes