Dataset Information

Multi-omic analysis of Yersinia response to temperature shift

ABSTRACT: A temporal multi-omic analysis of Y. pestis and Y. pseudotuberculosis at physiologically relevant temperatures was performed to gain insights into how an acute and highly lethal bacterial pathogen, Y. pestis, differs from its less virulent progenitor, Y. pseudotuberculosis. Associated transcriptomics data have been deposited in GEO under accession number GSE30634.

OTHER RELATED OMICS DATASETS IN: PRJNA144625

INSTRUMENT(S): LTQ Orbitrap Velos, LTQ

ORGANISM(S): Yersinia Pestis Yersinia Pseudotuberculosis

SUBMITTER: Matthew Monroe

PROVIDER: PXD000393 | Pride | 2013-10-07

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	SBEP_YPCO_009_R1_11Jan10_Andromeda_09-10-16.mgf	Mgf
	SBEP_YPCO_009_R1_11Jan10_Andromeda_09-10-16.raw	Raw
	SBEP_YPCO_009_R1_11Jan10_Andromeda_09-10-16_msgfplus.mzid	Mzid
	SBEP_YPCO_009_R2_22Jan10_Andromeda_09-10-16.mgf	Mgf
	SBEP_YPCO_009_R2_22Jan10_Andromeda_09-10-16.raw	Raw

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Publications

Comparative omics-driven genome annotation refinement: application across Yersiniae.

Schrimpe-Rutledge Alexandra C AC Jones Marcus B MB Chauhan Sadhana S Purvine Samuel O SO Sanford James A JA Monroe Matthew E ME Brewer Heather M HM Payne Samuel H SH Ansong Charles C Frank Bryan C BC Smith Richard D RD Peterson Scott N SN Motin Vladimir L VL Adkins Joshua N JN

PloS one 20120327 3

Genome sequencing continues to be a rapidly evolving technology, yet most downstream aspects of genome annotation pipelines remain relatively stable or are even being abandoned. The annotation process is now performed almost exclusively in an automated fashion to balance the large number of sequences generated. One possible way of reducing errors inherent to automated computational annotations is to apply data from omics measurements (i.e. transcriptional and proteomic) to the un-annotated genom ...[more]

PMID: 22479471

Similar Datasets

Project description:Yersinia pestis (Y. pestis) is the etiologic agent of the plague, an endemic zoonotic disease of critical clinical and historic importance. The species belongs to a genus comprising eleven members, three of which are human pathogens. Y. pestis and its closest extant relative, Yersinia pseudotuberculosis, are very similar in many respects, yet there is a distinct dichotomy between these species in terms of pathogenicity. Y. pseudotuberculosis produces a relatively benign food- or water-borne gastroenteritis with rare cases of potentially fatal bacteremia. In contrast, the characteristics of high infectivity and high mortality have made Y. pestis a pathogen of historic importance with devastating effects on the human populace over the course of three major pandemics. These qualities coupled with the emergence of multi-drug resistant variants make Y. pestis an ideal candidate for use as a bioterrorism agent. Consequentially, evolutionary biology of this organism has become a priority in the counter-terrorism research effort. The flow of genetic information within the Y. pseudotuberculosis/Y. pestis group motivated us to identify novel genes for the purpose of creating a pan-genome species DNA microarray to better understand the phylogenomic relationships among its members. Based on the sequence information be generated from the novel gene discovery project conducted at the PFGRC as well as other publicly available sources regarding Yersinia spp. genome sequences, we designed a species microarray which represents the hitherto known genetic repertoire of this taxonomic group. In order to create a species microarray that represents novel genes or genes with significant sequence variation, the ArrayOligoSelector software (http://arrayoligosel.sourceforge.net/) was used to design a 70-mer oligonucleotide for each of the annotated ORFs or partial ORFs. A detailed description of the 70-mer oligo design process and filters developed by the PFGRC can be found on the PFGRC web site at (http://pfgrc.tigr.org/presentations/seminars/oligo_design_final.pdf).