Transcriptomics

Dataset Information

2

Identification of new genomic areas within the genomes of Yersinia pestis and Yersinia pseudotuberculosis strains through targeted genome sequencing


ABSTRACT: 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). One hundred fifty six query strains were investigated in this study, with each query strain hybridized against the reference strain, CO92. Each strain has a single dye experiment. Each oligo is spotted on the Y. pestis species microarray once. Positive controls on the array consist of oligos designed from the sequenced reference genome, CO92, and negative controls on the array consist of oligos designed from the thale cress plant, Arabidopsis thaliana.The microarrays also had Agilent internal controls.

SUBMITTER: Qiang Sun   Mikeljon Nikolich  Timothy Minogue  Shaohua Jin  Scott N Peterson  Leka Papazisi  Dana M Cash  Sarah Akkoush  Luther Lindler  Robert D Fleischmann  Chunhua Wan  Eric Wester  A’Drian Pineda  Shashikala Ratnayake  Fatma Onmus  Xiaozhe Huang  Lakshmi M Appalla  Erik Snesrud 

PROVIDER: E-GEOD-23797 | ArrayExpress | 2010-09-02

SECONDARY ACCESSION(S): GSE23797PRJNA130705

REPOSITORIES: GEO, ArrayExpress

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