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Series GSE25601 Query DataSets for GSE25601
Status Public on Dec 07, 2010
Title Novel gene discovery in up to 10 ETEC strains and production of species microarray. Discovery of conserved and unique ETEC genes by comparative genome hybridization studies.
Organism Escherichia coli
Experiment type Genome variation profiling by array
Summary PFGRC has developed a cost effective alternative to complete genome sequencing in order to study the genetic differences between closely related species and/or strains. The comparative genomics approach combines Gene Discovery (GD) and Comparative Genomic Hybridization (CGH) techniques, resulting in the design and production of species microarrays that represent the diversity of a species beyond just the sequenced reference strain(s) used in the initial microarray design. These species arrays may then be used to interrogate hundreds of closely related strains in order to further unravel their evolutionary relationships.

Infectious diarrhea is a leading worldwide cause of infant mortality and secondary malnutrition. Enterotoxigenic E. coli (ETEC) is a principal etiology of travelers?diarrhea and a major endemic health threat, especially among children in developing nations where it is estimated to cause hundreds of thousands of deaths each year. Vaccine development for ETEC has been significantly hampered by the remarkable genetic plasticity of E. coli, a comparatively modest understanding of the basic pathogenesis of these organisms, and an uncertainty regarding the degree to which any given antigenic target might be conserved. While experimental and epidemiologic data suggest that a broadly protective vaccine can be achieved, this will most effectively be accomplished in a research environment that fosters sharing of vital resources and open, collaborative interactions among multiple investigators. The proposed project is aimed at providing critical leverage to ongoing international investigative efforts pertaining to ETEC pathogenesis and vaccinology.

The flow of genetic information within this group motivated us to identify novel genes for the purpose of creating a species DNA microarray to better understand the ancestral relationships among its members. Based on preliminary MLST genotyping, 11 diverse ETEC strains were selected for sequencing. Sequence information obtained from this project, and from other publicly available sources, led to the development of a comprehensive species microarray for ETEC group members. The availability of the ETEC species DNA microarray has allowed us to carry out a collaborative CGH genotyping project to validate this microarray as well as understand the phylogenomic relationships among members of ETEC group.
 
Overall design Two hundread sixteen query strains were investigated in this study, with each query strain hybridized against the reference strain, B7A. Each strain has a single dye experiment. Each oligo is spotted on the Etec species microarray once. Positive controls on the array consist of oligos designed from the sequenced reference genome, B7A, and negative controls on the array consist of oligos designed from the thale cress plant, Arabidopsis thaliana.The microarrays also had Agilent internal controls.
 
Contributor(s) Papazisi L, Snesrud E, Akkoush S, Wester E, Sun C, Ratnayake S, Appalla L, Liu J, Dracheva T, Wan C, Li J, Wei L, Braisted J, Saeed A, Belland MJ, Curtiss III R, Francis JD, Gomez-Duarte OG, Gormley RP, Moxley RA, Munson GP, Qadri F, Savarino SJ, Fleckenstein M, Hardwidge PR, Fleischmann RD, Peterson SN
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Submission date Nov 24, 2010
Last update date Mar 22, 2012
Contact name John Braisted
E-mail(s) jbraisted@jcvi.org
Organization name J Craig Venter Institute
Department PFGRC
Lab PFGRC_EXTSW
Street address 9704 Medical Center Dr
City Rockville
State/province MD
ZIP/Postal code 20850
Country USA
 
Platforms (1)
GPL10979 Agilent-029784 ETEC_CGH
Samples (216)
GSM627752 252978410001_B7A_CY5_BCE001MS16_CY3.mev.refIsIB.out
GSM627927 252978410001_B7A_CY5_BCE022DS6_CY3.mev.refIsIB.out
GSM628414 252978410007_B7A_CY5_BCE002_MS12_CY3.mev.refIsIB.out
Relations
BioProject PRJNA134243

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE25601_RAW.tar 2.7 Gb (http)(custom) TAR (of TXT)
Processed data included within Sample table
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