title: Streptococcus pneumoniae Supragenome Hybridization Arrays for Profiling of Genetic Content and Gene Expression.
abstract: There is extensive genomic diversity among Streptococcus pneumoniae isolates. Approximately half of the comprehensive set of genes in the species (the supragenome or pangenome) is present in all the isolates (core set), and the remaining is unevenly distributed among strains (distributed set). The Streptococcus pneumoniae Supragenome Hybridization (SpSGH) array provides coverage for an extensive set of genes and polymorphisms encountered within this species, capturing this genomic diversity. Further, the capture is quantitative. In this manner, the SpSGH array allows for both genomic and transcriptomic analyses of diverse S. pneumoniae isolates on a single platform. In this unit, we present the SpSGH array, and describe in detail its design and implementation for both genomic and transcriptomic analyses. The methodology can be applied to construction and modification of SpSGH array platforms, as well to other bacterial species as long as multiple whole-genome sequences are available that collectively capture the vast majority of the species supragenome.
authors: Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania.
authors: Anagha
authors: A
authors: Kadam
authors: Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania.
authors: Benjamin
authors: B
authors: Janto
authors: Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, Pennsylvania.
authors: Rory
authors: R
authors: Eutsey
authors: Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania.
authors: Joshua P
authors: JP
authors: Earl
authors: Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, Pennsylvania.
authors: Evan
authors: E
authors: Powell
authors: Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, Pennsylvania.
authors: Margaret E
authors: ME
authors: Dahlgren
authors: Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania.
authors: Fen Z
authors: FZ
authors: Hu
authors: Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania.
authors: Garth D
authors: GD
authors: Ehrlich
authors: Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania.|Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, Pennsylvania.
authors: N Luisa
authors: NL
authors: Hiller
mesh_terms: D020869:Gene Expression Profiling / Q000379:methods; D014644:Genetic Variation; D005827:Genetics, Microbial / Q000379:methods*; D023281:Genomics / Q000379:methods; D008967:Molecular Biology / Q000379:methods*; D009693:Nucleic Acid Hybridization / Q000379:methods*; D013296:Streptococcus pneumoniae / Q000145:classification* / Q000235:genetics*
keywords: Streptococcus pneumoniae; gene array; gene expression; genome content; pangenome; supragenome; transcriptional profiling
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