Streptococcus pneumoniae Supragenome Hybridization Arrays for Profiling of Genetic Content and Gene Expression

Anagha Kadam; Benjamin Janto; Rory Eutsey; Joshua P Earl; Evan Powell; Margaret E Dahlgren; Fen Z Hu; Garth D Ehrlich; N. Luisa Hiller

doi:10.1002/9780471729259.mc09d04s36

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Streptococcus pneumoniae Supragenome Hybridization Arrays for Profiling of Genetic Content and Gene Expression

Journal article

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Streptococcus pneumoniae Supragenome Hybridization Arrays for Profiling of Genetic Content and Gene Expression

Anagha Kadam, Benjamin Janto, Rory Eutsey, Joshua P Earl, Evan Powell, Margaret E Dahlgren, Fen Z Hu, Garth D Ehrlich and N. Luisa Hiller

Current protocols in microbiology (Online), v 36(1), pp 9D.4.1-9D.4.20

Feb 2015

DOI: https://doi.org/10.1002/9780471729259.mc09d04s36

PMID: 25641101

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Abstract

transcriptional profiling

supragenome

pangenome

gene array

gene expression

genome content

Streptococcus pneumoniae

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 as applied to other bacterial species as long as multiple whole genome sequences are available that collectively capture the vast majority of the species supragenome.

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Title: Streptococcus pneumoniae Supragenome Hybridization Arrays for Profiling of Genetic Content and Gene Expression
Creators: Anagha Kadam - Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
Benjamin Janto - Department of Microbiology & Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
Rory Eutsey - Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, PA, USA
Joshua P Earl - Department of Microbiology & Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
Evan Powell - Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, PA, USA
Margaret E Dahlgren - Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, PA, USA
Fen Z Hu - Department of Microbiology & Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
Garth D Ehrlich - Department of Microbiology & Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
N. Luisa Hiller - Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
Publication Details: Current protocols in microbiology (Online), v 36(1), pp 9D.4.1-9D.4.20
Publisher: Wiley
Resource Type: Journal article
Language: English
Academic Unit: Microbiology and Immunology
Scopus ID: 2-s2.0-84949231968
Other Identifier: 991014969751304721

Streptococcus pneumoniae Supragenome Hybridization Arrays for Profiling of Genetic Content and Gene Expression

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