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<PubmedArticle><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25641101</PMID><DateCompleted><Year>2016</Year><Month>09</Month><Day>07</Day></DateCompleted><DateRevised><Year>2022</Year><Month>10</Month><Day>05</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1934-8533</ISSN><JournalIssue CitedMedium="Internet"><Volume>36</Volume><PubDate><Year>2015</Year><Month>Feb</Month><Day>02</Day></PubDate></JournalIssue><Title>Current protocols in microbiology</Title><ISOAbbreviation>Curr Protoc Microbiol</ISOAbbreviation></Journal><ArticleTitle>Streptococcus pneumoniae Supragenome Hybridization Arrays for Profiling of Genetic Content and Gene Expression.</ArticleTitle><Pagination><StartPage>9D.4.1</StartPage><EndPage>9D.4.20</EndPage><MedlinePgn>9D.4.1-9D.4.20</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1002/9780471729259.mc09d04s36</ELocationID><Abstract><AbstractText>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.</AbstractText><CopyrightInformation>Copyright &#xa9; 2015 John Wiley &amp; Sons, Inc.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Kadam</LastName><ForeName>Anagha</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Janto</LastName><ForeName>Benjamin</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Eutsey</LastName><ForeName>Rory</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, Pennsylvania.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Earl</LastName><ForeName>Joshua P</ForeName><Initials>JP</Initials><AffiliationInfo><Affiliation>Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Powell</LastName><ForeName>Evan</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, Pennsylvania.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Dahlgren</LastName><ForeName>Margaret E</ForeName><Initials>ME</Initials><AffiliationInfo><Affiliation>Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, Pennsylvania.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hu</LastName><ForeName>Fen Z</ForeName><Initials>FZ</Initials><AffiliationInfo><Affiliation>Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ehrlich</LastName><ForeName>Garth D</ForeName><Initials>GD</Initials><AffiliationInfo><Affiliation>Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hiller</LastName><ForeName>N Luisa</ForeName><Initials>NL</Initials><AffiliationInfo><Affiliation>Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, Pennsylvania.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>R00 DC011322</GrantID><Acronym>DC</Acronym><Agency>NIDCD NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>AI080935</GrantID><Acronym>AI</Acronym><Agency>NIAID NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>K99 DC011322</GrantID><Acronym>DC</Acronym><Agency>NIDCD NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01 DC002148</GrantID><Acronym>DC</Acronym><Agency>NIDCD NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>DC011322</GrantID><Acronym>DC</Acronym><Agency>NIDCD NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>DC02148</GrantID><Acronym>DC</Acronym><Agency>NIDCD NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01 AI080935</GrantID><Acronym>AI</Acronym><Agency>NIAID NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2015</Year><Month>02</Month><Day>02</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Curr Protoc Microbiol</MedlineTA><NlmUniqueID>101257113</NlmUniqueID><ISSNLinking>1934-8525</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014644" MajorTopicYN="Y">Genetic Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005827" MajorTopicYN="N">Genetics, Microbial</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="N">Genomics</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008967" MajorTopicYN="N">Molecular Biology</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D009693" MajorTopicYN="N">Nucleic Acid Hybridization</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D013296" MajorTopicYN="N">Streptococcus pneumoniae</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="Y">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Streptococcus pneumoniae</Keyword><Keyword MajorTopicYN="N">gene array</Keyword><Keyword MajorTopicYN="N">gene expression</Keyword><Keyword MajorTopicYN="N">genome content</Keyword><Keyword MajorTopicYN="N">pangenome</Keyword><Keyword MajorTopicYN="N">supragenome</Keyword><Keyword MajorTopicYN="N">transcriptional profiling</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2015</Year><Month>2</Month><Day>3</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2015</Year><Month>2</Month><Day>3</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>9</Month><Day>8</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pmc-release"><Year>2016</Year><Month>2</Month><Day>2</Day></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">25641101</ArticleId><ArticleId IdType="mid">NIHMS662861</ArticleId><ArticleId 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