SrasV1, PubMed, Curation, bibRecord, 000F83

Genomic profiling of collaborative cross founder mice infected with respiratory viruses reveals novel transcripts and infection-related strain-specific gene and isoform expression.

Identifieur interne : 000F83 ( PubMed/Curation ); précédent : 000F82; suivant : 000F84

Genomic profiling of collaborative cross founder mice infected with respiratory viruses reveals novel transcripts and infection-related strain-specific gene and isoform expression.

Auteurs : Hao Xiong [États-Unis] ; Juliet Morrison [États-Unis] ; Martin T. Ferris [États-Unis] ; Lisa E. Gralinski [États-Unis] ; Alan C. Whitmore [États-Unis] ; Richard Green [États-Unis] ; Matthew J. Thomas [États-Unis] ; Jennifer Tisoncik-Go [États-Unis] ; Gary P. Schroth [États-Unis] ; Fernando Pardo-Manuel De Villena [États-Unis] ; Ralph S. Baric [États-Unis] ; Mark T. Heise [États-Unis] ; Xinxia Peng [États-Unis] ; Michael G. Katze [États-Unis]

Source :

G3 (Bethesda, Md.) [ 2160-1836 ] ; 2014.

RBID : pubmed:24902603

Descripteurs français

KwdFr :
- ARN (génétique), Analyse de profil d'expression de gènes, Analyse de séquence d'ARN, Animaux, Charge virale, Femelle, Génome, Infections à Orthomyxoviridae (génétique), Infections à Orthomyxoviridae (virologie), Phénotype, Poumon (métabolisme), Poumon (virologie), Régulation de l'expression des gènes, Souris, Spécificité d'espèce, Syndrome respiratoire aigu sévère (génétique), Syndrome respiratoire aigu sévère (virologie), Virus de la grippe A, Virus du SRAS.
MESH :
- génétique : ARN, Infections à Orthomyxoviridae, Syndrome respiratoire aigu sévère.
- métabolisme : Poumon.
- virologie : Infections à Orthomyxoviridae, Poumon, Syndrome respiratoire aigu sévère.
- Analyse de profil d'expression de gènes, Analyse de séquence d'ARN, Animaux, Charge virale, Femelle, Génome, Phénotype, Régulation de l'expression des gènes, Souris, Spécificité d'espèce, Virus de la grippe A, Virus du SRAS.

English descriptors

KwdEn :
- Animals, Female, Gene Expression Profiling, Gene Expression Regulation, Genome, Influenza A virus, Lung (metabolism), Lung (virology), Mice, Orthomyxoviridae Infections (genetics), Orthomyxoviridae Infections (virology), Phenotype, RNA (genetics), SARS Virus, Sequence Analysis, RNA, Severe Acute Respiratory Syndrome (genetics), Severe Acute Respiratory Syndrome (virology), Species Specificity, Viral Load.
MESH :
- chemical , genetics : RNA.
- genetics : Orthomyxoviridae Infections, Severe Acute Respiratory Syndrome.
- metabolism : Lung.
- virology : Lung, Orthomyxoviridae Infections, Severe Acute Respiratory Syndrome.
- Animals, Female, Gene Expression Profiling, Gene Expression Regulation, Genome, Influenza A virus, Mice, Phenotype, SARS Virus, Sequence Analysis, RNA, Species Specificity, Viral Load.

Abstract

Genetic variation between diverse mouse species is well-characterized, yet existing knowledge of the mouse transcriptome comes largely from one mouse strain (C57BL/6J). As such, it is unlikely to reflect the transcriptional complexity of the mouse species. Gene transcription is dynamic and condition-specific; therefore, to better understand the mouse transcriptional response to respiratory virus infection, we infected the eight founder strains of the Collaborative Cross with either influenza A virus or severe acute respiratory syndrome coronavirus and sequenced lung RNA samples at 2 and 4 days after infection. We found numerous instances of transcripts that were not present in the C57BL/6J reference annotation, indicating that a nontrivial proportion of the mouse genome is transcribed but poorly annotated. Of these novel transcripts, 2150 could be aligned to human or rat genomes, but not to existing mouse genomes, suggesting functionally conserved sequences not yet recorded in mouse genomes. We also found that respiratory virus infection induced differential expression of 4287 splicing junctions, resulting in strain-specific isoform expression. Of these, 59 were influenced by strain-specific mutations within 2 base pairs of key intron-exon boundaries, suggesting cis-regulated expression. Our results reveal the complexity of the transcriptional response to viral infection, previously undocumented genomic elements, and extensive diversity in the response across mouse strains. These findings identify hitherto unexplored transcriptional patterns and undocumented transcripts in genetically diverse mice. Host genetic variation drives the complexity and diversity of the host response by eliciting starkly different transcriptional profiles in response to a viral infection.

DOI: 10.1534/g3.114.011759
PubMed: 24902603

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<author><name sortKey="Katze, Michael G" sort="Katze, Michael G" uniqKey="Katze M" first="Michael G" last="Katze">Michael G. Katze</name>
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<sourceDesc><biblStruct><analytic><title xml:lang="en">Genomic profiling of collaborative cross founder mice infected with respiratory viruses reveals novel transcripts and infection-related strain-specific gene and isoform expression.</title>
<author><name sortKey="Xiong, Hao" sort="Xiong, Hao" uniqKey="Xiong H" first="Hao" last="Xiong">Hao Xiong</name>
<affiliation wicri:level="2"><nlm:affiliation>Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, Portland, Oregon.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
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<author><name sortKey="Morrison, Juliet" sort="Morrison, Juliet" uniqKey="Morrison J" first="Juliet" last="Morrison">Juliet Morrison</name>
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<country xml:lang="fr">États-Unis</country>
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<author><name sortKey="Ferris, Martin T" sort="Ferris, Martin T" uniqKey="Ferris M" first="Martin T" last="Ferris">Martin T. Ferris</name>
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<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Caroline du Nord</region>
</placeName>
<wicri:cityArea>Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, Portland, Oregon Department of Genetics, University of North Carolina-Chapel Hill, Chapel Hill</wicri:cityArea>
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<author><name sortKey="Gralinski, Lisa E" sort="Gralinski, Lisa E" uniqKey="Gralinski L" first="Lisa E" last="Gralinski">Lisa E. Gralinski</name>
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<country xml:lang="fr">États-Unis</country>
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</affiliation>
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<author><name sortKey="Whitmore, Alan C" sort="Whitmore, Alan C" uniqKey="Whitmore A" first="Alan C" last="Whitmore">Alan C. Whitmore</name>
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<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Caroline du Nord</region>
</placeName>
<wicri:cityArea>Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, Portland, Oregon Department of Genetics, University of North Carolina-Chapel Hill, Chapel Hill</wicri:cityArea>
</affiliation>
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<author><name sortKey="Green, Richard" sort="Green, Richard" uniqKey="Green R" first="Richard" last="Green">Richard Green</name>
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<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Oregon</region>
</placeName>
<wicri:cityArea>Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, Portland</wicri:cityArea>
</affiliation>
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<author><name sortKey="Thomas, Matthew J" sort="Thomas, Matthew J" uniqKey="Thomas M" first="Matthew J" last="Thomas">Matthew J. Thomas</name>
<affiliation wicri:level="2"><nlm:affiliation>Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, Portland, Oregon.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Oregon</region>
</placeName>
<wicri:cityArea>Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, Portland</wicri:cityArea>
</affiliation>
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<author><name sortKey="Tisoncik Go, Jennifer" sort="Tisoncik Go, Jennifer" uniqKey="Tisoncik Go J" first="Jennifer" last="Tisoncik-Go">Jennifer Tisoncik-Go</name>
<affiliation wicri:level="2"><nlm:affiliation>Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, Portland, Oregon.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Oregon</region>
</placeName>
<wicri:cityArea>Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, Portland</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Schroth, Gary P" sort="Schroth, Gary P" uniqKey="Schroth G" first="Gary P" last="Schroth">Gary P. Schroth</name>
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<country>États-Unis</country>
<placeName><region type="state">Californie</region>
</placeName>
<wicri:cityArea>Illumina, Inc., San Diego</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Pardo Manuel De Villena, Fernando" sort="Pardo Manuel De Villena, Fernando" uniqKey="Pardo Manuel De Villena F" first="Fernando" last="Pardo-Manuel De Villena">Fernando Pardo-Manuel De Villena</name>
<affiliation wicri:level="2"><nlm:affiliation>Department of Genetics, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Caroline du Nord</region>
</placeName>
<wicri:cityArea>Department of Genetics, University of North Carolina-Chapel Hill, Chapel Hill</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Baric, Ralph S" sort="Baric, Ralph S" uniqKey="Baric R" first="Ralph S" last="Baric">Ralph S. Baric</name>
<affiliation wicri:level="2"><nlm:affiliation>Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, Portland, Oregon Department of Epidemiology, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Caroline du Nord</region>
</placeName>
<wicri:cityArea>Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, Portland, Oregon Department of Epidemiology, University of North Carolina-Chapel Hill, Chapel Hill</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Heise, Mark T" sort="Heise, Mark T" uniqKey="Heise M" first="Mark T" last="Heise">Mark T. Heise</name>
<affiliation wicri:level="2"><nlm:affiliation>Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, Portland, Oregon Department of Genetics, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Caroline du Nord</region>
</placeName>
<wicri:cityArea>Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, Portland, Oregon Department of Genetics, University of North Carolina-Chapel Hill, Chapel Hill</wicri:cityArea>
</affiliation>
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<author><name sortKey="Peng, Xinxia" sort="Peng, Xinxia" uniqKey="Peng X" first="Xinxia" last="Peng">Xinxia Peng</name>
<affiliation wicri:level="2"><nlm:affiliation>Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, Portland, Oregon.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Oregon</region>
</placeName>
<wicri:cityArea>Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, Portland</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Katze, Michael G" sort="Katze, Michael G" uniqKey="Katze M" first="Michael G" last="Katze">Michael G. Katze</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, Portland, Oregon honey@uw.edu.</nlm:affiliation>
<country wicri:rule="url">États-Unis</country>
<wicri:regionArea>Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, Portland</wicri:regionArea>
</affiliation>
</author>
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<series><title level="j">G3 (Bethesda, Md.)</title>
<idno type="eISSN">2160-1836</idno>
<imprint><date when="2014" type="published">2014</date>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term>
<term>Female</term>
<term>Gene Expression Profiling</term>
<term>Gene Expression Regulation</term>
<term>Genome</term>
<term>Influenza A virus</term>
<term>Lung (metabolism)</term>
<term>Lung (virology)</term>
<term>Mice</term>
<term>Orthomyxoviridae Infections (genetics)</term>
<term>Orthomyxoviridae Infections (virology)</term>
<term>Phenotype</term>
<term>RNA (genetics)</term>
<term>SARS Virus</term>
<term>Sequence Analysis, RNA</term>
<term>Severe Acute Respiratory Syndrome (genetics)</term>
<term>Severe Acute Respiratory Syndrome (virology)</term>
<term>Species Specificity</term>
<term>Viral Load</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>ARN (génétique)</term>
<term>Analyse de profil d'expression de gènes</term>
<term>Analyse de séquence d'ARN</term>
<term>Animaux</term>
<term>Charge virale</term>
<term>Femelle</term>
<term>Génome</term>
<term>Infections à Orthomyxoviridae (génétique)</term>
<term>Infections à Orthomyxoviridae (virologie)</term>
<term>Phénotype</term>
<term>Poumon (métabolisme)</term>
<term>Poumon (virologie)</term>
<term>Régulation de l'expression des gènes</term>
<term>Souris</term>
<term>Spécificité d'espèce</term>
<term>Syndrome respiratoire aigu sévère (génétique)</term>
<term>Syndrome respiratoire aigu sévère (virologie)</term>
<term>Virus de la grippe A</term>
<term>Virus du SRAS</term>
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</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Orthomyxoviridae Infections</term>
<term>Severe Acute Respiratory Syndrome</term>
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<term>Infections à Orthomyxoviridae</term>
<term>Syndrome respiratoire aigu sévère</term>
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<term>Poumon</term>
<term>Syndrome respiratoire aigu sévère</term>
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<term>Orthomyxoviridae Infections</term>
<term>Severe Acute Respiratory Syndrome</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Animals</term>
<term>Female</term>
<term>Gene Expression Profiling</term>
<term>Gene Expression Regulation</term>
<term>Genome</term>
<term>Influenza A virus</term>
<term>Mice</term>
<term>Phenotype</term>
<term>SARS Virus</term>
<term>Sequence Analysis, RNA</term>
<term>Species Specificity</term>
<term>Viral Load</term>
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<keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term>
<term>Analyse de séquence d'ARN</term>
<term>Animaux</term>
<term>Charge virale</term>
<term>Femelle</term>
<term>Génome</term>
<term>Phénotype</term>
<term>Régulation de l'expression des gènes</term>
<term>Souris</term>
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<front><div type="abstract" xml:lang="en">Genetic variation between diverse mouse species is well-characterized, yet existing knowledge of the mouse transcriptome comes largely from one mouse strain (C57BL/6J). As such, it is unlikely to reflect the transcriptional complexity of the mouse species. Gene transcription is dynamic and condition-specific; therefore, to better understand the mouse transcriptional response to respiratory virus infection, we infected the eight founder strains of the Collaborative Cross with either influenza A virus or severe acute respiratory syndrome coronavirus and sequenced lung RNA samples at 2 and 4 days after infection. We found numerous instances of transcripts that were not present in the C57BL/6J reference annotation, indicating that a nontrivial proportion of the mouse genome is transcribed but poorly annotated. Of these novel transcripts, 2150 could be aligned to human or rat genomes, but not to existing mouse genomes, suggesting functionally conserved sequences not yet recorded in mouse genomes. We also found that respiratory virus infection induced differential expression of 4287 splicing junctions, resulting in strain-specific isoform expression. Of these, 59 were influenced by strain-specific mutations within 2 base pairs of key intron-exon boundaries, suggesting cis-regulated expression. Our results reveal the complexity of the transcriptional response to viral infection, previously undocumented genomic elements, and extensive diversity in the response across mouse strains. These findings identify hitherto unexplored transcriptional patterns and undocumented transcripts in genetically diverse mice. Host genetic variation drives the complexity and diversity of the host response by eliciting starkly different transcriptional profiles in response to a viral infection. </div>
</front>
</TEI>
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<DateCompleted><Year>2015</Year>
<Month>04</Month>
<Day>10</Day>
</DateCompleted>
<DateRevised><Year>2018</Year>
<Month>11</Month>
<Day>13</Day>
</DateRevised>
<Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">2160-1836</ISSN>
<JournalIssue CitedMedium="Internet"><Volume>4</Volume>
<Issue>8</Issue>
<PubDate><Year>2014</Year>
<Month>Jun</Month>
<Day>05</Day>
</PubDate>
</JournalIssue>
<Title>G3 (Bethesda, Md.)</Title>
<ISOAbbreviation>G3 (Bethesda)</ISOAbbreviation>
</Journal>
<ArticleTitle>Genomic profiling of collaborative cross founder mice infected with respiratory viruses reveals novel transcripts and infection-related strain-specific gene and isoform expression.</ArticleTitle>
<Pagination><MedlinePgn>1429-44</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1534/g3.114.011759</ELocationID>
<Abstract><AbstractText>Genetic variation between diverse mouse species is well-characterized, yet existing knowledge of the mouse transcriptome comes largely from one mouse strain (C57BL/6J). As such, it is unlikely to reflect the transcriptional complexity of the mouse species. Gene transcription is dynamic and condition-specific; therefore, to better understand the mouse transcriptional response to respiratory virus infection, we infected the eight founder strains of the Collaborative Cross with either influenza A virus or severe acute respiratory syndrome coronavirus and sequenced lung RNA samples at 2 and 4 days after infection. We found numerous instances of transcripts that were not present in the C57BL/6J reference annotation, indicating that a nontrivial proportion of the mouse genome is transcribed but poorly annotated. Of these novel transcripts, 2150 could be aligned to human or rat genomes, but not to existing mouse genomes, suggesting functionally conserved sequences not yet recorded in mouse genomes. We also found that respiratory virus infection induced differential expression of 4287 splicing junctions, resulting in strain-specific isoform expression. Of these, 59 were influenced by strain-specific mutations within 2 base pairs of key intron-exon boundaries, suggesting cis-regulated expression. Our results reveal the complexity of the transcriptional response to viral infection, previously undocumented genomic elements, and extensive diversity in the response across mouse strains. These findings identify hitherto unexplored transcriptional patterns and undocumented transcripts in genetically diverse mice. Host genetic variation drives the complexity and diversity of the host response by eliciting starkly different transcriptional profiles in response to a viral infection. </AbstractText>
<CopyrightInformation>Copyright © 2014 Xiong et al.</CopyrightInformation>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Xiong</LastName>
<ForeName>Hao</ForeName>
<Initials>H</Initials>
<AffiliationInfo><Affiliation>Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, Portland, Oregon.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Morrison</LastName>
<ForeName>Juliet</ForeName>
<Initials>J</Initials>
<AffiliationInfo><Affiliation>Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, Portland, Oregon.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Ferris</LastName>
<ForeName>Martin T</ForeName>
<Initials>MT</Initials>
<AffiliationInfo><Affiliation>Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, Portland, Oregon Department of Genetics, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Gralinski</LastName>
<ForeName>Lisa E</ForeName>
<Initials>LE</Initials>
<AffiliationInfo><Affiliation>Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, Portland, Oregon Department of Epidemiology, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Whitmore</LastName>
<ForeName>Alan C</ForeName>
<Initials>AC</Initials>
<AffiliationInfo><Affiliation>Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, Portland, Oregon Department of Genetics, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Green</LastName>
<ForeName>Richard</ForeName>
<Initials>R</Initials>
<AffiliationInfo><Affiliation>Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, Portland, Oregon.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Thomas</LastName>
<ForeName>Matthew J</ForeName>
<Initials>MJ</Initials>
<AffiliationInfo><Affiliation>Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, Portland, Oregon.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Tisoncik-Go</LastName>
<ForeName>Jennifer</ForeName>
<Initials>J</Initials>
<AffiliationInfo><Affiliation>Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, Portland, Oregon.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Schroth</LastName>
<ForeName>Gary P</ForeName>
<Initials>GP</Initials>
<AffiliationInfo><Affiliation>Illumina, Inc., San Diego, California.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Pardo-Manuel de Villena</LastName>
<ForeName>Fernando</ForeName>
<Initials>F</Initials>
<AffiliationInfo><Affiliation>Department of Genetics, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Baric</LastName>
<ForeName>Ralph S</ForeName>
<Initials>RS</Initials>
<AffiliationInfo><Affiliation>Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, Portland, Oregon Department of Epidemiology, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Heise</LastName>
<ForeName>Mark T</ForeName>
<Initials>MT</Initials>
<AffiliationInfo><Affiliation>Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, Portland, Oregon Department of Genetics, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Peng</LastName>
<ForeName>Xinxia</ForeName>
<Initials>X</Initials>
<AffiliationInfo><Affiliation>Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, Portland, Oregon.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Katze</LastName>
<ForeName>Michael G</ForeName>
<Initials>MG</Initials>
<AffiliationInfo><Affiliation>Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, Portland, Oregon honey@uw.edu.</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>
<Language>eng</Language>
<DataBankList CompleteYN="Y"><DataBank><DataBankName>GEO</DataBankName>
<AccessionNumberList><AccessionNumber>GSE52405</AccessionNumber>
</AccessionNumberList>
</DataBank>
</DataBankList>
<GrantList CompleteYN="Y"><Grant><GrantID>U19 AI100625</GrantID>
<Acronym>AI</Acronym>
<Agency>NIAID NIH HHS</Agency>
<Country>United States</Country>
</Grant>
<Grant><GrantID>U19 AI00625</GrantID>
<Acronym>AI</Acronym>
<Agency>NIAID NIH HHS</Agency>
<Country>United States</Country>
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<PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType>
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<Month>06</Month>
<Day>05</Day>
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<MedlineJournalInfo><Country>United States</Country>
<MedlineTA>G3 (Bethesda)</MedlineTA>
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<MeshHeadingList><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D005260" MajorTopicYN="N">Female</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName>
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<MeshHeading><DescriptorName UI="D005786" MajorTopicYN="N">Gene Expression Regulation</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D016678" MajorTopicYN="N">Genome</DescriptorName>
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<MeshHeading><DescriptorName UI="D009980" MajorTopicYN="N">Influenza A virus</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D008168" MajorTopicYN="N">Lung</DescriptorName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
<QualifierName UI="Q000821" MajorTopicYN="N">virology</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D051379" MajorTopicYN="N">Mice</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D009976" MajorTopicYN="N">Orthomyxoviridae Infections</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
<QualifierName UI="Q000821" MajorTopicYN="N">virology</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D010641" MajorTopicYN="N">Phenotype</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D012313" MajorTopicYN="N">RNA</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D045473" MajorTopicYN="N">SARS Virus</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D017423" MajorTopicYN="N">Sequence Analysis, RNA</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D045169" MajorTopicYN="N">Severe Acute Respiratory Syndrome</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
<QualifierName UI="Q000821" MajorTopicYN="N">virology</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D013045" MajorTopicYN="N">Species Specificity</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D019562" MajorTopicYN="N">Viral Load</DescriptorName>
</MeshHeading>
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<KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">RNA-seq</Keyword>
<Keyword MajorTopicYN="N">collaborative cross</Keyword>
<Keyword MajorTopicYN="N">isoform differential expression</Keyword>
<Keyword MajorTopicYN="N">mouse transcriptome annotation</Keyword>
<Keyword MajorTopicYN="N">viral infection</Keyword>
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   |texte=   Genomic profiling of collaborative cross founder mice infected with respiratory viruses reveals novel transcripts and infection-related strain-specific gene and isoform expression.
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Genomic profiling of collaborative cross founder mice infected with respiratory viruses reveals novel transcripts and infection-related strain-specific gene and isoform expression.

Genomic profiling of collaborative cross founder mice infected with respiratory viruses reveals novel transcripts and infection-related strain-specific gene and isoform expression.

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