Isolating Viral and Host RNA Sequences from Archival Material and Production of cDNA Libraries for High-Throughput DNA Sequencing.
Identifieur interne : 001A80 ( Ncbi/Checkpoint ); précédent : 001A79; suivant : 001A81Isolating Viral and Host RNA Sequences from Archival Material and Production of cDNA Libraries for High-Throughput DNA Sequencing.
Auteurs : Yongli Xiao [États-Unis] ; Zong-Mei Sheng [États-Unis] ; Jeffery K. Taubenberger [États-Unis]Source :
- Current protocols in microbiology [ 1934-8533 ] ; 2015.
Descripteurs français
- KwdFr :
- ARN viral (génétique), ARN viral (isolement et purification), Anatomopathologie moléculaire (), Banque de gènes, Humains, Pandémie de grippe de 1918-1919, Sous-type H1N1 du virus de la grippe A (génétique), Sous-type H1N1 du virus de la grippe A (isolement et purification), Séquençage nucléotidique à haut débit.
- MESH :
- génétique : ARN viral, Sous-type H1N1 du virus de la grippe A.
- isolement et purification : ARN viral, Sous-type H1N1 du virus de la grippe A.
- Anatomopathologie moléculaire, Banque de gènes, Humains, Pandémie de grippe de 1918-1919, Séquençage nucléotidique à haut débit.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : RNA, Viral.
- genetics : Influenza A Virus, H1N1 Subtype.
- isolation & purification : Influenza A Virus, H1N1 Subtype, RNA, Viral.
- methods : Pathology, Molecular.
- Gene Library, High-Throughput Nucleotide Sequencing, Humans, Influenza Pandemic, 1918-1919.
Abstract
The vast majority of surgical biopsy and post-mortem tissue samples are formalin-fixed and paraffin-embedded (FFPE), but this process leads to RNA degradation that limits gene expression analysis. As an example, the viral RNA genome of the 1918 pandemic influenza A virus was previously determined in a 9-year effort by overlapping RT-PCR from post-mortem samples. Using the protocols described here, the full genome of the 1918 virus was determined at high coverage in one high-throughput sequencing run of a cDNA library derived from total RNA of a 1918 FFPE sample after duplex-specific nuclease treatments. This basic methodological approach should assist in the analysis of FFPE tissue samples isolated over the past century from a variety of infectious diseases.
DOI: 10.1002/9780471729259.mc01e08s37
PubMed: 26344216
Affiliations:
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Taubenberger</name><affiliation wicri:level="2"><nlm:affiliation>Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Maryland</region></placeName><wicri:cityArea>Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda</wicri:cityArea></affiliation></author></analytic><series><title level="j">Current protocols in microbiology</title><idno type="eISSN">1934-8533</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Gene Library</term><term>High-Throughput Nucleotide Sequencing</term><term>Humans</term><term>Influenza A Virus, H1N1 Subtype (genetics)</term><term>Influenza A Virus, H1N1 Subtype (isolation & purification)</term><term>Influenza Pandemic, 1918-1919</term><term>Pathology, Molecular (methods)</term><term>RNA, Viral (genetics)</term><term>RNA, Viral (isolation & purification)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN viral (génétique)</term><term>ARN viral (isolement et purification)</term><term>Anatomopathologie moléculaire ()</term><term>Banque de gènes</term><term>Humains</term><term>Pandémie de grippe de 1918-1919</term><term>Sous-type H1N1 du virus de la grippe A (génétique)</term><term>Sous-type H1N1 du virus de la grippe A (isolement et purification)</term><term>Séquençage nucléotidique à haut débit</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA, Viral</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Influenza A Virus, H1N1 Subtype</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN viral</term><term>Sous-type H1N1 du virus de la grippe A</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Influenza A Virus, H1N1 Subtype</term><term>RNA, Viral</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>ARN viral</term><term>Sous-type H1N1 du virus de la grippe A</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Pathology, Molecular</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Gene Library</term><term>High-Throughput Nucleotide Sequencing</term><term>Humans</term><term>Influenza Pandemic, 1918-1919</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Anatomopathologie moléculaire</term><term>Banque de gènes</term><term>Humains</term><term>Pandémie de grippe de 1918-1919</term><term>Séquençage nucléotidique à haut débit</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The vast majority of surgical biopsy and post-mortem tissue samples are formalin-fixed and paraffin-embedded (FFPE), but this process leads to RNA degradation that limits gene expression analysis. As an example, the viral RNA genome of the 1918 pandemic influenza A virus was previously determined in a 9-year effort by overlapping RT-PCR from post-mortem samples. Using the protocols described here, the full genome of the 1918 virus was determined at high coverage in one high-throughput sequencing run of a cDNA library derived from total RNA of a 1918 FFPE sample after duplex-specific nuclease treatments. This basic methodological approach should assist in the analysis of FFPE tissue samples isolated over the past century from a variety of infectious diseases.</div></front></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>Maryland</li></region></list><tree><country name="États-Unis"><region name="Maryland"><name sortKey="Xiao, Yongli" sort="Xiao, Yongli" uniqKey="Xiao Y" first="Yongli" last="Xiao">Yongli Xiao</name></region><name sortKey="Sheng, Zong Mei" sort="Sheng, Zong Mei" uniqKey="Sheng Z" first="Zong-Mei" last="Sheng">Zong-Mei Sheng</name><name sortKey="Taubenberger, Jeffery K" sort="Taubenberger, Jeffery K" uniqKey="Taubenberger J" first="Jeffery K" last="Taubenberger">Jeffery K. Taubenberger</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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