tetano
Editor, Senior Moderator
J Pathol. 2012 Nov 26. doi: 10.1002/path.4145. [Epub ahead of print]
High-throughput RNA sequencing of a formalin-fixed, paraffin-embedded autopsy lung tissue sample from the 1918 influenza pandemic.
Xiao YL, Kash JC, Beres SB, Sheng ZM, Musser JM, Taubenberger JK.
Source
Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA.
Abstract
Most biopsy and autopsy tissues are formalin-fixed, and paraffin-embedded (FFPE), but this process leads to RNA degradation that limits gene expression analysis. The RNA genome of the 1918 pandemic influenza virus was previously determined in a 9-year effort by overlapping RT-PCR from postmortem samples. Here, the full genome of the 1918 virus at 3,000x coverage was determined in one high-throughput sequencing run of a library derived from total RNA of a 1918 FFPE sample after duplex specific nuclease treatments. Bacterial sequences associated with secondary bacterial pneumonias were also detected. Host transcripts were well represented in the library. Compared to a 2009 pandemic influenza virus FFPE postmortem library, the 1918 sample showed significant enrichment for host defense and cell death response genes, concordant with prior animal studies. This methodological approach should assist in the analysis of FFPE tissue samples isolated over the past century from a variety of diseases. Copyright ? 2012 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Copyright ? 2012 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
PMID:
23180419
[PubMed - as supplied by publisher]
http://www.ncbi.nlm.nih.gov/pubmed/23180419
High-throughput RNA sequencing of a formalin-fixed, paraffin-embedded autopsy lung tissue sample from the 1918 influenza pandemic.
Xiao YL, Kash JC, Beres SB, Sheng ZM, Musser JM, Taubenberger JK.
Source
Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA.
Abstract
Most biopsy and autopsy tissues are formalin-fixed, and paraffin-embedded (FFPE), but this process leads to RNA degradation that limits gene expression analysis. The RNA genome of the 1918 pandemic influenza virus was previously determined in a 9-year effort by overlapping RT-PCR from postmortem samples. Here, the full genome of the 1918 virus at 3,000x coverage was determined in one high-throughput sequencing run of a library derived from total RNA of a 1918 FFPE sample after duplex specific nuclease treatments. Bacterial sequences associated with secondary bacterial pneumonias were also detected. Host transcripts were well represented in the library. Compared to a 2009 pandemic influenza virus FFPE postmortem library, the 1918 sample showed significant enrichment for host defense and cell death response genes, concordant with prior animal studies. This methodological approach should assist in the analysis of FFPE tissue samples isolated over the past century from a variety of diseases. Copyright ? 2012 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Copyright ? 2012 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
PMID:
23180419
[PubMed - as supplied by publisher]
http://www.ncbi.nlm.nih.gov/pubmed/23180419