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Benefits of random-priming: Exhaustive survey of a cDNA library from lung tissue of a SARS patient
The severe acute respiratory syndrome (SARS) leads to severe injury in the lungs with multiple factors, though the pathogenesis is still largely unclear. This paper describes the particular analyses of the transcriptome of human lung tissue that was infected by SARS-associated coronavirus (SARS-CoV)...
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| Published in: | Journal of medical virology 2011-04, Vol.83 (4), p.574-586 |
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| container_end_page | 586 |
| container_issue | 4 |
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| container_title | Journal of medical virology |
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| creator | Wu, Hongkai Wang, Jinwen Deng, Riqiang Xing, Ke Xiong, Yuanyan Huang, Junfeng He, Xionglei Wang, Xunzhang |
| description | The severe acute respiratory syndrome (SARS) leads to severe injury in the lungs with multiple factors, though the pathogenesis is still largely unclear. This paper describes the particular analyses of the transcriptome of human lung tissue that was infected by SARS-associated coronavirus (SARS-CoV). Random primers were used to produce ESTs from total RNA samples of the lung tissue. The result showed a high diversity of the transcripts, covering much of the human genome, including loci which do not contain protein coding sequences. 10,801 ESTs were generated and assembled into 267 contigs plus 7,659 singletons. Sequences matching to SARS-CoV RNAs and other pneumonia-related microbes were found. The transcripts were well classified by functional annotation. Among the 7,872 assembled sequences that were identified as from human genome, 578 non-coding genes were revealed by BLAST search. The transcripts were mapped to the human genome with the restriction of identity = 100%, which found a candidate pool of 448 novel transcriptional loci where EST transcriptional signal was never found before. Among these, 13 loci were never reported to be transcriptional by other detection methods such as gene chips, tiling arrays, and paired-end ditags (PETs). The result showed that random-priming cDNA library is valid for the investigation of transcript diversity in the virus-infected tissue. The EST data could be a useful supplemental source for SARS pathology researches. J. Med. Virol. 83:574-586, 2011. |
| doi_str_mv | 10.1002/jmv.22012 |
| format | article |
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This paper describes the particular analyses of the transcriptome of human lung tissue that was infected by SARS-associated coronavirus (SARS-CoV). Random primers were used to produce ESTs from total RNA samples of the lung tissue. The result showed a high diversity of the transcripts, covering much of the human genome, including loci which do not contain protein coding sequences. 10,801 ESTs were generated and assembled into 267 contigs plus 7,659 singletons. Sequences matching to SARS-CoV RNAs and other pneumonia-related microbes were found. The transcripts were well classified by functional annotation. Among the 7,872 assembled sequences that were identified as from human genome, 578 non-coding genes were revealed by BLAST search. The transcripts were mapped to the human genome with the restriction of identity = 100%, which found a candidate pool of 448 novel transcriptional loci where EST transcriptional signal was never found before. Among these, 13 loci were never reported to be transcriptional by other detection methods such as gene chips, tiling arrays, and paired-end ditags (PETs). The result showed that random-priming cDNA library is valid for the investigation of transcript diversity in the virus-infected tissue. The EST data could be a useful supplemental source for SARS pathology researches. J. Med. Virol. 83:574-586, 2011.</description><identifier>ISSN: 0146-6615</identifier><identifier>EISSN: 1096-9071</identifier><identifier>DOI: 10.1002/jmv.22012</identifier><identifier>PMID: 21328370</identifier><identifier>CODEN: JMVIDB</identifier><language>eng</language><publisher>Hoboken: Wiley Subscription Services, Inc., A Wiley Company</publisher><subject>Adult ; Aged ; Biological and medical sciences ; cDNA library ; Chemistry ; DNA Primers - genetics ; Fundamental and applied biological sciences. Psychology ; Gene Expression Profiling ; Gene Library ; Human viral diseases ; Humans ; Infectious diseases ; Lung - pathology ; Lung - virology ; Male ; Medical sciences ; Microbiology ; Miscellaneous ; Pathology, Molecular - methods ; random primer ; SARS coronavirus ; SARS Virus - pathogenicity ; SARS-associated coronavirus ; Severe Acute Respiratory Syndrome - pathology ; Severe Acute Respiratory Syndrome - virology ; Severe acute respiratory syndrome coronavirus 2 ; transcript diversity ; Viral diseases ; Virology</subject><ispartof>Journal of medical virology, 2011-04, Vol.83 (4), p.574-586</ispartof><rights>Copyright © 2011 Wiley‐Liss, Inc.</rights><rights>2015 INIST-CNRS</rights><rights>Copyright © 2011 Wiley-Liss, Inc.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c5272-3e359edec8b96f95e1e91afe3bf867aca2ed904d8e3e45aae630bc6ccea35dbe3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1002%2Fjmv.22012$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fjmv.22012$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>230,315,786,790,891,27957,27958,50923,51032</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=23891142$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/21328370$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Wu, Hongkai</creatorcontrib><creatorcontrib>Wang, Jinwen</creatorcontrib><creatorcontrib>Deng, Riqiang</creatorcontrib><creatorcontrib>Xing, Ke</creatorcontrib><creatorcontrib>Xiong, Yuanyan</creatorcontrib><creatorcontrib>Huang, Junfeng</creatorcontrib><creatorcontrib>He, Xionglei</creatorcontrib><creatorcontrib>Wang, Xunzhang</creatorcontrib><title>Benefits of random-priming: Exhaustive survey of a cDNA library from lung tissue of a SARS patient</title><title>Journal of medical virology</title><addtitle>J. Med. Virol</addtitle><description>The severe acute respiratory syndrome (SARS) leads to severe injury in the lungs with multiple factors, though the pathogenesis is still largely unclear. This paper describes the particular analyses of the transcriptome of human lung tissue that was infected by SARS-associated coronavirus (SARS-CoV). Random primers were used to produce ESTs from total RNA samples of the lung tissue. The result showed a high diversity of the transcripts, covering much of the human genome, including loci which do not contain protein coding sequences. 10,801 ESTs were generated and assembled into 267 contigs plus 7,659 singletons. Sequences matching to SARS-CoV RNAs and other pneumonia-related microbes were found. The transcripts were well classified by functional annotation. Among the 7,872 assembled sequences that were identified as from human genome, 578 non-coding genes were revealed by BLAST search. The transcripts were mapped to the human genome with the restriction of identity = 100%, which found a candidate pool of 448 novel transcriptional loci where EST transcriptional signal was never found before. Among these, 13 loci were never reported to be transcriptional by other detection methods such as gene chips, tiling arrays, and paired-end ditags (PETs). The result showed that random-priming cDNA library is valid for the investigation of transcript diversity in the virus-infected tissue. The EST data could be a useful supplemental source for SARS pathology researches. J. Med. Virol. 83:574-586, 2011.</description><subject>Adult</subject><subject>Aged</subject><subject>Biological and medical sciences</subject><subject>cDNA library</subject><subject>Chemistry</subject><subject>DNA Primers - genetics</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gene Expression Profiling</subject><subject>Gene Library</subject><subject>Human viral diseases</subject><subject>Humans</subject><subject>Infectious diseases</subject><subject>Lung - pathology</subject><subject>Lung - virology</subject><subject>Male</subject><subject>Medical sciences</subject><subject>Microbiology</subject><subject>Miscellaneous</subject><subject>Pathology, Molecular - methods</subject><subject>random primer</subject><subject>SARS coronavirus</subject><subject>SARS Virus - pathogenicity</subject><subject>SARS-associated coronavirus</subject><subject>Severe Acute Respiratory Syndrome - pathology</subject><subject>Severe Acute Respiratory Syndrome - virology</subject><subject>Severe acute respiratory syndrome coronavirus 2</subject><subject>transcript diversity</subject><subject>Viral diseases</subject><subject>Virology</subject><issn>0146-6615</issn><issn>1096-9071</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</creationdate><recordtype>article</recordtype><recordid>eNp90V1v0zAUBuAIgVgZXPAHINKEgItsx3bsxFwglTHGRymCMnZpOe5J55KPYidl_fe4pBsfEuQmF3n8nuO8UXSfwCEBoEfLen1IKRB6IxoRkCKRkJGb0QhIKhIhCN-L7ni_BIBcUno72qOE0ZxlMIqKF9hgaTsft2XsdDNv62TlbG2bxbP45PJC976za4x979a42SIdm5fTcVzZwmm3iUvX1nHVN4u4s973OJDZ-NMsXunOYtPdjW6VuvJ4b_fej85enXw-fp1MPpy-OR5PEsNpRhOGjEuco8kLKUrJkaAkukRWlLnItNEU5xLSeY4MU641CgaFEcagZnxeINuPng-5q76ocW7CaKcrtb1NWFS12qo_vzT2Qi3atcqICA8PAY93Aa791qPvVG29warSDba9VzmnEoQAGuST_0rCBRAQRIpAD_6iy7Z3TfgRQaUcckEhC-rpoIxrvXdYXq9NQG07VqFj9bPjYB_8fs9reVVqAI92QHujqzLUaqz_5VguCUm3QUeD-24r3Px7onr7_svV6GQ4YX2Hl9cntPuqRMYyrs6np2pK380mU_iozoN_OPhSt0ovXNjibBaSGBCZZpBy9gNNP9av</recordid><startdate>201104</startdate><enddate>201104</enddate><creator>Wu, Hongkai</creator><creator>Wang, Jinwen</creator><creator>Deng, Riqiang</creator><creator>Xing, Ke</creator><creator>Xiong, Yuanyan</creator><creator>Huang, Junfeng</creator><creator>He, Xionglei</creator><creator>Wang, Xunzhang</creator><general>Wiley Subscription Services, Inc., A Wiley Company</general><general>Wiley</general><general>Wiley Subscription Services, Inc</general><scope>FBQ</scope><scope>BSCLL</scope><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7TK</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7TM</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>201104</creationdate><title>Benefits of random-priming: Exhaustive survey of a cDNA library from lung tissue of a SARS patient</title><author>Wu, Hongkai ; Wang, Jinwen ; Deng, Riqiang ; Xing, Ke ; Xiong, Yuanyan ; Huang, Junfeng ; He, Xionglei ; Wang, Xunzhang</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c5272-3e359edec8b96f95e1e91afe3bf867aca2ed904d8e3e45aae630bc6ccea35dbe3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2011</creationdate><topic>Adult</topic><topic>Aged</topic><topic>Biological and medical sciences</topic><topic>cDNA library</topic><topic>Chemistry</topic><topic>DNA Primers - genetics</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Gene Expression Profiling</topic><topic>Gene Library</topic><topic>Human viral diseases</topic><topic>Humans</topic><topic>Infectious diseases</topic><topic>Lung - pathology</topic><topic>Lung - virology</topic><topic>Male</topic><topic>Medical sciences</topic><topic>Microbiology</topic><topic>Miscellaneous</topic><topic>Pathology, Molecular - methods</topic><topic>random primer</topic><topic>SARS coronavirus</topic><topic>SARS Virus - pathogenicity</topic><topic>SARS-associated coronavirus</topic><topic>Severe Acute Respiratory Syndrome - pathology</topic><topic>Severe Acute Respiratory Syndrome - virology</topic><topic>Severe acute respiratory syndrome coronavirus 2</topic><topic>transcript diversity</topic><topic>Viral diseases</topic><topic>Virology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Wu, Hongkai</creatorcontrib><creatorcontrib>Wang, Jinwen</creatorcontrib><creatorcontrib>Deng, Riqiang</creatorcontrib><creatorcontrib>Xing, Ke</creatorcontrib><creatorcontrib>Xiong, Yuanyan</creatorcontrib><creatorcontrib>Huang, Junfeng</creatorcontrib><creatorcontrib>He, Xionglei</creatorcontrib><creatorcontrib>Wang, Xunzhang</creatorcontrib><collection>AGRIS</collection><collection>Istex</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Neurosciences Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Journal of medical virology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wu, Hongkai</au><au>Wang, Jinwen</au><au>Deng, Riqiang</au><au>Xing, Ke</au><au>Xiong, Yuanyan</au><au>Huang, Junfeng</au><au>He, Xionglei</au><au>Wang, Xunzhang</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Benefits of random-priming: Exhaustive survey of a cDNA library from lung tissue of a SARS patient</atitle><jtitle>Journal of medical virology</jtitle><addtitle>J. Med. Virol</addtitle><date>2011-04</date><risdate>2011</risdate><volume>83</volume><issue>4</issue><spage>574</spage><epage>586</epage><pages>574-586</pages><issn>0146-6615</issn><eissn>1096-9071</eissn><coden>JMVIDB</coden><notes>http://dx.doi.org/10.1002/jmv.22012</notes><notes>Subject of State Key Laboratory of Biocontrol, Sun Yat-sen University - No. SKLBC08B01</notes><notes>istex:060666D93DECD1F24B46DA7D439F0D9D0A8C0D42</notes><notes>ark:/67375/WNG-N2KSLN0Q-W</notes><notes>ArticleID:JMV22012</notes><notes>Science and Technology Project of Guangdong Province - No. 03-33200-4202224</notes><notes>Natural Science Foundation of Guangdong Province - No. 4203388</notes><notes>Natural Science Foundation of China - No. 30970139</notes><notes>ObjectType-Article-1</notes><notes>SourceType-Scholarly Journals-1</notes><notes>ObjectType-Feature-2</notes><notes>content type line 23</notes><notes>ObjectType-Feature-3</notes><notes>ObjectType-Undefined-2</notes><abstract>The severe acute respiratory syndrome (SARS) leads to severe injury in the lungs with multiple factors, though the pathogenesis is still largely unclear. This paper describes the particular analyses of the transcriptome of human lung tissue that was infected by SARS-associated coronavirus (SARS-CoV). Random primers were used to produce ESTs from total RNA samples of the lung tissue. The result showed a high diversity of the transcripts, covering much of the human genome, including loci which do not contain protein coding sequences. 10,801 ESTs were generated and assembled into 267 contigs plus 7,659 singletons. Sequences matching to SARS-CoV RNAs and other pneumonia-related microbes were found. The transcripts were well classified by functional annotation. Among the 7,872 assembled sequences that were identified as from human genome, 578 non-coding genes were revealed by BLAST search. The transcripts were mapped to the human genome with the restriction of identity = 100%, which found a candidate pool of 448 novel transcriptional loci where EST transcriptional signal was never found before. Among these, 13 loci were never reported to be transcriptional by other detection methods such as gene chips, tiling arrays, and paired-end ditags (PETs). The result showed that random-priming cDNA library is valid for the investigation of transcript diversity in the virus-infected tissue. The EST data could be a useful supplemental source for SARS pathology researches. J. Med. Virol. 83:574-586, 2011.</abstract><cop>Hoboken</cop><pub>Wiley Subscription Services, Inc., A Wiley Company</pub><pmid>21328370</pmid><doi>10.1002/jmv.22012</doi><tpages>13</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Adult Aged Biological and medical sciences cDNA library Chemistry DNA Primers - genetics Fundamental and applied biological sciences. Psychology Gene Expression Profiling Gene Library Human viral diseases Humans Infectious diseases Lung - pathology Lung - virology Male Medical sciences Microbiology Miscellaneous Pathology, Molecular - methods random primer SARS coronavirus SARS Virus - pathogenicity SARS-associated coronavirus Severe Acute Respiratory Syndrome - pathology Severe Acute Respiratory Syndrome - virology Severe acute respiratory syndrome coronavirus 2 transcript diversity Viral diseases Virology |
| title | Benefits of random-priming: Exhaustive survey of a cDNA library from lung tissue of a SARS patient |
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