Transcriptomic Analysis of Myocardial Ischemia Using the Blood of Rat
Myocardial ischemia is a pathological state of heart with reduced blood flow to heart and abnormal myocardial energy metabolism. This disease occurs commonly in middle aged and elderly people. Several studies have indicated that the rat was an appropriate animal model used to study myocardial ischem...
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| creator | Hou, Jincai Fu, Jianhua Li, Dan Han, Xiao Li, Lei Song, Wenting Yao, Mingjiang Liu, Jianxun |
| description | Myocardial ischemia is a pathological state of heart with reduced blood flow to heart and abnormal myocardial energy metabolism. This disease occurs commonly in middle aged and elderly people. Several studies have indicated that the rat was an appropriate animal model used to study myocardial ischemia. In this study, in order to gain insights into the pathogenesis of myocardial ischemia, we sequenced the transcriptomes of three normal rats as control and the same number of myocardial ischemia rats. We sequenced the genomes of 6 rats, including 3 cases (myocardial ischemia) and 3 controls using Illumina HiSeq 2000. Then we calculated the gene expression values and identified differentially expressed genes based on reads per kilobase transcriptome per million (RPKM). Meanwhile we performed a GO enrichment analysis and predicted novel transcripts. In our study, we found that 707 genes were up-regulated and 21 genes were down-regulated in myocardial ischemia rats by at least 2-fold compared with controls. By the distribution of reads and the annotation of reference genes, we found 1,703 and 1,552 novel transcripts in cases and controls, respectively. At the same time, we refined the structure of 9,587 genes in controls and 10,301 in cases. According to the results of GO term and pathway analysis of differentially expressed genes, we found that the immune response, stimulus response, response to stress and some diseases may be associated with myocardial ischemia. Since many diseases, especially immune diseases, are associated with myocardial ischemia, we should pay more attention to the complications which might result from myocardial ischemia. |
| doi_str_mv | 10.1371/journal.pone.0141915 |
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This disease occurs commonly in middle aged and elderly people. Several studies have indicated that the rat was an appropriate animal model used to study myocardial ischemia. In this study, in order to gain insights into the pathogenesis of myocardial ischemia, we sequenced the transcriptomes of three normal rats as control and the same number of myocardial ischemia rats. We sequenced the genomes of 6 rats, including 3 cases (myocardial ischemia) and 3 controls using Illumina HiSeq 2000. Then we calculated the gene expression values and identified differentially expressed genes based on reads per kilobase transcriptome per million (RPKM). Meanwhile we performed a GO enrichment analysis and predicted novel transcripts. In our study, we found that 707 genes were up-regulated and 21 genes were down-regulated in myocardial ischemia rats by at least 2-fold compared with controls. By the distribution of reads and the annotation of reference genes, we found 1,703 and 1,552 novel transcripts in cases and controls, respectively. At the same time, we refined the structure of 9,587 genes in controls and 10,301 in cases. According to the results of GO term and pathway analysis of differentially expressed genes, we found that the immune response, stimulus response, response to stress and some diseases may be associated with myocardial ischemia. Since many diseases, especially immune diseases, are associated with myocardial ischemia, we should pay more attention to the complications which might result from myocardial ischemia.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0141915</identifier><identifier>PMID: 26540270</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Animal models ; Animals ; Annotations ; Bioinformatics ; Blood ; Blood flow ; Complications ; Diabetes ; Diseases ; Down-Regulation - genetics ; Energy metabolism ; Gene expression ; Gene Expression - genetics ; Gene Expression Profiling - methods ; Genes ; Genomes ; Geriatrics ; Heart ; Heart attacks ; Heart failure ; Hospitals ; Immune response ; Immune system ; Immunological diseases ; Ischemia ; Laboratory animals ; Male ; Metabolism ; Molecular Sequence Annotation - methods ; Myocardial ischemia ; Myocardial Ischemia - blood ; Myocardial Ischemia - genetics ; Older people ; Pathogenesis ; Pharmacology ; Rats ; Rats, Wistar ; Rodents ; Studies ; Transcriptome - genetics ; Up-Regulation - genetics</subject><ispartof>PloS one, 2015-11, Vol.10 (11), p.e0141915-e0141915</ispartof><rights>2015 Hou et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2015 Hou et al 2015 Hou et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c526t-5bf1033fe79f62499397e5d596e62ec4c3ad6da6a3e28be01cca4372e1b1864a3</citedby><cites>FETCH-LOGICAL-c526t-5bf1033fe79f62499397e5d596e62ec4c3ad6da6a3e28be01cca4372e1b1864a3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4634849/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4634849/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26540270$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Jiang, Yongshuai</contributor><creatorcontrib>Hou, Jincai</creatorcontrib><creatorcontrib>Fu, Jianhua</creatorcontrib><creatorcontrib>Li, Dan</creatorcontrib><creatorcontrib>Han, Xiao</creatorcontrib><creatorcontrib>Li, Lei</creatorcontrib><creatorcontrib>Song, Wenting</creatorcontrib><creatorcontrib>Yao, Mingjiang</creatorcontrib><creatorcontrib>Liu, Jianxun</creatorcontrib><title>Transcriptomic Analysis of Myocardial Ischemia Using the Blood of Rat</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Myocardial ischemia is a pathological state of heart with reduced blood flow to heart and abnormal myocardial energy metabolism. This disease occurs commonly in middle aged and elderly people. Several studies have indicated that the rat was an appropriate animal model used to study myocardial ischemia. In this study, in order to gain insights into the pathogenesis of myocardial ischemia, we sequenced the transcriptomes of three normal rats as control and the same number of myocardial ischemia rats. We sequenced the genomes of 6 rats, including 3 cases (myocardial ischemia) and 3 controls using Illumina HiSeq 2000. Then we calculated the gene expression values and identified differentially expressed genes based on reads per kilobase transcriptome per million (RPKM). Meanwhile we performed a GO enrichment analysis and predicted novel transcripts. In our study, we found that 707 genes were up-regulated and 21 genes were down-regulated in myocardial ischemia rats by at least 2-fold compared with controls. By the distribution of reads and the annotation of reference genes, we found 1,703 and 1,552 novel transcripts in cases and controls, respectively. At the same time, we refined the structure of 9,587 genes in controls and 10,301 in cases. According to the results of GO term and pathway analysis of differentially expressed genes, we found that the immune response, stimulus response, response to stress and some diseases may be associated with myocardial ischemia. Since many diseases, especially immune diseases, are associated with myocardial ischemia, we should pay more attention to the complications which might result from myocardial ischemia.</description><subject>Animal models</subject><subject>Animals</subject><subject>Annotations</subject><subject>Bioinformatics</subject><subject>Blood</subject><subject>Blood flow</subject><subject>Complications</subject><subject>Diabetes</subject><subject>Diseases</subject><subject>Down-Regulation - genetics</subject><subject>Energy metabolism</subject><subject>Gene expression</subject><subject>Gene Expression - genetics</subject><subject>Gene Expression Profiling - methods</subject><subject>Genes</subject><subject>Genomes</subject><subject>Geriatrics</subject><subject>Heart</subject><subject>Heart attacks</subject><subject>Heart failure</subject><subject>Hospitals</subject><subject>Immune response</subject><subject>Immune system</subject><subject>Immunological diseases</subject><subject>Ischemia</subject><subject>Laboratory animals</subject><subject>Male</subject><subject>Metabolism</subject><subject>Molecular Sequence Annotation - methods</subject><subject>Myocardial ischemia</subject><subject>Myocardial Ischemia - blood</subject><subject>Myocardial Ischemia - genetics</subject><subject>Older people</subject><subject>Pathogenesis</subject><subject>Pharmacology</subject><subject>Rats</subject><subject>Rats, Wistar</subject><subject>Rodents</subject><subject>Studies</subject><subject>Transcriptome - genetics</subject><subject>Up-Regulation - genetics</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNptkl1r2zAUhsXYWD__wdgMvelNMn1buhl0pdsCHYPRXotj-ThRsK1Mcgb593Uat7RjVxLScx6dI15CPjA6Z6Jkn9dxm3po55vY45wyySxTb8gxs4LPNKfi7Yv9ETnJeU2pEkbr9-SIayUpL-kxublL0GefwmaIXfDF1ajc5ZCL2BQ_d9FDqgO0xSL7FXYBivsc-mUxrLD42sZY77HfMJyRdw20Gc-n9ZTcf7u5u_4xu_31fXF9dTvziuthpqqGUSEaLG2jubRW2BJVraxGzdFLL6DWNWgQyE2FlHkPUpQcWcWMliBOyaeDd9PG7KYfyI6VgmojOZcjsTgQdYS126TQQdq5CME9HsS0dJCG4Ft0DUojKmu811o2pamkNFY1QCtkVoEfXV-m17ZVh7XHfkjQvpK-vunDyi3jXye1kEbaUXA5CVL8s8U8uC5kj20LPcbtY9-sNJwxNaIX_6D_n04eKJ9izgmb52YYdftUPFW5fSrclIqx7OPLQZ6LnmIgHgDyQbUo</recordid><startdate>20151105</startdate><enddate>20151105</enddate><creator>Hou, Jincai</creator><creator>Fu, Jianhua</creator><creator>Li, Dan</creator><creator>Han, Xiao</creator><creator>Li, Lei</creator><creator>Song, Wenting</creator><creator>Yao, Mingjiang</creator><creator>Liu, Jianxun</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><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>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20151105</creationdate><title>Transcriptomic Analysis of Myocardial Ischemia Using the Blood of Rat</title><author>Hou, Jincai ; Fu, Jianhua ; Li, Dan ; Han, Xiao ; Li, Lei ; Song, Wenting ; Yao, Mingjiang ; Liu, Jianxun</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c526t-5bf1033fe79f62499397e5d596e62ec4c3ad6da6a3e28be01cca4372e1b1864a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Animal models</topic><topic>Animals</topic><topic>Annotations</topic><topic>Bioinformatics</topic><topic>Blood</topic><topic>Blood flow</topic><topic>Complications</topic><topic>Diabetes</topic><topic>Diseases</topic><topic>Down-Regulation - 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By the distribution of reads and the annotation of reference genes, we found 1,703 and 1,552 novel transcripts in cases and controls, respectively. At the same time, we refined the structure of 9,587 genes in controls and 10,301 in cases. According to the results of GO term and pathway analysis of differentially expressed genes, we found that the immune response, stimulus response, response to stress and some diseases may be associated with myocardial ischemia. Since many diseases, especially immune diseases, are associated with myocardial ischemia, we should pay more attention to the complications which might result from myocardial ischemia.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>26540270</pmid><doi>10.1371/journal.pone.0141915</doi><oa>free_for_read</oa></addata></record> |
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| subjects | Animal models Animals Annotations Bioinformatics Blood Blood flow Complications Diabetes Diseases Down-Regulation - genetics Energy metabolism Gene expression Gene Expression - genetics Gene Expression Profiling - methods Genes Genomes Geriatrics Heart Heart attacks Heart failure Hospitals Immune response Immune system Immunological diseases Ischemia Laboratory animals Male Metabolism Molecular Sequence Annotation - methods Myocardial ischemia Myocardial Ischemia - blood Myocardial Ischemia - genetics Older people Pathogenesis Pharmacology Rats Rats, Wistar Rodents Studies Transcriptome - genetics Up-Regulation - genetics |
| title | Transcriptomic Analysis of Myocardial Ischemia Using the Blood of Rat |
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