Development of a DNA Microarray for Toxicology Based on Hepatotoxin-Regulated Sequences
Toxicogenomics is an emerging field combining genomics and bioinformatics to identify and characterize mechanisms of toxicity of compounds. One of the main tools used in toxicogenomics is DNA microarrays. We have used a novel strategy to create a library highly enriched for genes expressed in the li...
Gespeichert in:
| Veröffentlicht in: | Environmental health perspectives 2003-05, Vol.111 (6), p.863-870 |
|---|---|
| Hauptverfasser: | , , , , , , , , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 870 |
|---|---|
| container_issue | 6 |
| container_start_page | 863 |
| container_title | Environmental health perspectives |
| container_volume | 111 |
| creator | Waring, Jeffrey F. Cavet, Guy Jolly, Robert A. McDowell, Jeff Dai, Hongye Ciurlionis, Rita Zhang, Chunsheng Stoughton, Roland Lum, Pek Ferguson, Allan Roberts, Christopher J. Ulrich, Roger G. |
| description | Toxicogenomics is an emerging field combining genomics and bioinformatics to identify and characterize mechanisms of toxicity of compounds. One of the main tools used in toxicogenomics is DNA microarrays. We have used a novel strategy to create a library highly enriched for genes expressed in the liver under hepatotoxic conditions. Using this library, we have created a new oligonucleotide microarray dedicated to the study of rat liver function. Oligonucleotide probes for these genes were designed and used in experimental hybridization studies to deduce the correct sequence orientation and to determine those sequences exhibiting differential regulation under a variety of toxicity-related treatments and conditions. The final array was benchmarked on treatments with 3-methylcholanthrene, Aroclor 1254, and cyclopropane carboxylic acid. Our results showed that the subtractive hybridization greatly enriched for genes regulated during a hepatotoxic response. Overall, our strategy for design of a new rat toxicology microarray can be applied to other systems as well and should aid greatly in the development of microarrays targeted for specific scientific areas. |
| doi_str_mv | 10.1289/ehp.5998 |
| format | Article |
| fullrecord | <record><control><sourceid>gale_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_1241508</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A105367015</galeid><jstor_id>3435129</jstor_id><sourcerecordid>A105367015</sourcerecordid><originalsourceid>FETCH-LOGICAL-c542t-84ec859733059afa4d3669bd8e050e0579f666c20e9248e0bb24ff6fc9282b333</originalsourceid><addsrcrecordid>eNqNkk1r3DAQhk1podu00B_Qg0-hPXir77UuhW3SNIG0gSRtj0KWR14HW3IlOWT_fRQ2hC7kUIQQzDzzMjN6i-I9RktMavkZNtOSS1m_KBaYc1JJSdjLYoGQxJVYCf66eBPjDUII10Isij_HcAuDn0ZwqfS21OXxz3X5ozfB6xD0trQ-lNf-rjd-8N22_KojtKV35SlMOvmUM666hG4edMqJK_g7gzMQ3xavrB4ivHt8D4pfJ9-uj06r84vvZ0fr88pwRlJVMzA1lytKEZfaatZSIWTT1oA4ynclrRDCEAR5jBxsGsKsFdZIUpOGUnpQfNnpTnMzQmvyGEEPagr9qMNWed2r_YzrN6rztwoThjmqs8Dho0DwufeY1NhHA8OgHfg5KsyEYEiwDFY7sNMDqN5Zn_VMBw6yrHdg-xxeY8SpWCHMM798hs-nhTFv87mCT3sFmUlwlzo9x6jOri7_n734vc8e_sNuQA9pE_0wp967uA9-3IH582MMYJ_WiJF6MJfK5lIP5srohx16E5MPTxxllGMi6T1AfckE</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>14664064</pqid></control><display><type>article</type><title>Development of a DNA Microarray for Toxicology Based on Hepatotoxin-Regulated Sequences</title><source>DOAJ Directory of Open Access Journals</source><source>Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals</source><source>PubMed Central Open Access</source><source>JSTOR Archive Collection A-Z Listing</source><source>PubMed Central</source><creator>Waring, Jeffrey F. ; Cavet, Guy ; Jolly, Robert A. ; McDowell, Jeff ; Dai, Hongye ; Ciurlionis, Rita ; Zhang, Chunsheng ; Stoughton, Roland ; Lum, Pek ; Ferguson, Allan ; Roberts, Christopher J. ; Ulrich, Roger G.</creator><creatorcontrib>Waring, Jeffrey F. ; Cavet, Guy ; Jolly, Robert A. ; McDowell, Jeff ; Dai, Hongye ; Ciurlionis, Rita ; Zhang, Chunsheng ; Stoughton, Roland ; Lum, Pek ; Ferguson, Allan ; Roberts, Christopher J. ; Ulrich, Roger G.</creatorcontrib><description>Toxicogenomics is an emerging field combining genomics and bioinformatics to identify and characterize mechanisms of toxicity of compounds. One of the main tools used in toxicogenomics is DNA microarrays. We have used a novel strategy to create a library highly enriched for genes expressed in the liver under hepatotoxic conditions. Using this library, we have created a new oligonucleotide microarray dedicated to the study of rat liver function. Oligonucleotide probes for these genes were designed and used in experimental hybridization studies to deduce the correct sequence orientation and to determine those sequences exhibiting differential regulation under a variety of toxicity-related treatments and conditions. The final array was benchmarked on treatments with 3-methylcholanthrene, Aroclor 1254, and cyclopropane carboxylic acid. Our results showed that the subtractive hybridization greatly enriched for genes regulated during a hepatotoxic response. Overall, our strategy for design of a new rat toxicology microarray can be applied to other systems as well and should aid greatly in the development of microarrays targeted for specific scientific areas.</description><identifier>ISSN: 0091-6765</identifier><identifier>EISSN: 1552-9924</identifier><identifier>DOI: 10.1289/ehp.5998</identifier><language>eng</language><publisher>National Institute of Environmental Health Sciences. National Institutes of Health. Department of Health, Education and Welfare</publisher><subject>Gene expression regulation ; Genes ; Libraries ; Liver ; Oligonucleotide probes ; Polychlorinated biphenyls ; Rats ; RNA ; Toxicity ; Toxicogenomics ; Toxicology</subject><ispartof>Environmental health perspectives, 2003-05, Vol.111 (6), p.863-870</ispartof><rights>COPYRIGHT 2003 National Institute of Environmental Health Sciences</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c542t-84ec859733059afa4d3669bd8e050e0579f666c20e9248e0bb24ff6fc9282b333</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/3435129$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/3435129$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>230,315,728,781,785,804,865,886,27926,27927,53793,53795,58019,58252</link.rule.ids></links><search><creatorcontrib>Waring, Jeffrey F.</creatorcontrib><creatorcontrib>Cavet, Guy</creatorcontrib><creatorcontrib>Jolly, Robert A.</creatorcontrib><creatorcontrib>McDowell, Jeff</creatorcontrib><creatorcontrib>Dai, Hongye</creatorcontrib><creatorcontrib>Ciurlionis, Rita</creatorcontrib><creatorcontrib>Zhang, Chunsheng</creatorcontrib><creatorcontrib>Stoughton, Roland</creatorcontrib><creatorcontrib>Lum, Pek</creatorcontrib><creatorcontrib>Ferguson, Allan</creatorcontrib><creatorcontrib>Roberts, Christopher J.</creatorcontrib><creatorcontrib>Ulrich, Roger G.</creatorcontrib><title>Development of a DNA Microarray for Toxicology Based on Hepatotoxin-Regulated Sequences</title><title>Environmental health perspectives</title><description>Toxicogenomics is an emerging field combining genomics and bioinformatics to identify and characterize mechanisms of toxicity of compounds. One of the main tools used in toxicogenomics is DNA microarrays. We have used a novel strategy to create a library highly enriched for genes expressed in the liver under hepatotoxic conditions. Using this library, we have created a new oligonucleotide microarray dedicated to the study of rat liver function. Oligonucleotide probes for these genes were designed and used in experimental hybridization studies to deduce the correct sequence orientation and to determine those sequences exhibiting differential regulation under a variety of toxicity-related treatments and conditions. The final array was benchmarked on treatments with 3-methylcholanthrene, Aroclor 1254, and cyclopropane carboxylic acid. Our results showed that the subtractive hybridization greatly enriched for genes regulated during a hepatotoxic response. Overall, our strategy for design of a new rat toxicology microarray can be applied to other systems as well and should aid greatly in the development of microarrays targeted for specific scientific areas.</description><subject>Gene expression regulation</subject><subject>Genes</subject><subject>Libraries</subject><subject>Liver</subject><subject>Oligonucleotide probes</subject><subject>Polychlorinated biphenyls</subject><subject>Rats</subject><subject>RNA</subject><subject>Toxicity</subject><subject>Toxicogenomics</subject><subject>Toxicology</subject><issn>0091-6765</issn><issn>1552-9924</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2003</creationdate><recordtype>article</recordtype><recordid>eNqNkk1r3DAQhk1podu00B_Qg0-hPXir77UuhW3SNIG0gSRtj0KWR14HW3IlOWT_fRQ2hC7kUIQQzDzzMjN6i-I9RktMavkZNtOSS1m_KBaYc1JJSdjLYoGQxJVYCf66eBPjDUII10Isij_HcAuDn0ZwqfS21OXxz3X5ozfB6xD0trQ-lNf-rjd-8N22_KojtKV35SlMOvmUM666hG4edMqJK_g7gzMQ3xavrB4ivHt8D4pfJ9-uj06r84vvZ0fr88pwRlJVMzA1lytKEZfaatZSIWTT1oA4ynclrRDCEAR5jBxsGsKsFdZIUpOGUnpQfNnpTnMzQmvyGEEPagr9qMNWed2r_YzrN6rztwoThjmqs8Dho0DwufeY1NhHA8OgHfg5KsyEYEiwDFY7sNMDqN5Zn_VMBw6yrHdg-xxeY8SpWCHMM798hs-nhTFv87mCT3sFmUlwlzo9x6jOri7_n734vc8e_sNuQA9pE_0wp967uA9-3IH582MMYJ_WiJF6MJfK5lIP5srohx16E5MPTxxllGMi6T1AfckE</recordid><startdate>20030515</startdate><enddate>20030515</enddate><creator>Waring, Jeffrey F.</creator><creator>Cavet, Guy</creator><creator>Jolly, Robert A.</creator><creator>McDowell, Jeff</creator><creator>Dai, Hongye</creator><creator>Ciurlionis, Rita</creator><creator>Zhang, Chunsheng</creator><creator>Stoughton, Roland</creator><creator>Lum, Pek</creator><creator>Ferguson, Allan</creator><creator>Roberts, Christopher J.</creator><creator>Ulrich, Roger G.</creator><general>National Institute of Environmental Health Sciences. National Institutes of Health. Department of Health, Education and Welfare</general><general>National Institute of Environmental Health Sciences</general><scope>AAYXX</scope><scope>CITATION</scope><scope>IOV</scope><scope>ISR</scope><scope>7ST</scope><scope>C1K</scope><scope>SOI</scope><scope>5PM</scope></search><sort><creationdate>20030515</creationdate><title>Development of a DNA Microarray for Toxicology Based on Hepatotoxin-Regulated Sequences</title><author>Waring, Jeffrey F. ; Cavet, Guy ; Jolly, Robert A. ; McDowell, Jeff ; Dai, Hongye ; Ciurlionis, Rita ; Zhang, Chunsheng ; Stoughton, Roland ; Lum, Pek ; Ferguson, Allan ; Roberts, Christopher J. ; Ulrich, Roger G.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c542t-84ec859733059afa4d3669bd8e050e0579f666c20e9248e0bb24ff6fc9282b333</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2003</creationdate><topic>Gene expression regulation</topic><topic>Genes</topic><topic>Libraries</topic><topic>Liver</topic><topic>Oligonucleotide probes</topic><topic>Polychlorinated biphenyls</topic><topic>Rats</topic><topic>RNA</topic><topic>Toxicity</topic><topic>Toxicogenomics</topic><topic>Toxicology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Waring, Jeffrey F.</creatorcontrib><creatorcontrib>Cavet, Guy</creatorcontrib><creatorcontrib>Jolly, Robert A.</creatorcontrib><creatorcontrib>McDowell, Jeff</creatorcontrib><creatorcontrib>Dai, Hongye</creatorcontrib><creatorcontrib>Ciurlionis, Rita</creatorcontrib><creatorcontrib>Zhang, Chunsheng</creatorcontrib><creatorcontrib>Stoughton, Roland</creatorcontrib><creatorcontrib>Lum, Pek</creatorcontrib><creatorcontrib>Ferguson, Allan</creatorcontrib><creatorcontrib>Roberts, Christopher J.</creatorcontrib><creatorcontrib>Ulrich, Roger G.</creatorcontrib><collection>CrossRef</collection><collection>Gale In Context: Opposing Viewpoints</collection><collection>Gale In Context: Science</collection><collection>Environment Abstracts</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Environment Abstracts</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Environmental health perspectives</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Waring, Jeffrey F.</au><au>Cavet, Guy</au><au>Jolly, Robert A.</au><au>McDowell, Jeff</au><au>Dai, Hongye</au><au>Ciurlionis, Rita</au><au>Zhang, Chunsheng</au><au>Stoughton, Roland</au><au>Lum, Pek</au><au>Ferguson, Allan</au><au>Roberts, Christopher J.</au><au>Ulrich, Roger G.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Development of a DNA Microarray for Toxicology Based on Hepatotoxin-Regulated Sequences</atitle><jtitle>Environmental health perspectives</jtitle><date>2003-05-15</date><risdate>2003</risdate><volume>111</volume><issue>6</issue><spage>863</spage><epage>870</epage><pages>863-870</pages><issn>0091-6765</issn><eissn>1552-9924</eissn><abstract>Toxicogenomics is an emerging field combining genomics and bioinformatics to identify and characterize mechanisms of toxicity of compounds. One of the main tools used in toxicogenomics is DNA microarrays. We have used a novel strategy to create a library highly enriched for genes expressed in the liver under hepatotoxic conditions. Using this library, we have created a new oligonucleotide microarray dedicated to the study of rat liver function. Oligonucleotide probes for these genes were designed and used in experimental hybridization studies to deduce the correct sequence orientation and to determine those sequences exhibiting differential regulation under a variety of toxicity-related treatments and conditions. The final array was benchmarked on treatments with 3-methylcholanthrene, Aroclor 1254, and cyclopropane carboxylic acid. Our results showed that the subtractive hybridization greatly enriched for genes regulated during a hepatotoxic response. Overall, our strategy for design of a new rat toxicology microarray can be applied to other systems as well and should aid greatly in the development of microarrays targeted for specific scientific areas.</abstract><pub>National Institute of Environmental Health Sciences. National Institutes of Health. Department of Health, Education and Welfare</pub><doi>10.1289/ehp.5998</doi><tpages>8</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0091-6765 |
| ispartof | Environmental health perspectives, 2003-05, Vol.111 (6), p.863-870 |
| issn | 0091-6765 1552-9924 |
| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_1241508 |
| source | DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central Open Access; JSTOR Archive Collection A-Z Listing; PubMed Central |
| subjects | Gene expression regulation Genes Libraries Liver Oligonucleotide probes Polychlorinated biphenyls Rats RNA Toxicity Toxicogenomics Toxicology |
| title | Development of a DNA Microarray for Toxicology Based on Hepatotoxin-Regulated Sequences |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-18T06%3A21%3A08IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Development%20of%20a%20DNA%20Microarray%20for%20Toxicology%20Based%20on%20Hepatotoxin-Regulated%20Sequences&rft.jtitle=Environmental%20health%20perspectives&rft.au=Waring,%20Jeffrey%20F.&rft.date=2003-05-15&rft.volume=111&rft.issue=6&rft.spage=863&rft.epage=870&rft.pages=863-870&rft.issn=0091-6765&rft.eissn=1552-9924&rft_id=info:doi/10.1289/ehp.5998&rft_dat=%3Cgale_pubme%3EA105367015%3C/gale_pubme%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=14664064&rft_id=info:pmid/&rft_galeid=A105367015&rft_jstor_id=3435129&rfr_iscdi=true |