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Transcriptomics tool for the human Schistosoma blood flukes using microarray gene expression profiling
We report the design, fabrication, and validation of a microarray covering the majority of the Schistosoma japonicum and Schistosoma mansoni transcriptomes. The oligonucleotide microarray contains 12,166 S. mansoni and 7055 S. japonicum target sequences. A confidence threshold of ⩽0.001 ( P value) w...
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| Published in: | Experimental parasitology 2006-11, Vol.114 (3), p.160-172 |
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| container_title | Experimental parasitology |
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| creator | Gobert, Geoffrey N. McInnes, Russell Moertel, Luke Nelson, Charles Jones, Malcolm K. Hu, Wei McManus, Donald P. |
| description | We report the design, fabrication, and validation of a microarray covering the majority of the
Schistosoma japonicum and
Schistosoma mansoni transcriptomes. The oligonucleotide microarray contains 12,166
S. mansoni and 7055
S. japonicum target sequences. A confidence threshold of ⩽0.001 (
P value) was used in all analyses. The cross hybridization potential of the microarray was representative of 10,362 probes detected in both channels, while 12,052 probes hybridised to
S. japonicum and 11,254 probes hybridised to
S. mansoni. Differential hybridisation consisted of 3422 probes to
S. mansoni mRNA and 3103 probes to
S. japonicum mRNA. Important biological functions, such as transport, metabolism, immune evasion and host–parasite immunological interplay, cell communication, and sexual maturation are represented on this microarray. This is the first microarray commercially manufactured for studying schistosomes, and the large size and verified quality of the resource demonstrate its power for characterising the schistosome transcriptome. |
| doi_str_mv | 10.1016/j.exppara.2006.03.003 |
| format | article |
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Schistosoma japonicum and
Schistosoma mansoni transcriptomes. The oligonucleotide microarray contains 12,166
S. mansoni and 7055
S. japonicum target sequences. A confidence threshold of ⩽0.001 (
P value) was used in all analyses. The cross hybridization potential of the microarray was representative of 10,362 probes detected in both channels, while 12,052 probes hybridised to
S. japonicum and 11,254 probes hybridised to
S. mansoni. Differential hybridisation consisted of 3422 probes to
S. mansoni mRNA and 3103 probes to
S. japonicum mRNA. Important biological functions, such as transport, metabolism, immune evasion and host–parasite immunological interplay, cell communication, and sexual maturation are represented on this microarray. This is the first microarray commercially manufactured for studying schistosomes, and the large size and verified quality of the resource demonstrate its power for characterising the schistosome transcriptome.</description><identifier>ISSN: 0014-4894</identifier><identifier>EISSN: 1090-2449</identifier><identifier>DOI: 10.1016/j.exppara.2006.03.003</identifier><identifier>PMID: 16631746</identifier><identifier>CODEN: EXPAAA</identifier><language>eng</language><publisher>San Diego, CA: Elsevier Inc</publisher><subject>Animals ; Biological and medical sciences ; Biomphalaria ; CTP ; Cy3 ; Cy5 ; cyanine3 ; cyanine5 ; cytidine 5′-triphosphate ; Female ; Fertility - genetics ; Fundamental and applied biological sciences. Psychology ; GEML ; Gene expression ; gene expression markup language ; Gene Expression Profiling - methods ; Gene Expression Regulation - genetics ; Gene Ontologies ; Helminth ; Host-Parasite Interactions - immunology ; hours ; In Situ Hybridization, Fluorescence ; Invertebrates ; Life cycle. Host-agent relationship. Pathogenesis ; locally weighed scatter plot smoothing ; LOWESS ; Male ; Mice ; Microarray ; min ; minute ; nanogram ; Nemathelminthia. Plathelmintha ; Oligonucleotide Array Sequence Analysis - methods ; Oligonucleotide Array Sequence Analysis - standards ; PBS ; phosphate buffer saline ; photomultiplier tube ; PMT ; Protozoa ; QIMR ; Queensland Institute of Medical Research ; reverse transcriptase ; Reverse Transcriptase Polymerase Chain Reaction ; revolutions per minute ; RNA, Helminth - analysis ; RNA, Helminth - genetics ; RNA, Messenger - analysis ; RNA, Messenger - genetics ; rpm ; Schistosoma ; Schistosoma japonicum ; Schistosoma japonicum - genetics ; Schistosoma japonicum - immunology ; Schistosoma japonicum - physiology ; Schistosoma mansoni ; Schistosoma mansoni - genetics ; Schistosoma mansoni - immunology ; Schistosoma mansoni - physiology ; second ; Signal Transduction - genetics ; sodium chloride/sodium phosphate/EDTA buffer ; SSPE ; TAE ; Transcription, Genetic ; Transcriptome ; Trematoda ; Tris/acetate/EDTA buffer ; w/v ; weight/volume</subject><ispartof>Experimental parasitology, 2006-11, Vol.114 (3), p.160-172</ispartof><rights>2006 Elsevier Inc.</rights><rights>2006 INIST-CNRS</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c490t-b07c6618c5ba28702e6cacdd5fed024c805e5f3c127f359778866794b10abd4a3</citedby><cites>FETCH-LOGICAL-c490t-b07c6618c5ba28702e6cacdd5fed024c805e5f3c127f359778866794b10abd4a3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27924,27925</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=18256333$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/16631746$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Gobert, Geoffrey N.</creatorcontrib><creatorcontrib>McInnes, Russell</creatorcontrib><creatorcontrib>Moertel, Luke</creatorcontrib><creatorcontrib>Nelson, Charles</creatorcontrib><creatorcontrib>Jones, Malcolm K.</creatorcontrib><creatorcontrib>Hu, Wei</creatorcontrib><creatorcontrib>McManus, Donald P.</creatorcontrib><title>Transcriptomics tool for the human Schistosoma blood flukes using microarray gene expression profiling</title><title>Experimental parasitology</title><addtitle>Exp Parasitol</addtitle><description>We report the design, fabrication, and validation of a microarray covering the majority of the
Schistosoma japonicum and
Schistosoma mansoni transcriptomes. The oligonucleotide microarray contains 12,166
S. mansoni and 7055
S. japonicum target sequences. A confidence threshold of ⩽0.001 (
P value) was used in all analyses. The cross hybridization potential of the microarray was representative of 10,362 probes detected in both channels, while 12,052 probes hybridised to
S. japonicum and 11,254 probes hybridised to
S. mansoni. Differential hybridisation consisted of 3422 probes to
S. mansoni mRNA and 3103 probes to
S. japonicum mRNA. Important biological functions, such as transport, metabolism, immune evasion and host–parasite immunological interplay, cell communication, and sexual maturation are represented on this microarray. This is the first microarray commercially manufactured for studying schistosomes, and the large size and verified quality of the resource demonstrate its power for characterising the schistosome transcriptome.</description><subject>Animals</subject><subject>Biological and medical sciences</subject><subject>Biomphalaria</subject><subject>CTP</subject><subject>Cy3</subject><subject>Cy5</subject><subject>cyanine3</subject><subject>cyanine5</subject><subject>cytidine 5′-triphosphate</subject><subject>Female</subject><subject>Fertility - genetics</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>GEML</subject><subject>Gene expression</subject><subject>gene expression markup language</subject><subject>Gene Expression Profiling - methods</subject><subject>Gene Expression Regulation - genetics</subject><subject>Gene Ontologies</subject><subject>Helminth</subject><subject>Host-Parasite Interactions - immunology</subject><subject>hours</subject><subject>In Situ Hybridization, Fluorescence</subject><subject>Invertebrates</subject><subject>Life cycle. Host-agent relationship. Pathogenesis</subject><subject>locally weighed scatter plot smoothing</subject><subject>LOWESS</subject><subject>Male</subject><subject>Mice</subject><subject>Microarray</subject><subject>min</subject><subject>minute</subject><subject>nanogram</subject><subject>Nemathelminthia. Plathelmintha</subject><subject>Oligonucleotide Array Sequence Analysis - methods</subject><subject>Oligonucleotide Array Sequence Analysis - standards</subject><subject>PBS</subject><subject>phosphate buffer saline</subject><subject>photomultiplier tube</subject><subject>PMT</subject><subject>Protozoa</subject><subject>QIMR</subject><subject>Queensland Institute of Medical Research</subject><subject>reverse transcriptase</subject><subject>Reverse Transcriptase Polymerase Chain Reaction</subject><subject>revolutions per minute</subject><subject>RNA, Helminth - analysis</subject><subject>RNA, Helminth - genetics</subject><subject>RNA, Messenger - analysis</subject><subject>RNA, Messenger - genetics</subject><subject>rpm</subject><subject>Schistosoma</subject><subject>Schistosoma japonicum</subject><subject>Schistosoma japonicum - genetics</subject><subject>Schistosoma japonicum - immunology</subject><subject>Schistosoma japonicum - physiology</subject><subject>Schistosoma mansoni</subject><subject>Schistosoma mansoni - genetics</subject><subject>Schistosoma mansoni - immunology</subject><subject>Schistosoma mansoni - physiology</subject><subject>second</subject><subject>Signal Transduction - genetics</subject><subject>sodium chloride/sodium phosphate/EDTA buffer</subject><subject>SSPE</subject><subject>TAE</subject><subject>Transcription, Genetic</subject><subject>Transcriptome</subject><subject>Trematoda</subject><subject>Tris/acetate/EDTA buffer</subject><subject>w/v</subject><subject>weight/volume</subject><issn>0014-4894</issn><issn>1090-2449</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2006</creationdate><recordtype>article</recordtype><recordid>eNqFkUFv1DAQhS0EotvCTwD5ArcN48RxnBNCFVCkShwoZ8txxl0vSRw8SUX_PV5tpB57msv33sy8x9g7AYUAoT4dC_w3zzbZogRQBVQFQPWC7QS0sC-lbF-yHYCQe6lbecEuiY4AoEUpX7MLoVQlGql2zN8lO5FLYV7iGBzxJcaB-5j4ckB-WEc78V_uEGiJFEfLuyHGnvth_YPEVwrTPc-yFG1K9pHf44Q835WQKMSJzyn6MGToDXvl7UD4dptX7Pe3r3fXN_vbn99_XH-53TvZwrLvoHFKCe3qzpa6gRKVs67va489lNJpqLH2lRNl46u6bRqtlWpa2QmwXS9tdcU-nn3z5r8r0mLGQA6HwU4YVzJKt42uQT0L5lBbaLXIYH0G85NECb2ZUxhtejQCzKkJczRbEyeRMlCZ3ETWvd8WrN2I_ZNqiz4DHzbAkrODzz24QE-cLmtVVSejz2cOc24PAZMhF3By2IeEbjF9DM-c8h87fquc</recordid><startdate>20061101</startdate><enddate>20061101</enddate><creator>Gobert, Geoffrey N.</creator><creator>McInnes, Russell</creator><creator>Moertel, Luke</creator><creator>Nelson, Charles</creator><creator>Jones, Malcolm K.</creator><creator>Hu, Wei</creator><creator>McManus, Donald P.</creator><general>Elsevier Inc</general><general>Elsevier</general><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>7QO</scope><scope>7TM</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20061101</creationdate><title>Transcriptomics tool for the human Schistosoma blood flukes using microarray gene expression profiling</title><author>Gobert, Geoffrey N. ; McInnes, Russell ; Moertel, Luke ; Nelson, Charles ; Jones, Malcolm K. ; Hu, Wei ; McManus, Donald P.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c490t-b07c6618c5ba28702e6cacdd5fed024c805e5f3c127f359778866794b10abd4a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2006</creationdate><topic>Animals</topic><topic>Biological and medical sciences</topic><topic>Biomphalaria</topic><topic>CTP</topic><topic>Cy3</topic><topic>Cy5</topic><topic>cyanine3</topic><topic>cyanine5</topic><topic>cytidine 5′-triphosphate</topic><topic>Female</topic><topic>Fertility - genetics</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>GEML</topic><topic>Gene expression</topic><topic>gene expression markup language</topic><topic>Gene Expression Profiling - methods</topic><topic>Gene Expression Regulation - genetics</topic><topic>Gene Ontologies</topic><topic>Helminth</topic><topic>Host-Parasite Interactions - immunology</topic><topic>hours</topic><topic>In Situ Hybridization, Fluorescence</topic><topic>Invertebrates</topic><topic>Life cycle. Host-agent relationship. Pathogenesis</topic><topic>locally weighed scatter plot smoothing</topic><topic>LOWESS</topic><topic>Male</topic><topic>Mice</topic><topic>Microarray</topic><topic>min</topic><topic>minute</topic><topic>nanogram</topic><topic>Nemathelminthia. Plathelmintha</topic><topic>Oligonucleotide Array Sequence Analysis - methods</topic><topic>Oligonucleotide Array Sequence Analysis - standards</topic><topic>PBS</topic><topic>phosphate buffer saline</topic><topic>photomultiplier tube</topic><topic>PMT</topic><topic>Protozoa</topic><topic>QIMR</topic><topic>Queensland Institute of Medical Research</topic><topic>reverse transcriptase</topic><topic>Reverse Transcriptase Polymerase Chain Reaction</topic><topic>revolutions per minute</topic><topic>RNA, Helminth - analysis</topic><topic>RNA, Helminth - genetics</topic><topic>RNA, Messenger - analysis</topic><topic>RNA, Messenger - genetics</topic><topic>rpm</topic><topic>Schistosoma</topic><topic>Schistosoma japonicum</topic><topic>Schistosoma japonicum - genetics</topic><topic>Schistosoma japonicum - immunology</topic><topic>Schistosoma japonicum - physiology</topic><topic>Schistosoma mansoni</topic><topic>Schistosoma mansoni - genetics</topic><topic>Schistosoma mansoni - immunology</topic><topic>Schistosoma mansoni - physiology</topic><topic>second</topic><topic>Signal Transduction - genetics</topic><topic>sodium chloride/sodium phosphate/EDTA buffer</topic><topic>SSPE</topic><topic>TAE</topic><topic>Transcription, Genetic</topic><topic>Transcriptome</topic><topic>Trematoda</topic><topic>Tris/acetate/EDTA buffer</topic><topic>w/v</topic><topic>weight/volume</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Gobert, Geoffrey N.</creatorcontrib><creatorcontrib>McInnes, Russell</creatorcontrib><creatorcontrib>Moertel, Luke</creatorcontrib><creatorcontrib>Nelson, Charles</creatorcontrib><creatorcontrib>Jones, Malcolm K.</creatorcontrib><creatorcontrib>Hu, Wei</creatorcontrib><creatorcontrib>McManus, Donald P.</creatorcontrib><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>Biotechnology Research Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Experimental parasitology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Gobert, Geoffrey N.</au><au>McInnes, Russell</au><au>Moertel, Luke</au><au>Nelson, Charles</au><au>Jones, Malcolm K.</au><au>Hu, Wei</au><au>McManus, Donald P.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Transcriptomics tool for the human Schistosoma blood flukes using microarray gene expression profiling</atitle><jtitle>Experimental parasitology</jtitle><addtitle>Exp Parasitol</addtitle><date>2006-11-01</date><risdate>2006</risdate><volume>114</volume><issue>3</issue><spage>160</spage><epage>172</epage><pages>160-172</pages><issn>0014-4894</issn><eissn>1090-2449</eissn><coden>EXPAAA</coden><abstract>We report the design, fabrication, and validation of a microarray covering the majority of the
Schistosoma japonicum and
Schistosoma mansoni transcriptomes. The oligonucleotide microarray contains 12,166
S. mansoni and 7055
S. japonicum target sequences. A confidence threshold of ⩽0.001 (
P value) was used in all analyses. The cross hybridization potential of the microarray was representative of 10,362 probes detected in both channels, while 12,052 probes hybridised to
S. japonicum and 11,254 probes hybridised to
S. mansoni. Differential hybridisation consisted of 3422 probes to
S. mansoni mRNA and 3103 probes to
S. japonicum mRNA. Important biological functions, such as transport, metabolism, immune evasion and host–parasite immunological interplay, cell communication, and sexual maturation are represented on this microarray. This is the first microarray commercially manufactured for studying schistosomes, and the large size and verified quality of the resource demonstrate its power for characterising the schistosome transcriptome.</abstract><cop>San Diego, CA</cop><pub>Elsevier Inc</pub><pmid>16631746</pmid><doi>10.1016/j.exppara.2006.03.003</doi><tpages>13</tpages></addata></record> |
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| ispartof | Experimental parasitology, 2006-11, Vol.114 (3), p.160-172 |
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| subjects | Animals Biological and medical sciences Biomphalaria CTP Cy3 Cy5 cyanine3 cyanine5 cytidine 5′-triphosphate Female Fertility - genetics Fundamental and applied biological sciences. Psychology GEML Gene expression gene expression markup language Gene Expression Profiling - methods Gene Expression Regulation - genetics Gene Ontologies Helminth Host-Parasite Interactions - immunology hours In Situ Hybridization, Fluorescence Invertebrates Life cycle. Host-agent relationship. Pathogenesis locally weighed scatter plot smoothing LOWESS Male Mice Microarray min minute nanogram Nemathelminthia. Plathelmintha Oligonucleotide Array Sequence Analysis - methods Oligonucleotide Array Sequence Analysis - standards PBS phosphate buffer saline photomultiplier tube PMT Protozoa QIMR Queensland Institute of Medical Research reverse transcriptase Reverse Transcriptase Polymerase Chain Reaction revolutions per minute RNA, Helminth - analysis RNA, Helminth - genetics RNA, Messenger - analysis RNA, Messenger - genetics rpm Schistosoma Schistosoma japonicum Schistosoma japonicum - genetics Schistosoma japonicum - immunology Schistosoma japonicum - physiology Schistosoma mansoni Schistosoma mansoni - genetics Schistosoma mansoni - immunology Schistosoma mansoni - physiology second Signal Transduction - genetics sodium chloride/sodium phosphate/EDTA buffer SSPE TAE Transcription, Genetic Transcriptome Trematoda Tris/acetate/EDTA buffer w/v weight/volume |
| title | Transcriptomics tool for the human Schistosoma blood flukes using microarray gene expression profiling |
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