Library on a slide for bacterial comparative genomics
<p>Abstract</p> <p>Background</p> <p>We describe a novel application of microarray technology for comparative genomics of bacteria in which libraries of entire genomes rather than the sequence of a single genome or sets of genes are arrayed on the slide and then probed...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2004-03-01
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| Series: | BMC Microbiology |
| Online Access: | http://www.biomedcentral.com/1471-2180/4/12 |
| _version_ | 1818443636769030144 |
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| author | Gilsdorf Janet R Ghosh Debashis Marrs Carl F Srinivasan Usha Zhang Lixin Foxman Betsy |
| author_facet | Gilsdorf Janet R Ghosh Debashis Marrs Carl F Srinivasan Usha Zhang Lixin Foxman Betsy |
| author_sort | Gilsdorf Janet R |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>We describe a novel application of microarray technology for comparative genomics of bacteria in which libraries of entire genomes rather than the sequence of a single genome or sets of genes are arrayed on the slide and then probed for the presence or absence of specific genes and/or gene alleles.</p> <p>Results</p> <p>We first adopted a 96-well high throughput working protocol to efficiently isolate high quality genomic DNA. We then optimized conditions to print genomic DNA onto a glass slide with high density (up to 15000 spots) and to sensitively detect gene targets in each genome spot using fluorescently labeled DNA probe. Finally, we created an <it>E. coli </it>reference collection array and probed it for the presence or absence of the hemolysin (<it>hly</it>) gene using a dual channel non-competing hybridization strategy. Results from the array hybridization matched perfectly with previous tests.</p> <p>Conclusions</p> <p>This new form of microarray technology, Library on a Slide, is an efficient way for sharing and utilizing large strain collections in comparative genomic analyses.</p> |
| first_indexed | 2024-12-14T19:03:12Z |
| format | Article |
| id | doaj.art-b32a226abe4f4a82ae1ffdf7927f0766 |
| institution | Directory Open Access Journal |
| issn | 1471-2180 |
| language | English |
| last_indexed | 2024-12-14T19:03:12Z |
| publishDate | 2004-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Microbiology |
| spelling | doaj.art-b32a226abe4f4a82ae1ffdf7927f07662022-12-21T22:50:55ZengBMCBMC Microbiology1471-21802004-03-01411210.1186/1471-2180-4-12Library on a slide for bacterial comparative genomicsGilsdorf Janet RGhosh DebashisMarrs Carl FSrinivasan UshaZhang LixinFoxman Betsy<p>Abstract</p> <p>Background</p> <p>We describe a novel application of microarray technology for comparative genomics of bacteria in which libraries of entire genomes rather than the sequence of a single genome or sets of genes are arrayed on the slide and then probed for the presence or absence of specific genes and/or gene alleles.</p> <p>Results</p> <p>We first adopted a 96-well high throughput working protocol to efficiently isolate high quality genomic DNA. We then optimized conditions to print genomic DNA onto a glass slide with high density (up to 15000 spots) and to sensitively detect gene targets in each genome spot using fluorescently labeled DNA probe. Finally, we created an <it>E. coli </it>reference collection array and probed it for the presence or absence of the hemolysin (<it>hly</it>) gene using a dual channel non-competing hybridization strategy. Results from the array hybridization matched perfectly with previous tests.</p> <p>Conclusions</p> <p>This new form of microarray technology, Library on a Slide, is an efficient way for sharing and utilizing large strain collections in comparative genomic analyses.</p>http://www.biomedcentral.com/1471-2180/4/12 |
| spellingShingle | Gilsdorf Janet R Ghosh Debashis Marrs Carl F Srinivasan Usha Zhang Lixin Foxman Betsy Library on a slide for bacterial comparative genomics BMC Microbiology |
| title | Library on a slide for bacterial comparative genomics |
| title_full | Library on a slide for bacterial comparative genomics |
| title_fullStr | Library on a slide for bacterial comparative genomics |
| title_full_unstemmed | Library on a slide for bacterial comparative genomics |
| title_short | Library on a slide for bacterial comparative genomics |
| title_sort | library on a slide for bacterial comparative genomics |
| url | http://www.biomedcentral.com/1471-2180/4/12 |
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