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Library on a slide for bacterial comparative genomics
BACKGROUND: 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 ge...
Autores principales: | , , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2004
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC394321/ https://www.ncbi.nlm.nih.gov/pubmed/15035675 http://dx.doi.org/10.1186/1471-2180-4-12 |
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author | Zhang, Lixin Srinivasan, Usha Marrs, Carl F Ghosh, Debashis Gilsdorf, Janet R Foxman, Betsy |
author_facet | Zhang, Lixin Srinivasan, Usha Marrs, Carl F Ghosh, Debashis Gilsdorf, Janet R Foxman, Betsy |
author_sort | Zhang, Lixin |
collection | PubMed |
description | BACKGROUND: 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. RESULTS: 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 E. coli reference collection array and probed it for the presence or absence of the hemolysin (hly) gene using a dual channel non-competing hybridization strategy. Results from the array hybridization matched perfectly with previous tests. CONCLUSIONS: 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. |
format | Text |
id | pubmed-394321 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2004 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-3943212004-04-22 Library on a slide for bacterial comparative genomics Zhang, Lixin Srinivasan, Usha Marrs, Carl F Ghosh, Debashis Gilsdorf, Janet R Foxman, Betsy BMC Microbiol Methodology Article BACKGROUND: 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. RESULTS: 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 E. coli reference collection array and probed it for the presence or absence of the hemolysin (hly) gene using a dual channel non-competing hybridization strategy. Results from the array hybridization matched perfectly with previous tests. CONCLUSIONS: 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. BioMed Central 2004-03-22 /pmc/articles/PMC394321/ /pubmed/15035675 http://dx.doi.org/10.1186/1471-2180-4-12 Text en Copyright © 2004 Zhang et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL. |
spellingShingle | Methodology Article Zhang, Lixin Srinivasan, Usha Marrs, Carl F Ghosh, Debashis Gilsdorf, Janet R Foxman, Betsy Library on a slide for bacterial comparative genomics |
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 |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC394321/ https://www.ncbi.nlm.nih.gov/pubmed/15035675 http://dx.doi.org/10.1186/1471-2180-4-12 |
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