ArticleBMC genomics2003
A novel design of whole-genome microarray probes for Saccharomyces cerevisiae which minimizes cross-hybridization.
Article in BMC genomics, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers, 1 of them a synthesis that pooled it.
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17 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Strengthening insights into host responses to mastitis infection in ruminants by combining heterogeneous microarray data sources.BMC genomics · 2011Pooled it
- Insights into the Quorum Sensing Regulon of the Acidophilic Acidithiobacillus ferrooxidans Revealed by Transcriptomic in the Presence of an Acyl Homoserine Lactone Superagonist Analog.Frontiers in microbiology · 2016Article
- BOND: Basic OligoNucleotide Design.BMC bioinformatics · 2013Article
- Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments.Silence · 2011Article
- An evaluation of custom microarray applications: the oligonucleotide design challenge.Nucleic acids research · 2009Article
- In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation.BMC bioinformatics · 2007Article
- Effect of 21 different nitrogen sources on global gene expression in the yeast Saccharomyces cerevisiae.Molecular and cellular biology · 2007Article
- An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes.Nucleic acids research · 2006Article
- A multivariate prediction model for microarray cross-hybridization.BMC bioinformatics · 2006Article
- Expression profiling of laser-microdissected intrapulmonary arteries in hypoxia-induced pulmonary hypertension.Respiratory research · 2005Article
- Multiple locus linkage analysis of genomewide expression in yeast.PLoS biology · 2005Article
- Comparison of transcript profiling on Arabidopsis microarray platform technologies.Plant molecular biology · 2005Article
- A generic approach for the design of whole-genome oligoarrays, validated for genomotyping, deletion mapping and gene expression analysis on Staphylococcus aureus.BMC genomics · 2005Article
- The landscape of genetic complexity across 5,700 gene expression traits in yeast.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
- CYGD: the Comprehensive Yeast Genome Database.Nucleic acids research · 2005Article
- Methods for transcriptional profiling in plants. Be fruitful and replicate.Plant physiology · 2004Review
- Large-scale exploration of growth inhibition caused by overexpression of genomic fragments in Saccharomyces cerevisiae.Genome biology · 2004Article
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundNumerous DNA microarray hybridization experiments have been performed in yeast over the last years using either synthetic oligonucleotides or PCR-amplified coding sequences as probes. The design and quality of the microarray probes are of critical importance for hybridization experiments as well as subsequent analysis of the data.
resultsWe present here a novel design of Saccharomyces cerevisiae microarrays based on a refined annotation of the genome and with the aim of reducing cross-hybridization between related sequences. An effort was made to design probes of similar lengths, preferably located in the 3'-end of reading frames. The sequence of each gene was compared against the entire yeast genome and optimal sub-segments giving no predicted cross-hybridization were selected. A total of 5660 novel probes (more than 97% of the yeast genes) were designed. For the remaining 143 genes, cross-hybridization was unavoidable. Using a set of 18 deletant strains, we have experimentally validated our cross-hybridization procedure. Sensitivity, reproducibility and dynamic range of these new microarrays have been measured. Based on this experience, we have written a novel program to design long oligonucleotides for microarray hybridizations of complete genome sequences.
conclusionsA validated procedure to predict cross-hybridization in microarray probe design was defined in this work. Subsequently, a novel Saccharomyces cerevisiae microarray (which minimizes cross-hybridization) was designed and constructed. Arrays are available at Eurogentec S. A. Finally, we propose a novel design program, OliD, which allows automatic oligonucleotide design for microarrays. The OliD program is available from authors.
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