ArticleBMC bioinformatics2006
Improvement in the reproducibility and accuracy of DNA microarray quantification by optimizing hybridization conditions.
Article in BMC bioinformatics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 37 citations in OpenAlex.
- Current Technologies and Recent Developments for Screening of HPV-Associated Cervical and Oropharyngeal Cancers.Cancers · 2016Review
- Ribosomal RNA depletion or exclusion has negligible effect on the detection of viruses in a pan viral microarray.Journal of virological methods · 2014Article
- Microarray-based RNA profiling of breast cancer: batch effect removal improves cross-platform consistency.BioMed research international · 2014Article
- Signal oscillation is another reason for variability in microarray-based gene expression quantification.PloS one · 2013Article
- Impact of the spotted microarray preprocessing method on fold-change compression and variance stability.BMC bioinformatics · 2011Article
- The impact of quantitative optimization of hybridization conditions on gene expression analysis.BMC bioinformatics · 2011Article
- Microarray meta-analysis database (M(2)DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database.BMC bioinformatics · 2010Article
- Washing scaling of GeneChip microarray expression.BMC bioinformatics · 2010Article
- Transcriptome for photobiological hydrogen production induced by sulfur deprivation in the green alga Chlamydomonas reinhardtii.Eukaryotic cell · 2008Article
- Proceedings of the Fourth Annual Conference of the MidSouth Computational Biology and Bioinformatics Society.BMC bioinformatics · 2007Article
- Optimization of cDNA microarrays procedures using criteria that do not rely on external standards.BMC genomics · 2007Article
- Interferon-mediated immunopathological events are associated with atypical innate and adaptive immune responses in patients with severe acute respiratory syndrome.Journal of virology · 2007Article
- Review of the literature examining the correlation among DNA microarray technologies.Environmental and molecular mutagenesis · 2007Review
- Elimination of laboratory ozone leads to a dramatic improvement in the reproducibility of microarray gene expression measurements.BMC biotechnology · 2007Article
- Revision of the nonequilibrium thermal dissociation and stringent washing approaches for identification of mixed nucleic acid targets by microarrays.Nucleic acids research · 2007Article
- Proceedings of the Third Annual Conference of the MidSouth Computational Biology and Bioinformatics Society. Introduction.BMC bioinformatics · 2006Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDNA microarrays, which have been increasingly used to monitor mRNA transcripts at a global level, can provide detailed insight into cellular processes involved in response to drugs and toxins. This is leading to new understandings of signaling networks that operate in the cell, and the molecular basis of diseases. Custom printed oligonucleotide arrays have proven to be an effective way to facilitate the applications of DNA microarray technology. A successful microarray experiment, however, involves many steps: well-designed oligonucleotide probes, printing, RNA extraction and labeling, hybridization, and imaging. Optimization is essential to generate reliable microarray data.
resultsHybridization and washing steps are crucial for a successful microarray experiment. By following the hybridization and washing conditions recommended by an oligonucleotide provider, it was found that the expression ratios were compressed greater than expected and data analysis revealed a high degree of non-specific binding. A series of experiments was conducted using rat mixed tissue RNA reference material (MTRRM) and other RNA samples to optimize the hybridization and washing conditions. The optimized hybridization and washing conditions greatly reduced the non-specific binding and improved the accuracy of spot intensity measurements.
conclusionThe results from the optimized hybridization and washing conditions greatly improved the reproducibility and accuracy of expression ratios. These experiments also suggested the importance of probe designs using better bioinformatics approaches and the need for common reference RNA samples for platform performance evaluation in order to fulfill the potential of DNA microarray technology.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.