Use of Microarrays with Different Probe Sizes for Monitoring GeneExpression

doi:https://doi.org/10.1128/AEM.71.9.5154-5162.2005

Title: Use of Microarrays with Different Probe Sizes for Monitoring GeneExpression

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Abstract

Microarrays with oligonucleotides of different lengths wereused to monitor gene expression at a whole-genome level. To determinewhat length of oligonucleotide is a better alternative to PCR-generatedprobes, the performance of oligonucleotide probes was systematicallycompared to that of their PCR-generated counterparts for 96 genes fromShewanella oneidensis MR-1 in terms of overall signal intensity, numbersof genes detected, specificity, sensitivity, and differential geneexpression under experimental conditions. Hybridizations conducted at42oC, 45oC, 50oC, and 60oC indicated that good sensitivities wereobtained at 45oC for oligonucleotide probes in the presence of 50 percentformamide, under which conditions specific signals were detected by bothPCR and oligonucleotide probes. Signal intensity increased as the lengthof the oligonucleotide probe increased, and the 70-mer oligonucleotideprobes produced signal intensities similar to the intensities obtainedwith the PCR probes and detected numbers of open reading frames similarto the numbers detected with the PCR probes. PCR amplicon, 70-mer,60-mer, and 50-mer arrays had detection sensitivities of 5.0, 25, 100,and 100 ng of genomic DNA, which were equivalent to approximately 1.9 x106, 9.2 x 106, 3.7 x 107, and 3.7 x 107 copies, respectively, when thearray was hybridized with genomic DNA. To evaluate differential geneexpression under experimental conditions, S. oneidensis MR-1 cells wereexposed to low- or high-pH conditions for 30more »« less

Authors:: He, Z; Wu, L; Fields, M; Zhou, J -Z

Publication Date:: 2005-03-22

Research Org.:: COLLABORATION - OakRidge

OSTI Identifier:: 903373

Report Number(s):: LBNL-60467
Journal ID: ISSN 0099-2240; AEMIDF; R&D Project: VGTLJK; BnR: KP1102010; TRN: US200720%%305

DOE Contract Number:: DE-AC02-05CH11231

Resource Type:: Journal Article

Journal Name:: Applied and Environmental Microbiology

Additional Journal Information:: Journal Volume: 71; Journal Issue: 9; Related Information: Journal Publication Date: Sept./2005; Journal ID: ISSN 0099-2240

Country of Publication:: United States

Language:: English

Subject:: 59; DETECTION; DNA; FORMAMIDE; GENES; MONITORING; MONITORS; OLIGONUCLEOTIDES; PERFORMANCE; PROBES; SENSITIVITY; SPECIFICITY; Microarrays

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                    He, Z, Wu, L, Fields, M, and Zhou, J -Z. Use of Microarrays with Different Probe Sizes for Monitoring GeneExpression.  United States: N. p., 2005. 
        Web.  doi:10.1128/AEM.71.9.5154-5162.2005.

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                    He, Z, Wu, L, Fields, M, & Zhou, J -Z. Use of Microarrays with Different Probe Sizes for Monitoring GeneExpression.  United States.  https://doi.org/10.1128/AEM.71.9.5154-5162.2005

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                    He, Z, Wu, L, Fields, M, and Zhou, J -Z. Tue .  
        "Use of Microarrays with Different Probe Sizes for Monitoring GeneExpression".  United States.  https://doi.org/10.1128/AEM.71.9.5154-5162.2005.

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@article{osti_903373,

  title        = {Use of Microarrays with Different Probe Sizes for Monitoring GeneExpression},

  author       = {He, Z and Wu, L and Fields, M and Zhou, J -Z},

  abstractNote = {Microarrays with oligonucleotides of different lengths wereused to monitor gene expression at a whole-genome level. To determinewhat length of oligonucleotide is a better alternative to PCR-generatedprobes, the performance of oligonucleotide probes was systematicallycompared to that of their PCR-generated counterparts for 96 genes fromShewanella oneidensis MR-1 in terms of overall signal intensity, numbersof genes detected, specificity, sensitivity, and differential geneexpression under experimental conditions. Hybridizations conducted at42oC, 45oC, 50oC, and 60oC indicated that good sensitivities wereobtained at 45oC for oligonucleotide probes in the presence of 50 percentformamide, under which conditions specific signals were detected by bothPCR and oligonucleotide probes. Signal intensity increased as the lengthof the oligonucleotide probe increased, and the 70-mer oligonucleotideprobes produced signal intensities similar to the intensities obtainedwith the PCR probes and detected numbers of open reading frames similarto the numbers detected with the PCR probes. PCR amplicon, 70-mer,60-mer, and 50-mer arrays had detection sensitivities of 5.0, 25, 100,and 100 ng of genomic DNA, which were equivalent to approximately 1.9 x106, 9.2 x 106, 3.7 x 107, and 3.7 x 107 copies, respectively, when thearray was hybridized with genomic DNA. To evaluate differential geneexpression under experimental conditions, S. oneidensis MR-1 cells wereexposed to low- or high-pH conditions for 30 and 60 min, and thetranscriptional profiles detected by oligonucleotide probes (50-mer,60-mer, and 70-mer) were closely correlated with those detected by thePCR probes. The results demonstrated that 70-mer oligonucleotides canprovide the performance most comparable to the performance obtained withPCR-generated probes.},

  doi          = {10.1128/AEM.71.9.5154-5162.2005},

  url          = {https://www.osti.gov/biblio/903373},
  journal      = {Applied and Environmental Microbiology},

  issn         = {0099-2240},

  number       = 9,

  volume       = 71,

  place        = {United States},

  year         = {2005},

  month        = {3}

}

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