2004
DOI: 10.1093/nar/gnh099
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Optimization of probe length and the number of probes per gene for optimal microarray analysis of gene expression

Abstract: Gene-specific oligonucleotide probes are currently used in microarrays to avoid cross-hybridization of highly similar sequences. We developed an approach to determine the optimal number and length of gene-specific probes for accurate transcriptional profiling studies. The study surveyed probe lengths from 25 to 1000 nt. Long probes yield better signal intensity than short probes. The signal intensity of short probes can be improved by addition of spacers or using higher probe concentration for spotting. We als… Show more

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Cited by 170 publications
(157 citation statements)
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“…Lengthening the probe sequences on the 2 nd generation chip by between 18 to 25 nucleotides increased the signal intensity, which has been reported previously by Chou et al (2004). However, a number of non-specific cross-hybridisation was observed with the initial 1 st generation 58 °C hybridisation temperature step .…”
Section: Cross Reactivity Testing: Microarraysupporting
confidence: 83%
See 2 more Smart Citations
“…Lengthening the probe sequences on the 2 nd generation chip by between 18 to 25 nucleotides increased the signal intensity, which has been reported previously by Chou et al (2004). However, a number of non-specific cross-hybridisation was observed with the initial 1 st generation 58 °C hybridisation temperature step .…”
Section: Cross Reactivity Testing: Microarraysupporting
confidence: 83%
“…The reason why there was extensive cross reactivity observed in the 1 st generation microarray may be that the oligonucleotides routinely used for FISH hybridisation were too short, produced weak signal intensities or that the probes had inaccessible secondary structures to achieve specific hybridisation reactions in a microarray format (Chou et al 2004;Metfies and Medlin 2008a). Lengthening the probe sequences on the 2 nd generation chip by between 18 to 25 nucleotides increased the signal intensity, which has been reported previously by Chou et al (2004).…”
Section: Cross Reactivity Testing: Microarraymentioning
confidence: 99%
See 1 more Smart Citation
“…The low signal-to-noise ratio often seen in microarray experiments can generally be improved by synthesizing multiple copies of the (same) probe. Chou et al [60] showed that accurate gene-expression measurement can be achieved with multiple probes per gene, and fewer probes are needed if longer probes rather than shorter probes are used. To further reduce error, standards for reporting microarray data have been established: minimum information about a microarray experiment (MI-AME) [61].…”
Section: Discussionmentioning
confidence: 99%
“…In contrast to dsDNA microarray probes, the length of oligonucleotide probes usually ranges from 20 to 80 nucleotides. Use of shorter probe lengths increases the microarray specificity and enables efficient detection of minor genetic changes between the probe and target (Chou et al, 2004). For more efficient attachment of oligonucleotide probes to the functional groups on the surface of chemically activated glass slides (usually aldehyde, epoxy, and succinimide groups), the 5' or 3' end of the probes contain primary amino groups introduced during chemical synthesis.…”
mentioning
confidence: 99%