TY - JOUR
T1 - A microarray platform comparison for neuroscience applications
AU - Parrish, Mark L.
AU - Wei, Nan
AU - Duenwald, Sven
AU - Tokiwa, George Y.
AU - Wang, Yanqun
AU - Holder, Daniel
AU - Dai, Hongyue
AU - Zhang, Xiaohua
AU - Wright, Christopher
AU - Hodor, Paul
AU - Cavet, Guy
AU - Phillips, Robert L.
AU - Sun, Benjamin I.
AU - Fare, Thomas L.
PY - 2004/1/15
Y1 - 2004/1/15
N2 - To address the need for high sensitivity in gene expression profiling of small neural tissue samples (~100ng total RNA), we compared a novel RT-PCR-IVT protocol using fluor-reverse pairs on inkjet oligonucleotide microarrays and an RT-IVT protocol using 33P labeling on nylon cDNA arrays. The comparison protocol was designed to evaluate these systems for sensitivity, specificity, reproducibility, and linearity. We developed parameters, thresholds, and testing conditions that could be used to differentiate various systems that spanned detection chemistry and instrumentation; probe number and selection criteria; and sample processing protocols. We concluded that the inkjet system had better performance in sensitivity, specificity, and reproducibility than the nylon system, and similar performance in linearity. Between these two platforms, the data indicates that the inkjet system would perform better for the transcriptional profiling of 100ng total RNA samples for neuroscience studies.
AB - To address the need for high sensitivity in gene expression profiling of small neural tissue samples (~100ng total RNA), we compared a novel RT-PCR-IVT protocol using fluor-reverse pairs on inkjet oligonucleotide microarrays and an RT-IVT protocol using 33P labeling on nylon cDNA arrays. The comparison protocol was designed to evaluate these systems for sensitivity, specificity, reproducibility, and linearity. We developed parameters, thresholds, and testing conditions that could be used to differentiate various systems that spanned detection chemistry and instrumentation; probe number and selection criteria; and sample processing protocols. We concluded that the inkjet system had better performance in sensitivity, specificity, and reproducibility than the nylon system, and similar performance in linearity. Between these two platforms, the data indicates that the inkjet system would perform better for the transcriptional profiling of 100ng total RNA samples for neuroscience studies.
KW - Expression profiling
KW - Microarray
KW - Nylon membrane
KW - Platform comparison
KW - Receiver operator characteristic
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U2 - 10.1016/j.jneumeth.2003.09.013
DO - 10.1016/j.jneumeth.2003.09.013
M3 - Article
C2 - 14687675
AN - SCOPUS:10744221835
SN - 0165-0270
VL - 132
SP - 57
EP - 68
JO - Journal of Neuroscience Methods
JF - Journal of Neuroscience Methods
IS - 1
ER -