A microarray platform comparison for neuroscience applications.
To address the need for high sensitivity in gene expression profiling of small neural tissue samples ( approximately 100 ng 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 100 ng total RNA samples for neuroscience studies.
Parrish
Mark L
ML
Rosetta Inpharmatics LLC, a wholly owned subsidiary Merck & Co. Inc., Kirkland, WA 98034, USA. mark_parrish@merck.com
Wei
Nan
N
Duenwald
Sven
S
Tokiwa
George Y
GY
Wang
Yanqun
Y
Holder
Daniel
D
Dai
Hongyue
H
Zhang
Xiaohua
X
Wright
Christopher
C
Hodor
Paul
P
Cavet
Guy
G
Phillips
Robert L
RL
Sun
Benjamin I
BI
Fare
Thomas L
TL
D000818:Animals; D001921:Brain / Q000033:anatomy & histology / Q000378:metabolism; D020869:Gene Expression Profiling; D017403:In Situ Hybridization; D007281:Ink; D016014:Linear Models; D051379:Mice; D009488:Neurosciences / Q000379:methods*; D009757:Nylons; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010759:Phosphorus Isotopes / Q000378:metabolism; D012313:RNA; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods; D012680:Sensitivity and Specificity
D009757:Nylons; D010759:Phosphorus Isotopes; D012313:RNA