title: A microarray platform comparison for neuroscience applications.
abstract: 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.
authors.affiliation: Rosetta Inpharmatics LLC, a wholly owned subsidiary Merck & Co. Inc., Kirkland, WA 98034, USA. mark_parrish@merck.com
authors.forename: Mark L
authors.initials: ML
authors.lastname: Parrish
authors.forename: Nan
authors.initials: N
authors.lastname: Wei
authors.forename: Sven
authors.initials: S
authors.lastname: Duenwald
authors.forename: George Y
authors.initials: GY
authors.lastname: Tokiwa
authors.forename: Yanqun
authors.initials: Y
authors.lastname: Wang
authors.forename: Daniel
authors.initials: D
authors.lastname: Holder
authors.forename: Hongyue
authors.initials: H
authors.lastname: Dai
authors.forename: Xiaohua
authors.initials: X
authors.lastname: Zhang
authors.forename: Christopher
authors.initials: C
authors.lastname: Wright
authors.forename: Paul
authors.initials: P
authors.lastname: Hodor
authors.forename: Guy
authors.initials: G
authors.lastname: Cavet
authors.forename: Robert L
authors.initials: RL
authors.lastname: Phillips
authors.forename: Benjamin I
authors.initials: BI
authors.lastname: Sun
authors.forename: Thomas L
authors.initials: TL
authors.lastname: Fare
mesh_terms: 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
chemical_list: D009757:Nylons; D010759:Phosphorus Isotopes; D012313:RNA