Microarray data derived from WT-Pico amplified pan-neural samples are reproducible and enriched for neural genes. A-B. Pairwise comparisons of individual hybridizations. Coefficient of determination (R2) values for A., all pairwise combinations of reference hybridizations and for B., all pairwise combinations of larval pan-neural data sets are indicative of reproducible results for both reference and experimental samples. C. Scatter plot of intensity values (log2) for a representative hybridization (298-DMM-8) (red) isolated from all larval cells (reference) compared to the average intensity of the reference data set (green). D. Scatter plot (log2) of representative pan-neural hybridization (298-DMM-3) (red) compared to the average intensities for all five pan-neural hybridizations (green). E. A representative WT-Pico-amplified pan-neural sample (298-DMM-3) (red) compared to the average of WT-Pico amplified reference samples (green). F. A representative IVT-amplified pan-neural sample (DMW43) (red) compared to the average of IVT-amplified reference samples (green). R2 = Coefficient of determination. Selected genes enriched in both the WT-Pico-amplified and IVT-amplified pan-neural samples are: snb-1(synaptobrevin), flp-11 (neuropeptide); unc-30 (homeodomain trancription factor). Transcripts exclusively enriched in the WT-Pico sample include rpm-1 (E3 ubiquitin ligase) and pag-3 (Zn-finger transcription factor). The nicotinic acetylcholine receptor unc-38 is selectively enriched in the IVT data set. Examples of transcripts that are depleted in both pan-neural samples are: him-4 (hemicentin, body muscle), myo-2 (myosin heavy chain, pharyngeal muscle), myo-3 (myosin heavy chain, body wall muscle).
Watson et al. BMC Genomics 2008 9:84 doi:10.1186/1471-2164-9-84