Journal: BMC Research Notes

Article Title: Development and application of a microarray meter tool to optimize microarray experiments

doi: 10.1186/1756-0500-1-45

Figure Lengend Snippet: A: Coefficient of variation (CV) in probe signal intensities on cDNA microarrays . printed with (a) BioRobotics Microgrid II equipped with MicroSpot 10 K pins, (b) QArrayMini equipped with Telechem ChipMaker Pins, and (c) Molecular Dynamics GenIII spotter. The microarray meter probes were printed from stocks at 200, 20 and 2 ng/μl as described in the text with every capillary pin. B: Signal dynamic range analysis (cDNA microarrays) . The signal intensities derived from hybridization of Cy5 labeled dynamic range spikes to increasing concentrations of complementary array probes (2, 20 and 200 ng/μl) was determined and plotted against the abundance of a particular sequence (expressed as an arbitrary copy number) in the hybridization reaction. C: Coefficient of variation (CV) in probe signal intensities on oligonucleotide microarrays printed with (a) Molecular Dynamics GenIII spotter and (b) QArrayMini equipped with Telechem ChipMaker Pins. The microarray meter probes were printed from oligonucleotide stocks at 200, 20 and 2 ng/μl as described in the text with every capillary pin. D: Signal dynamic range analysis (oligonucleotide microarrays) . The signal intensities derived from hybridization of Cy5 labeled dynamic range spikes to increasing concentrations of complementary array probes was determined and plotted against the abundance of a particular sequence (expressed as an arbitrary copy number) in the hybridization reaction. For the CV analysis presented in A and C , each robot's 12 pins printed 7 probes at the three different dilutions as 8 replicate spots on a slide. The mean values of the variation observed with each probe across all pins are represented as bars. The error bars denote one standard deviation. Data are plotted on a logarithmic scale in C and D . Each data point represents the mean of 96 measurements, (each of the 12 pins printed 8 replicate spots per probe per slide).

Article Snippet: The CV for each pin across all 7 probes at each dilution range was examined and values were determined to be lowest for the Molecular Dynamics GenIII spotter/GenIII pins (mean, 4.8%), followed by the BioRobotics MicroGrid II/MicroSpot 10 K pins (mean, 7.1%) and the QArrayMini/ChipMaker pins (mean, 11.8%).

Techniques: Microarray, Derivative Assay, Hybridization, Labeling, Sequencing, Standard Deviation