Development of a Microarray Meter

Abstract

Background:

Successful microarray experimentation requires a complex interplay between the slide chemistry, the printing pins, the nucleic acid probes and targets, and the hybridization milieu. Optimization of these parameters and a careful evaluation of emerging slide chemistries are a prerequisite to any large scale array fabrication effort. We have developed a microarray meter tool which assesses the inherent variation associated with microarray measurements prior to embarking on large scale projects.

Results:

The microarray meter consists of nucleic acid target (reference and dynamic range control) and probe components. Two different designs containing identical probe material were formulated to accommodate different robotic and pin designs. We examined the variability in probe quality and quantity (as judged by the amount of DNA printed and remaining post-hybridization) using three robots equipped with capillary printing pins.

Conclusions:

Generation of microarray data with minimal variation requires consistent quality control of the (DNA microarray) manufacturing and experimental processes. Spot reproducibility is a measure primarily of the variation associated with printing. The microarray meter assesses array quality by measuring the DNA content for every feature. It provides a post-hybridization analysis of array quality by scoring probe performance using three metrics, a) a measure of variability in the signal intensities, b) a measure of variability of the spot morphologies, and c) a measure of the signal dynamic range.

Notes and Figures

• Rouse_et_al_manuscript.pdf
• Rouse_et_al_SUPPLEMENTAL_figures.pdf
• GH_note_figures.pdf
• Rouse_et_al_Tables.pdf