Expression Array Detection
Troubleshooting Guide

3DNA Array 900, Array 350 and Array 50 V2 Kits
	Section I. Troubleshooting: General Recommendations   Section II. Procedural Problems   1. Unable to carry out reverse transcription reaction in     recommended volume.   2. Microcon column: low volume or no volume recovered.   3. Microcon column: reservoir collapsed into collection tube     during elution spin.   4. EtOH precipitation: no visible pellet.   5. Formation of bubbles under coverslip.   6. Coverslip stuck to array surface   Section III. Background Porblems   1. High, uniform background.   2. High, nonuniform background.   3. Grainy background.   4. Array coating damage.   5. Visible haze on array surface.     Section IV. Signal Problems   1. Low/absent signal in both channels.   2. Low/absent signal in one channel.   3. Uneven signal across array.     Section V. Data Problems   1. Strong signal/poor differential.   2. False positives.   3. Poor spot morphology.   4. Poor reproducibility.     Appendix A. RNA Gels     Appendix B. cDNA Gels     Appendix C. Hybridization Volume/Coverslip Table and Microarray Loading Technique
The Complete 3DNA Troubleshooting Guide in Acrobat PDF Format. ( Array 900, Array 350 and Array 50 V2 Kits )
3DNA Array 900MPX and Array 350RP Kits
	Section I. Troubleshooting: General Recommendations   Section II. Procedural Problems   1. Unable to carry out reverse transcription reaction in     recommended volume.   2. Excessive elution volume (Qiagen clean-up columns).   3. Low elution volume (Qiagen clean-up columns).   4. Microcon column: low volume or no volume recovered.   5. Microcon column: reservoir collapsed into collection tube     during elution spin.   6. EtOH precipitation: no visible pellet.   7. Formation of bubbles under coverslip.   8. Coverslip stuck to array surface (either cDNA or 3DNA washes).     Section III. Background Problems   1. High, uniform background.   2. High, nonuniform background.   3. Grainy background.   4. Array coating damage.   5. Visible haze on array surface.     Section IV. Signal Problems   1. Low/absent signal in both channels.   2. Low/absent signal in one channel.   3. Uneven signal across array.     Section V. Data Problems   1. Strong signal/poor differential.   2. False positives.   3. Poor spot morphology.   4. Poor reproducibility.   5. Low correlation with dT data.     Appendix A. RNA Gels     Appendix B. cDNA Gels     Appendix C. Hybridization Volume/Coverslip Table and Microarray Loading Technique
	The Complete 3DNA Troubleshooting Guide in Acrobat PDF Format. (Array 900MPX and Array 350RP Kits)