Table 2.

Troubleshooting table.

Step	Problem	Possible reason	Solution
11	Low chromosome yield	Low mitotic index	Optimize incubation time with metaphase- arresting drug
		Undissociated chromosome clusters	Extend vortexing time or syringe the suspension to release the chromosomes into suspension
18	High percentage of debris	Check pH of hypotonic solution and polyamine isolation buffer	Replace reagents (Hypotonic and polyamine isolation buffer)
		Chromosome fragmentation due to physical force	Reduce vortexing time
	Poor data resolution	Insufficient staining time	Extend fluorescence dyes staining time
		Effect from sodium sulfite and sodium citrate	Omit either reagent
30	Low yield after GenomePlex WGA	Derivative chromosome DNA is degraded or was considerably < 10 ng	Increase the amount of input DNA
		Fragmentation time was not optimal	A 4-min fragmentation time is crucial
	Negative control produced a product	Reagents contaminated	Replace reagents
47	Flow through is brightly colored and the membrane has retained only a small amount of color	Cleanup column membrane failed	Retrieve the sample by putting flow through back into a new column and clean up as described in the protocol
54	Low yield and low SA after labeling	Klenow inactive	Test reagents
83	No fluorescent signal on microarray	Check the slide was in the correct orientation during hybridization	Repeat experiment
	Low signal	Poor atmospheric conditions	Monitor the ozone levels, temperature and humidity in the laboratory where the experiment was conducted and, in particular, in the proximity of the scanner