Table 4.

A recipe for TAG-array PCR.

Ingredient	Quantity
2 x Extaq premix (Takara, RR003)	30 μl
Primer mixture	3 μl
Genomic DNA template (~200 ng/μl)	1 μl
MilliQ water	26 μl
Total	60 μl
94°C 5′; 50 x (94°C 10″; 50°C 10″; 72°C 20″); hold at 4°C

Note: If multiple samples are to be analyzed simultaneously, one should make a master mixture excluding the template genomic DNA for each of the four types of PCR reactions: Uptag Cy5, Uptag Cy3, Downtag Cy5, and Downtag Cy3. Aliquots of the master mixture are then added to PCR tubes containing the individual template DNA samples, from which the TAGs are amplified.