. Author manuscript; available in PMC: 2013 Dec 30.

Published in final edited form as: Methods. 2012 Nov 5;58(3):10.1016/j.ymeth.2012.10.011. doi: 10.1016/j.ymeth.2012.10.011

Table 4.

Example of a controlled 5C annealing reaction^*.

Ligation number	Sample name	^** Volume of 3C library (µl)	Volume of wate (µl)	Salmon testes DNA (1 µg/µl) (µl)	5C primer master mix (µl)
1	^*** Cellular 5C	2.5	4.6	0.9	2.0
2	Cellular 5C “no ligase”	2.5	4.6	0.9	2.0
3	Control “no template”	0	7.1	0.9	2.0
4	Cellular 5C “no 5C primers”	2.5	6.6	0.9	0

Total annealing volume is 10 µl. We do annealing in 20uL volume in 1X NEBuffer 4, NEB

^**

Based on a 3C library concentration of 240 ng/ul and an optimal amount of 600 ng

^***

More than one cellular 5C library will be required for analysis with either DNA sequencing or onto microarrays. This number should be adjusted based onto the 5C library complexity and desired sequencing depth. Consult Table 5 to select a number of reactions.