Skip to main content
. Author manuscript; available in PMC: 2015 Dec 1.
Published in final edited form as: Methods. 2014 Sep 8;70(0):89–96. doi: 10.1016/j.ymeth.2014.08.018

Table 3.

DNA yield and antibody efficiency. d

Antibody H3K9ac (10 min fixation) H3K14ac RNA pol II Negative
Sample Clean Up (50 ul) IP Sup* Clean Up (50 ul) IP Sup Input (10 ul) IP Sup Input (10 ul) IP Sup
DNA (ng/ul) 47.3 1.23 16.6 48.6 0.057 44.55 24.4 1.475 55.72 24.4 0.84 50.68
DNA (ng) 1892 12.3 664 1944 0.57 1782 976 14.75 2229 976 8.4 2027
Theoretical per IP ug 5.12 1.80 5.27 4.83 6.04 5.49
d

Four different antibodies have been utilized for IP. H3K9ac, (ab10812) H3K14ac (ac46984), RNA pol II (Active Motif 39097), and a negative antibody (Active Motif 53026) were used to pull down DNA from MDM. The samples are from the clean-up step (Section 2.6), or input (Section 2.7), the IP, and the supernatant. The clean-up and input samples are directly from the stock solution of chromatin; they are simply different proportions of the stock solution. The concentrations for the input and IP samples were measured by the Qubit®, while the clean-up and supernatant samples were measured by the NanoDrop. Theoretical per IP is the amount of DNA that could be obtained from each IP tube; there are six tubes per 20 ×106 MDM.

*

Sup- Supernatant