PT  - JOURNAL ARTICLE
AU  - Michele Busby
AU  - Cathy Xue
AU  - Yossi Farjoun
AU  - Elizabeth Gienger
AU  - Ido Yofe
AU  - Adrianne Gladden
AU  - Chad Nusbaum
AU  - Alon Goren
TI  - Systematic comparison of monoclonal versus polyclonal antibodies for mapping histone modifications by ChIP-seq
AID  - 10.1101/054387
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 054387
4099  - http://biorxiv.org/content/early/2016/05/19/054387.short
4100  - http://biorxiv.org/content/early/2016/05/19/054387.full
AB  - The robustness of ChIP-seq datasets is highly dependent upon the antibodies used. Currently, polyclonal antibodies are the standard despite several limitations: they are non-renewable, vary in performance between lots, and need to be validated with each new lot. In contrast, monoclonal antibody lots are renewable and provide consistent performance. To increase ChIP-seq standardization, we investigated whether monoclonal antibodies could replace polyclonal antibodies. We compared monoclonal antibodies that target five key histone modifications (H3K4me1, H3K4me3, H3K9me3, H3K27ac and H3K27me3) to their polyclonal counterparts. Overall performance was highly similar for four monoclonal/polyclonal pairs. In contrast, the binding patterns for H3K27ac differed substantially between polyclonal and monoclonal antibodies. However, this was most likely due to the distinct immunogen used rather than the clonality of the antibody. Altogether, we found that monoclonal antibodies as a class perform as well as polyclonal antibodies. Accordingly, we recommend the use of monoclonal antibodies in ChIP-seq experiments.