Table 1

Controls for ChIP and QPCR
Controls	Primers sets to test	Purpose

(a) Controls for ChIP
Input Sample	All primer sets	Positive control for presence of chromatin, used to calculate %IP
No Antibody control	All primer sets	Determines background signal level

(b) Controls for QPCR
Calibration line	All primer sets	Positive control for QPCR, used for quantification of QPCR signals
Melting curve	All primer sets	Tests for amplification of the correct fragment
No-template PCR	All primer sets	Negative control for QPCR, indicates primer artifacts

(c) Controls for data interpretation
ChIP control (+)	Control gene primer set	Positive control for ChIP (e.g. actin for H3K4me2)
ChIP control (-)	Control gene primer set	Negative control for ChIP (e.g. actin for H3K9me2)

Haring et al. Plant Methods 2007 3:11 doi:10.1186/1746-4811-3-11