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