Table 1 Controls for ChIP and QPCR
From: Chromatin immunoprecipitation: optimization, quantitative analysis and data normalization
Controls | Primers sets to test | Purpose |
|---|---|---|
(a) Controls for ChIP | Â | Â |
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 | Â | Â |
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 | Â | Â |
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) |