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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   
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)