Cross peak biological samples

Biological replication and appropriate controls are essential to ChIP experiments to assess reproducibility because of the nonrandom shearability of DNA and off-target effects of enrichment. A minimum of two replicates are recommended for both experimental and control samples. Control samples consist of two types a library consisting of formaldehyde-treated and -sheared DNA without antibody (input control) and a library where nonspecific, nonnuclear antibody is used for enrichment to the cross-linked DNA (mock library). Peaks in mapped reads from the enrichment library can be compared to peaks found from mapped reads control libraries to separate real and falsepositive peaks (Figure 4A). 

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