Ch IP-sequencing - Sensitivity

Sensitivity

Sensitivity of this technology depends on the depth of the sequencing run (i.e. the number of mapped sequence tags), the size of the genome and the distribution of the target factor. The sequencing depth is directly correlated with cost. If abundant binders in large genomes have to be mapped with high sensitivity, costs are high as an enormously high number of sequence tags will be required. This is in contrast to ChIP-chip in which the costs are not correlated with sensitivity.

Unlike microarray-based ChIP methods, the precision of the ChIP-seq assay is not limited by the spacing of predetermined probes. By integrating a large number of short reads, highly precise binding site localization is obtained. Compared to ChIP-chip, ChIP-seq data can be used to locate the binding site within few tens of base pairs of the actual protein binding site. Tag densities at the binding sites are a good indicator of protein–DNA binding affinity, which makes it easier to quantify and compare binding affinities of a protein to different DNA sites.