Less concerning limitations of DNase-seq are that it requires many cells and involves many sample preparation and enzyme titration steps. Success of this assay depends on the quality of nuclei preparations and small-scale preliminary experiments are essential to ascertain the exact amount of detergent needed for cell lysis [76]. Also, DNase I concentrations may need to be adjusted empirically depending on initial type and number of cells, the lot of DNase I used and the exact purpose of the experiment [84]. Overall, DNase-seq represents a reliable and robust way to identify active regulatory elements across the genome and in any cell type from a sequenced species, without a priori knowledge of additional epigenetic information. Its reliability as a TF footprint detection assay in a temporal scale is questionable and needs to be investigated further in detail.
