of the human genome. FAIRE-seq Any cell type 100,000 to 10 million cellsPaired-end or Single-endBased on the phenol-chloroform separation of nucleosome-bound and free sonicated areas of a genome, in the interphase and aqueous phase respectivelyMaps open chromatin1. Low signal-to-noise ratio, making computational data interpretation very difficult.[86–90]2. Results depend highly on fixation efficiency.3. Requires 20 to 50 million reads for standard accessibility studies of the human genome. ATAC-seq 500 to 50,000 freshly isolated cellsPaired-endUnfixed nuclei are tagged in vitro with adapters for NGS by purified Tn5 transposase. Adapters are integrated into regions of accessible chromatinMaps open chromatin, TF and nucleosome occupancy1. Contamination of generated data with mitochondrial DNA.[103]2. Immature data analysis tools.3. Requires 60 to 100 million reads for standard accessibility studies of the human genome.ATAC: assay for transposase-accessible chromatin; DNase I: deoxyribonuclease I; FAIRE: formaldehyde-assisted isolation of regulatory elements; MNase: micrococcal nuclease.
