ATAC-seq (Assay For Transposase-Accessible Chromatin Sequencing) is a fast and sensitive high-throughput sequencing method for epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. ATAC-seq uses hyperactive Tn5 transposase (Goryshin and Reznikoff, 1998; Adey et al., 2010) to simultaneously cut and ligate adapters for high-throughput sequencing at regions of increased accessibility. This technique will allow multidimensional assays of the regulatory landscape of chromatin with a relatively simple and fast protocol. Unlike methods such as MNase-seq (Zaret, 2005), ChIP-seq (Landt et al., 2012), and DNase-seq (Song and Crawford, 2010) which often require tens to hundreds of millions of cells as input material, ATAT-seq can be carried out with a standard sample size of 50,000 cells. Therefore, ATAC-seq is a fast and sensitive alternative to DNase-Seq for assaying genome-wide chromatin accessibility, or to MNase for assaying nucleosome positions in accessible regions of the genome.
Cell number: 25,000 - 75,000 cells recommended
Cell Collection: Cells should be intact and in a homogenous single cell suspension, fixatives can reduce transposition frequency and are not recommended.
PCR and Fragmentation distribution: 5 cycles of PCR to generate DNA fragments and fragment size window of 100–1000 bps recommended
Library Quantitation: qPCR method to quantify ATAC-seq libraries using the KAPA Library Quant Kit. Alternatively, Bioanalyzer can be used to estimate library concentration. Do not use Qubit, as it can give misleading and inaccurate results.
Sequencing: > 50M reads Paired-end 50-100 bp recommended
4-5 weeks depend on projects