scATAC-Seq (Microfluidics variation)

Single-Cell Assay for Transposase-Accessible Chromatin

This version of scATAC-seq is integrated into a programmable microfluidics platform (Buenrostro et al., 2015). The method is similar to scATAC-seq (combinatorial indexing version), which relies on indexing to identify single cells (Cusanovich et al., 2015). In this protocol the cells are captured in a fluidics device, lysed, and treated with Tn5 transposases. The ends of the Tn5 fragments are extended, and the fragments are PCR-amplified with dual-index primers, pooled, purified, and sequenced.


  • Maps the accessible genome of individual cells


  • Requires dedicated fluidics


Illumina Library prep and Array Kit Selector


Liu S. and Trapnell C. Single-cell transcriptome sequencing: recent advances and remaining challenges. F1000Res. 2016;5:

Lu F., Liu Y., Inoue A., Suzuki T., Zhao K., et al. Establishing Chromatin Regulatory Landscape during Mouse Preimplantation Development. Cell. 2016;165:1375-1388


Buenrostro J. D., Wu B., Litzenburger U. M., et al. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature. 2015;523:486-490