scATAC-Seq (Cell index variation)

Single-Cell Assay for Transposase-Accessible Chromatin

This version of scATAC-seq uses combinatorial cellular indexing to measure chromatin accessibility in thousands of single cells per assay. This method avoids the need for compartmentalization of individual cells, which makes the system scalable to analyze thousands of cells at a time (Cusanovich et al., 2015).

In this method, nuclei are isolated and molecularly tagged in bulk with barcoded Tn5 transposases in wells. Next, the nuclei are pooled and a limited number redistributed into a second set of wells. A second barcode is introduced during the PCR amplification step, and the fragments are pooled for library preparation and sequencing.


  • High throughput and scalable


  • None reported


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. and Zhang Y. Establishing Chromatin Regulatory Landscape during Mouse Preimplantation Development. Cell. 2016;165:1375-1388


Corces M. R., Buenrostro J. D., Wu B., et al. Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution. Nat Genet. 2016;48:1193-1203

Cusanovich D. A., Daza R., Adey A., et al. Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing. Science. 2015;348:910-914