Lan-lab / SPATAC-seq

SPATAC-seq: split-pool ligation-based scATAC-seq method

Overview of the molecular structure of SPATAC-seq

Dependiencies

• Python 3.0

• BWA

• FASTX-Toolkit

• Cell Ranger ATAC v1.2

• Sinto

• Signac

• ArchR

Citation

1. Cusanovich DA, Daza R, Adey A, et al. Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing. Science. 2015;348(6237):910-914. doi:10.1126/science.aab1601.
2. Amini S, Pushkarev D, Christiansen L, et al. Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing. Nat Genet. 2014;46(12):1343-1349. doi:10.1038/ng.3119.
3. Rosenberg AB, Roco CM, Muscat RA, et al. Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding. Science. 2018;360(6385):176-182. doi:10.1126/science.aam8999.
4. Ma S, Zhang B, LaFave LM, et al. Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin. Cell. 2020;183(4):1103-1116.e20. doi:10.1016/j.cell.2020.09.056.