Question: Can I sort nuclei for Single Cell ATAC sequencing?
Answer: Sorting nuclei to be used for single cell ATAC is not recommended for a number of reasons. Sorting and additional handling of nuclei can further compromise the nuclear membrane, leading to leakage of nuclear content. Additionally, certain dyes used for nuclei sorting, intercalate between the DNA and disrupt chromatin structure.
In the plot below, nuclei were stained with propidium iodide (PI), an intercalating dye, and sorted based on the population staining positive for PI. After sorting, the sample had a reduced number of unique fragments per barcode, reduced targeting, and lower clustering resolution within the tSNE plot.
Other sorting dyes tested shown to impact data quality: DAPI, Ethidium Homodimer, Vybrant Dyecycle Green, Zombie Violet
Alternatives: 7-Aminoactinomycin D (7-AAD) has shown promising results for a limited number of samples, please use with caution.
Products: Single Cell ATAC