Single-cell epigenome library prep drops from a week to a day: droplet microfluidics with nanopore long reads handles about 5,000 cells at once
Single-cell epigenome sequencing has moved its barcoding step off the plate and into droplets. Long-read single-cell ATAC and CUT&Tag previously ran well by well, needing at least a week of library work for about 5,000 cells at high cost. Now nuclei are co-encapsulated with barcoded beads on a commercial microfluidic chip and read on Nanopore: about 5,000 cells per run, one day of library prep instead of a week, and roughly $0.39 per cell instead of $1.98. In GM12878, 10,000 input nuclei produced 66 Gb, with 82.8% of reads on valid cell barcodes.