Single cell atac gel beads v 1

On the Chromium Next GEM Chip H (10x Genomics #2000180), unused channels were loaded with 70 μl (row 1), 50 μl (row 2) and 40 μl (row 3) of 50% glycerol solution (Sigma #G5516-100ML). Per sample, we added a mix of 41.9 μl of nuclease-free water, 12 μl of 10x Ampligase Reaction Buffer (Lucigen #A0102K), 2.3 μl of 100 U/μl Ampligase (Lucigen #A0102K), 1.5 μl of Reducing Agent B (10x Genomics #2000087) and 2.3 μl of 100 μM Bridge Oligo (sequence provided in Supplementary Table 1) immediately before the run. Seventy microliters of cell suspension in thermoligation master mix was loaded into the Chromium Next GEM Chip H (row 1), along with 50 μl of Single Cell ATAC Gel Beads v.1.1 (row 2, 10x Genomics #2000210) and 40 μl of Partitioning Oil (row 3, 10x Genomics #2000190), and the chip was run on the Chromium system.

The Chromium Single Cell ATAC v.1.0 E Chip (10x Genomics #2000121) was loaded with 80 μl of 1x Nuclei Buffer (10x Genomics #2000153) into inlet 1, 40 μl of Single Cell ATAC Gel Beads (10x Genomics #2000132) into inlet 2, and 240 μl of Partitioning Oil (10x Genomics #220088) into inlet 3. The Chromium Single Cell ATAC v.1.1 Next GEM H Chip (10x Genomics #20000180) was loaded with 70 μl of 1x Nuclei Buffer (10x Genomics #2000153) into inlet 1, 50 μl of Single Cell ATAC Gel Beads v.1.1 (10x Genomics #2000210) into inlet 2, and 40 μl of Partitioning Oil (10x Genomics #220088) into the outlet, labeled as row 3. Because we omitted Reducing Agent B, the gel beads remained intact throughout the microfluidic run, such that they could be visualized inside the emulsion droplets using a standard light microscope. Our fill rate calculations are based on a total of 1,265 (scATAC v.1.0) or 1,610 (scATAC v.1.1 Next GEM) droplets that were manually counted from microscopic images.