GM12878 cells were counted five times using a manual hemocytometer. The
mean cell count was used to resuspend the cells to a concentration of 500 cells
per 100 μl by the addition of PBS. From this diluted cell mixture, 100
μl (500 cells) were deposited into a 0.5-ml DNA LoBind tube (Eppendorf
#022431005) containing 400 μl of cold ATAC-seq RSB. This was
done to simulate a work-flow involving FACS sorting. These tubes were
centrifuged at 500 r.c.f. for 10 min in a pre-chilled (4 °C) fixed-angle
centrifuge with 0.6-ml tube adapters. All of the supernatant was removed using
the two pipetting steps described above, first by removing 400 μl with a
P1000 pipette tip followed by removal of the remaining volume with a P200
pipette tip. We note that a gradual but constant removal of supernatant is
crucial and that the final supernatant removal step should be completed in a
single motion to avoid disrupting the cell pellet. After supernatant removal,
lysis and transposition were performed simultaneously to avoid cell loss, and
the total reaction volume was reduced for the same reason. As such, 10
μl of transposition mix (3.3 μl PBS, 1.15 μl water, 5
μl 2× TD Buffer, 0.25 μl 1:10 diluted Tn5
enzyme26 (link), 0.1
μl 1% digitonin, 0.1 μl 10% Tween-20, and 0.1
μl 10% NP40) was added directly to the invisible cell pellet,
and the pellet was resuspended by pipetting up and down six times. The
transposition reaction was incubated at 37 °C for 30 min in a
thermomixer with shaking at 1,000 r.p.m. Note that Tn5 should be diluted in
1× TD Buffer (for example, 5 μl 2× TD Buffer, 4
μl of water, 1 μl Tn5).
mean cell count was used to resuspend the cells to a concentration of 500 cells
per 100 μl by the addition of PBS. From this diluted cell mixture, 100
μl (500 cells) were deposited into a 0.5-ml DNA LoBind tube (Eppendorf
#022431005) containing 400 μl of cold ATAC-seq RSB. This was
done to simulate a work-flow involving FACS sorting. These tubes were
centrifuged at 500 r.c.f. for 10 min in a pre-chilled (4 °C) fixed-angle
centrifuge with 0.6-ml tube adapters. All of the supernatant was removed using
the two pipetting steps described above, first by removing 400 μl with a
P1000 pipette tip followed by removal of the remaining volume with a P200
pipette tip. We note that a gradual but constant removal of supernatant is
crucial and that the final supernatant removal step should be completed in a
single motion to avoid disrupting the cell pellet. After supernatant removal,
lysis and transposition were performed simultaneously to avoid cell loss, and
the total reaction volume was reduced for the same reason. As such, 10
μl of transposition mix (3.3 μl PBS, 1.15 μl water, 5
μl 2× TD Buffer, 0.25 μl 1:10 diluted Tn5
enzyme26 (link), 0.1
μl 1% digitonin, 0.1 μl 10% Tween-20, and 0.1
μl 10% NP40) was added directly to the invisible cell pellet,
and the pellet was resuspended by pipetting up and down six times. The
transposition reaction was incubated at 37 °C for 30 min in a
thermomixer with shaking at 1,000 r.p.m. Note that Tn5 should be diluted in
1× TD Buffer (for example, 5 μl 2× TD Buffer, 4
μl of water, 1 μl Tn5).