GSM9278496: KRAS negative control, AT2 cells, replicate 02, ATAC; Mus musculus; ATAC-seq
Mouse lungs were harvested, dissociated and sorted for 100,000 tdT+ AT2 cells. Cells were centrifuged in 4°C at 1098 rcf  for 5 minutes in a fixed angle centrifuge. The supernatant was discarded, and the pellets were resuspended in 50 µL of cold ATAC-RSB lysis buffer (0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin, 10 mM Tris-HCl pH 8.1, 10 mM NaCl, 3 mM MgCl2). The resuspension was incubated on ice for 3 minutes followed by the addition of 1mL of cold ATAC-RSB+Tween (10 mM Tris-HCl pH 8.1, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20) and inverted 3 times to mix. Nuclei were pelleted through centrifugation in 4°C at 1098 rcffor 10 minutes in a fixed angle centrifuge. The supernatant was discarded, and the pellet was resuspended in 50 µL of transposition buffer that included the following: 22.5 µL of Tn5 Reaction Mix (PBS, 2.2% Digitonin, 2.2% Tween-20), 25 µL of Tn5 Buffer (10 mM MgCl2, 20 mM Tris-HCl, 20% Dimethyl Formamide), and 2.5 µL of Tn5 Enzyme (NX#-TDE1, Tagment DNA Enzyme, 15027865, Illumina). The reaction was incubated in a thermocycler at 37°C for 30 minutes. DNA was purified using the Qiagen MinElute PCR Purification Kit (29004) following the manufacturer instructions with one modification of eluting with 10 µL of distilled water. Sample barcoding and PCR amplification was performed using the Greenleaf ATAC primers (Buenrostro et al., 2013) following the OMNI-ATAC protocol PCR parameters.  To assess amplification efficiency, 5 µL of each sample was saved and set aside while the remainder of each sample continued to size selection purification using SPRIselect beads (Beckman Coulter, B23318). Following the manufacturer instructions for double size selection, the sample was incubated for upper size selection with 0.5X the volume and for lower size selection at 1.8X the volume. Size selection was verified using agarose gel electrophoresis with 1 µL of final sample as well as the previously saved pre size selection sample. Final DNA quantification was measured using the Qubit HS dsDNA assay (Thermo Fisher Scientific, Q32851).