GSM4676838: ATAC-seq_MPP6; Mus musculus; ATAC-seq
Omni-ATAC was performed as previously described (Corces et al., 2017) with optimization suited for both MPP cells (50,000 per sample) and HSCs (10,000 per sample). Cell pellets were resuspended in 50 μl of ATAC-seq RSB containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin and allowed to lyse for 3 minutes on ice. After lysis, 1 ml of ATAC-seq RSB containing 0.1% Tween-20 (without NP40 or digitonin) was added, and the tubes were inverted to mix. Nuclei were centrifuged for 10 minutes at 500 rcf at 4 °C. Nuclei were resuspended in 50 μl of transposition mix [25 μl 2× TD buffer, transposase (1.75 uL for MPP – 1 uL for HSC), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, and water (5.75 uL for MPP – 6.5 uL for HSC)] by pipetting up and down six times. Transposition reactions were incubated at 37 °C for 30 minutes in a thermomixer with shaking at 1,000 rpm. Reactions were cleaned with a Qiagen MinElute Reaction Cleanup kit. The ATAC-seq library preparation was performed as previously described  (Buenrostro et al., 2015).