title: GSM9458884: Extraembryonic mesoderm, rep 2; Mus musculus; ATAC-seq
library_construction_protocol: Cells were centrifuged at 500 × g for 5 min at 4 ˚C. Pellet was resuspended in 50 µl ice-cold resuspension buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% Tween-20). Nuclei were centrifuged at 500 × g for 10 min at 4 ˚C. Pellet was resuspended in 50 µl transposition buffer (10 mM Tris-HCl pH 7.6, 5 mM MgCl₂, 10% dimethyl formamide, 100 nM transposase, 0.01% digitonin, 0.1% Tween-20, 33% PBS) and incubated at 37 ˚C for 30 min in a thermomixer set to 1000 rpm. DNA was eluted in 20 µl elution buffer using a commercial DNA purification kit (Zymo Research). Libraries were amplified using 20 µl DNA with NEBNext HiFi 2X PCR Master Mix, universal i5 primer, and uniquely indexed i7 primers (1.25 µM each). PCR conditions were 72 °C for 5 min, 98 °C for 30 s, followed by 5 cycles of 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min. Libraries were eluted in 20 µl elution buffer using the same DNA purification kit.