title: GSM4600941: Maize_B73_ATAC_root_rep2; Zea mays; ATAC-seq
library_construction_protocol: ATAC-seq was performed as described previously (Lu et al 2017). For each replicate, approximately 100 mg of maize staple roots were harvested and immediately chopped with a razor blade and placed in 2 ml of pre-chilled lysis buffer (15 mM Tris–HCl pH 7.5, 20 mM sodium chloride, 80 mM potassium chloride, 0.5 mM spermine, 5 mM 2-mercaptoethanol and 0.2% TritonX-100). The chopped slurry was filtered twice through miracloth. The crude nuclei were stained with 4,6-diamidino- 2-phenylindole and loaded into a flow cytometer (Beckman Coulter MoFlo XDP). Nuclei were purified by flow sorting and washed in accordance with (Lu et al 2017). The sorted nuclei (50,000 nuclei per reaction) were incubated with 2 μl of transposome in 40 μl of tagmentation buffer (10 mM TAPS–sodium hydroxide pH 8.0, 5 mM magnesium chloride) at 37 °C for 30 min without rotation. The integration products were purified using a NEB Monarch PCR Purification Kit and then amplified using Phusion DNA polymerase for 11 cycles (Buenrostro et al 2013). Amplified libraries were purified with AMPure beads to remove primers.
attributes.tag: GEO Accession
attributes.value: GSM4600941