title: GSM6599884: Nip-ATAC-Normal-Rep1; Oryza sativa; ATAC-seq
library_construction_protocol: Primary root tips with 5 mm in length from the 3-day-old rice seedlings were harvested and fixed with cold paraformaldehyde solution (2%) for 30 min. Then the root tips were transferred to Dounce grinder (kimble), which was filled with cold lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 1 mM MgCl2, 1% BSA) and 0.2% Tween 20, 0.2% NP-40, 0.0075% Digitonin. 0.5% 2-ME (v/v) were added and then the roots were grinded completely. The homogenate was filtered with a 20 μm mesh (Sysmex) following by centrifuge at 480 rcf for 5 min at 4℃. After removing supernatant, 1% BSA buffer (10 mM Tris-HCl (pH7.4), 10 mM NaCl, 3 mM MgCl2, 1% BSA (v/v)) was added to resuspend pellet. Then, the mixture was placed on 80% percoll and following by centrifuge at 300 rcf for 25 min at 4℃. After removing 150 μl supernatant, nuclei were transferred to a new eppendorf tube and washed twice with 1% BSA buffer. Bulk ATAC-seq was performed as described previously (Liang et al., 2021 BMC biology. PMID: 33740972)