title: GSM4273171: FAIRE_4h_rep2; Oryza sativa; OTHER
library_construction_protocol: The isolated nuclei pellet was resuspended in 400 ml of Sonic-FAIRE buffer (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5% SDS, and protease inhibitor cocktail) and fragmented into 200–400-bp pieces by sonication in a Bioruptor (Diagenode). Lysates were centrifuged at 20,000 × g for 10 min at 4 °C, and the supernatant was transferred to a new tube. To prepare FAIRE DNA, 1 volume of phenol:chloroform:isoamyl alcohol was added to the supernatant; the mixture was vortex-mixed and centrifuged at 20,000 × g for 10 min; and the supernatant was transferred to a new tube. These steps were repeated at least twice to remove nucleosome-coated DNA. After ethanol precipitation, FAIRE DNA was resuspended in TE buffer. DNA libraries were prepared using an NEBNext® Ultra™ II DNA library prep kit for Illumina® (New England BioLabs, E7645).
attributes.tag: GEO Accession
attributes.value: GSM4273171