GSM4633549: Tinaja_2 [ATAC-seq]; Astyanax mexicanus; ATAC-seq
ATAC was performed as per Buenos et al. with some modifications to accommodate the use of whole tissues as starting material instead of cells. Livers were homogenized (30-40 strokes) using the loose pestle of Dounce homogenizer in lysis buffer (10 mM Tris·Cl, pH 7.4, 10 mM NaCl, 3 mMMgCl2, 0.1% (v/v) Igepal CA-630) to prepare nuclei. Rupturing of cell membrane and obtainment of nuclei was confirmed using Trypan blue staining under a phase contrast microscope. ~70000 nuclei were taken and spun down at 1500g at 4deg. Nuclei were resuspended in transposition mixture (25 μl TD of 2× reaction buffer from Nextera kit, 2.5 μl TDE1 Tn5 Transposase, 22.5 μl nuclease-free water) and incubated at 37deg for 22-24 min. The reaction was purified, and library was prepared following manufacturer instructions. Paired-end sequencing was done in Illumina Next-seq Mid-output mode.