GSM5396321: Shield_dnmt1_mKD_ATAC_seq_rep1; Danio rerio; ATAC-seq
The miniATAC-seq procedure was performed as previously described (Wu et al., 2018a) with modifications to adapt it for zebrafish embryos. Briefly, dispersed cells from deyolked zebrafish embryos were transferred into 6 µl lysis buffer (10 mM Tris-HCl, pH = 7.4; 10 mM NaCl; 3 mM MgCl2; and 0.02% digitonin) in ice for 16 min. The ATAC reaction was performed by adding 4 µl ddH2O, 4 µl 5 X TTBL, and 5 µl TTE mix V5 (Vazyme, Cat TD502) at 37℃ for 30 min, then stopped by adding 5 µl 5 X TS stop buffer at room temperature for 5 min. The DNA was extracted by phenol chloroform and ethanol purification after adding 40 ng carrier RNA and 103 µl Tris-EDTA. Then the DNA was PCR amplified with 10 µl index (Vayzme, Cat TD202), 10 µl 5 X TAB and 1 µl TAE (Vayzme, Cat TD502), with the program of 72℃ for 3 min, 98℃ for 30s, (98℃ for 15s, 60℃ for 30s, and 72℃ for 3min) with 18 cycles, and 72℃ for 5 min. The amplified DNA was size-selected using AMPure Beads for 200-800 bp DNA fragments. All libraries were sequenced by Illumina Hi-Seq 1500 or 2506 or XTen platform according to manufacturer's instruction.