Embryos for ATAC-seq were harvested at five different developmental stages: 64-cell (2 hpf), 256-cell (2.5 hpf), 1k-cell (3 hpf), oblong (3.7 hpf), and dome (4.5 hpf). The ATAC-seq analyses of the zebrafish embryos involved a slightly modified approach that was based on the original method (Buenrostro et al. 2013 (link)); see Supplemental Methods . The libraries were sequenced by Illumina HiSeq X Ten sequencing. Public ATAC-seq data were collected from Bogdanovic et al. (2016) (link) (Supplemental Table S2 ).
Sequenced reads were mapped to the zebrafish genome (zv9 assembly) using Bowtie 2 (version 2.2.3) with default parameters (Langmead and Salzberg 2012 (link)), and peak calling was performed using MACS (version 1.4.2 20120305) (Zhang et al. 2008 (link)) with the following parameters: -f BED −g 1.4 × 109 --keep-dup all --nomodel --shiftsize 25. Peaks with P-value ≤ 1 × 10−10 and fold ≥10 were kept. SeeSupplemental Methods for details.
Sequenced reads were mapped to the zebrafish genome (zv9 assembly) using Bowtie 2 (version 2.2.3) with default parameters (Langmead and Salzberg 2012 (link)), and peak calling was performed using MACS (version 1.4.2 20120305) (Zhang et al. 2008 (link)) with the following parameters: -f BED −g 1.4 × 109 --keep-dup all --nomodel --shiftsize 25. Peaks with P-value ≤ 1 × 10−10 and fold ≥10 were kept. See
