For each sample, approximately 30 embryos at stage 9 were collected and dissociated into single cells after pipetting with calcium- and magnesium-free medium [7.5 mM tris (pH 7.6), 2.4 mM NaHCO3, 88 mM NaCl, and 1 mM KCl]. The cells were
collected by centrifugation. The ChIP library was constructed following the manual of the Hyperactive In-situ ChIP Library Prep Kit for Illumina (Vazyme, #TD901), and 10 μg of H3K4me3 antibody (Abcam, ab8580) was added to each sample. High-throughput sequencing was performed using the NovaSeq platform and the PE 150 sequencing strategy. Quality control of the
ChIP-seq data was performed using FastQC, after which low-quality bases and adaptor contamination were filtered using Trim galore. After quality control and data filtering were performed, the
data were mapped to the X. laevis genome using bowtie2 software. Peak calling was performed using MACS 2.0, and significant enrichments were identified with a threshold level set at a q value of <0.05. Peak annotation was performed as reported (51 (link)). Some of the ChIP-seq data of X. laevis and X. tropicalis used in our analysis were downloaded from the Gene Expression Omnibus database under the accession numbers SRR5110212–SRR5110215 and SRR5110218–SRR5110221.
collected by centrifugation. The ChIP library was constructed following the manual of the Hyperactive In-situ ChIP Library Prep Kit for Illumina (Vazyme, #TD901), and 10 μg of H3K4me3 antibody (Abcam, ab8580) was added to each sample. High-throughput sequencing was performed using the NovaSeq platform and the PE 150 sequencing strategy. Quality control of the
ChIP-seq data was performed using FastQC, after which low-quality bases and adaptor contamination were filtered using Trim galore. After quality control and data filtering were performed, the
data were mapped to the X. laevis genome using bowtie2 software. Peak calling was performed using MACS 2.0, and significant enrichments were identified with a threshold level set at a q value of <0.05. Peak annotation was performed as reported (51 (link)). Some of the ChIP-seq data of X. laevis and X. tropicalis used in our analysis were downloaded from the Gene Expression Omnibus database under the accession numbers SRR5110212–SRR5110215 and SRR5110218–SRR5110221.