GSM9138309: Input control; Danio rerio; ChIP-Seq
At 20-22 ss, embryos (50-100 per library) were homogenized and fixed by formaldehyde crosslinking, quenched, and nuclei were isolated. Chromatin was sheared using a Bioruptor Pico (Diagenode; 4 cycles of 30 s ON/30 s OFF) to around 200-500 bp fragments. After preclearing with Dynabeads Protein A (Life Technologies), biotinylated Sox10‑DNA complexes were captured using Dynabeads Streptavidin M‑280 (Invitrogen). One‑twentieth of the sample was reserved as input DNA. Beads were washed under stringent conditions, crosslinks were reversed, and DNA was purified. ChIP and input DNAs were prepared into sequencing libraries using the MicroPlex Library Preparation Kit v3 (Diagenode) following the manufacturer's instructions. PCR amplification was 14 cycles for ChIP and 12 cycles for input libraries. Libraries were sequenced on an Illumina NovaSeq with 150‑bp paired‑end reads.