Construction of zebrafish chromatin accessibility landscape at a single-cell level using CH-ATAC-seq

The assay for transposase-accessible chromatin using sequencing (ATAC-seq) at single-cell level can provide different perspectives of regulatory patterns based on cell type-specific accessible regions. While human genomic elements have been well studied, understanding how nuclear acid sequence regulates the expression of target genes in a genome-wide level in other organisms remains a major challenge. Batch effects, expensive machines are still constraints nowadays to build a cross-species landscape for further analysis, a platform with high throughput and low cost will be extremely required.Here, we constructed a cross-species accessible chromatin landscape by combinatorial-hybridization-based single-cell ATAC-seq, a single-cell ATAC-seq platform with high throughput and signal-noise ratio using fresh nuclei as input. Overall design: Whole bodies of wild-type strain AB zebrafishes at 4 months were dissociated into single-nucleus suspensions, followed by single-cell DNA library construction, high-throughput sequencing, and bioinformatics analysis.