Abstract
The scarcity of zebrafish-specific motif databases presents a challenge to the analysis of transcription factor (TF) motif within zebrafish single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) data, thus hindering the identification of regulatory elements throughout zebrafish embryonic development. Here, we provide a protocol to analyze single-nucleus chromatin accessibility dataset during zebrafish early embryogenesis. We describe steps for fragment file retrieval, sample integration, quality control, Latent Semantic Indexing (LSI) clustering, and peak calling via ArchR. Crucially, we detail procedures for zebrafish-specific motif database construction, motif enrichment, and TF footprinting analysis. For complete details on the use and execution of this protocol, please refer to Lin et al.(1).