Zhou Jie, Yang Xueqian, Lin Xiumei, Zhao Kaichen, Wang Xue, Dong Zhiqiang, Liu Chuanyu, Liu Chang
BGI Research, Shenzhen 518083, China; BGI Research, Hangzhou 310030, China.
College of Biomedicine and Health, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
STAR Protoc. 2024 Dec 20;5(4):103501. doi: 10.1016/j.xpro.2024.103501. Epub 2024 Dec 12.
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..
斑马鱼特异性基序数据库的稀缺给利用测序技术进行斑马鱼转座酶可及染色质单细胞分析（scATAC-seq）数据中的转录因子（TF）基序分析带来了挑战，从而阻碍了对整个斑马鱼胚胎发育过程中调控元件的识别。在此，我们提供了一个用于分析斑马鱼早期胚胎发生过程中单细胞核染色质可及性数据集的方案。我们描述了片段文件检索、样本整合、质量控制、潜在语义索引（LSI）聚类以及通过ArchR进行峰识别的步骤。至关重要的是，我们详细介绍了斑马鱼特异性基序数据库构建、基序富集和TF足迹分析的程序。有关本方案使用和执行的完整详细信息，请参考Lin等人的研究。
