Systematic Enhancer Mapping and Functional Analysis in Zebrafish with Optimized CRISPR Interference

Optimization and Application of CRISPRi for Cis-Regulatory Element Analysis in Zebrafish Embryos ATAC-seq Publicly available ATAC-seq data for wild-type zebrafish embryos at 48 hpf were obtained from the NCBI Sequence Read Archive (SRA) under the following accessions: SRA run: SRR12435907 (corresponding to SRX8931602) SRA run: SRR12435908 (corresponding to SRX8931603) ATAC-seq data analysis was conducted using the workflow described in the document available at the following link: ATAC Workflow ChIP-Seq Publicly available ChIP-Seq (H3k27ac) data for wild-type zebrafish embryos at 48 hpf were obtained from NCBI under the accession number: PRJNA821001 ; This dataset is also available from the DANIO-CODE database (https://danio-code.zfin.org/dataExport/). The data processing workflow for ChIP-Seq can be found in this file: ./ChIP-Seq.sh Hi-C The raw sequencing data generated by our assays has been deposited on China National Center for Bioinformation (CNCB, https://www.cncb.ac.cn/ ), with the project number: PRJCA049852 In this study, we employed the following files as part of the Hi-C data analysis pipeline: ./Hi-C_code.sh Other Datasets The bw, BED, and BEDPE files used or generated in this study have also been uploaded. Contact Jiulin Chan ( [e-mail] ) Peng Hu ( [e-mail] ) Xiaolong Li ( [e-mail] )