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) The initial raw data were retrieved using the following command: SRR12435907_1="ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR124/007/SRR12435907/SRR12435907_1.fastq.gz"SRR12435907_2="ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR124/007/SRR12435907/SRR12435907_2.fastq.gz" SRR12435908_1="ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR124/008/SRR12435908/SRR12435908_1.fastq.gz"SRR12435908_2="ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR124/008/SRR12435908/SRR12435908_2.fastq.gz" ATAC-seq data analysis was conducted using the workflow described in the document available at the following link: ATAC Workflow CUT&Tag The data processing workflow for CUT&Tag can be found in this file: ./CUT_Tag.sh Hi-C In this study, we employed the following files as part of the Hi-C data analysis pipeline: ./up_demo_hic_code.sh Other Datasets The bw, BED, and BEDPE files used in this study have also been uploaded. Contact Jiulin Chan ( [e-mail] ) Peng Hu ( [e-mail] ) Xiaolong Li ( [e-mail] )