Zebrafish ReguloMap
Zebrafish ReguloMap focuses on mapping regulatory interactions (like enhancer-promoter loops) in zebrafish while emphasizing the integration of multi-omics data and Hi-C for comprehensive visualization.
It's concise, descriptive, and user-friendly for the research community.
More information:
Figure: Zebrafish ReguloMap
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- Danio_rerio: Danio_rerio.GRCz11.110.fa.gz — contains the reference genome sequence for the zebrafish (Danio rerio) in FASTA format for version GRCz11.
- GFF: Danio_rerio.GRCz11.110.gff.gz — is a General Feature Format file detailing gene models and annotations for the zebrafish GRCz11 genome.
- GTF: Danio_rerio.GRCz11.110.gtf.gff.gz — provides gene annotations in GTF (Gene Transfer Format) for the zebrafish GRCz11 genome version.
- bed_48hpf_ATAC_peaks: 48hpf_ATAC_peaks.narrowPeak.bed — lists transcriptionally active regions identified by ATAC-seq in zebrafish embryos at 48 hours post-fertilization.
- bed_48hpf_H3K27_peaks: 48hpf_H3K27_peaks.narrowPeak.bed — contains peak data for H3K27ac histone modification, indicating active enhancer regions at 48 hours post-fertilization.
- bed_48hpf_H3K4me3_peaks: 48hpf_H3K4me3_peaks.narrowPeak.bed — details peaks for the H3K4me3 histone modification showing promoter regions active at 48 hpf.
- bed_UCNEs_danRer7_to_DanRer11: result_new_UCNEs_danRer7_to_DanRer11.bed — includes ultra-conserved non-coding elements mapped from zebrafish genome version danRer7 to DanRer11.
- bed_48hpf_EP_LOOP: 48hpf_EP_LOOP.bedpe.bed — identifies enhancer-promoter loops in zebrafish embryos at 48 hours as BEDPE format.
- bw_ATAC-merged_bin1: 48hpf_ATAC-seq.bw — is a bigWig file representing merged ATAC-seq data to illustrate open chromatin regions in 48 hpf zebrafish embryos.
- bw_48hpf_H3K27ac: 48hpf_H3K27ac.bw — displays tags per base pair for the H3K27ac modification in 48 hpf zebrafish embryos using the bigWig format.
- bw_48hpf_H3K4me3: 48hpf_H3K4me3.bw — provides bigWig formatted data for H3K4me3 histone marks, indicative of active transcriptional start sites at 48 hpf.
- bw_48hpf_RNA-seq: 48hpf_RNA-seq.bw — contains RNA-seq expression data in bigWig format for zebrafish at 48 hours post-fertilization.
- 48hpf_embryo_hic: zebrafish_48h_embryo.hic — consists of a Hi-C data file revealing chromosomal architecture in zebrafish embryos at 48 hours post-fertilization.
Contact
If you have any questions, please do not hesitate to contact us:
- Jiulin Chan: jlchan@shou.edu.cn
- Peng Hu: phu@shou.edu.cn
- Xiaolong LI: lixllil@163.com