GSM915199	Embryo_24hpf	NA	GSE32483	 whole embryo	H3K27ac_24hpf, danRer7		 24hpf		H3K27ac	ChIP-Seq	Zv9	Reads were mapped to the D. rerio genome (ENSEMBL version Zv9) with the ELAND software (from Illumina CASAVA 1.8.2) using default settings. Reads with 0 or 1 mismatch were kept.	H3K27ac_24hpf, danRer7	bd_0_1_2_6_dr10	UsingSRR
GSM803832	Embryo_24hpf	NA	GSE32483	 whole embryo	H3K27ac_24hpf, danRer6		 24hpf		H3K27ac	ChIP-Seq	Zv8	Reads were mapped to the D. rerio genome (ENSEMBL version Zv8) with the ELAND software (Ilumina pipeline). Only the alignments within 2 mismatches were included in further analysis.	H3K27ac_24hpf, danRer6	bd_0_1_2_6_dr10	UsingSRR
GSM915195	Embryo_24hpf	NA	GSE32483	 whole embryo	H3K4me1_24hpf, danRer7		 24hpf		H3K4me1	ChIP-Seq	Zv9	Reads were mapped to the D. rerio genome (ENSEMBL version Zv9) with the ELAND software (from Illumina CASAVA 1.8.2) using default settings. Reads with 0 or 1 mismatch were kept.	H3K4me1_24hpf, danRer7	bd_0_1_2_6_dr10	UsingSRR
GSM803828	Embryo_24hpf	NA	GSE32483	 whole embryo	H3K4me1_24hpf, danRer6		 24hpf		H3K4me1	ChIP-Seq	Zv8	Reads were mapped to the D. rerio genome (ENSEMBL version Zv8) with the ELAND software (Ilumina pipeline). Only the alignments within 2 mismatches were included in further analysis.	H3K4me1_24hpf, danRer6	bd_0_1_2_6_dr10	UsingSRR
GSM686660	Embryo_24hpf	NA	GSE20600	 whole embryo	whole embryo at 24 hours post fertilization, H3K4me1 ChIP		 24 hours post fertilization		H3K4me1	ChIP-Seq	Zv7	Alignments: Sequence reads were obtained and mapped to the zebrafish (Zv7) genomes using the Illumina Genome Analyzer Pipeline. All reads uniquely mapped with two or fewer mismatches were retained for subsequent peak detection.	H3K4me1_ChIPSeq rep2	bd_0_1_2_6_dr10	UsingSRR
GSM520620	Embryo_24hpf	NA	GSE20600	 whole embryo	whole embryo at 24 hours post fertilization, H3K4me1 ChIP		 24 hours post fertilization		H3K4me1	ChIP-Seq	Zv7	Alignments: Sequence reads were obtained and mapped to the zebrafish (Zv7) genome using the Illumina Genome Analyzer Pipeline. All reads uniquely mapped with two or fewer mismatches were retained for subsequent peak detection. The alignment files are in bed format.	H3K4me1_ChIPSeq	bd_0_1_2_6_dr10	UsingSRR
GSM3494513	Embryo_24hpf	NA	GSE123059		Whole embryo		 24hpf		p63	ChIP-Seq	GRCz10	Reads were aligned using Bowtie	ChIPseq of p63 in zebrafish wild type embryos at 24hpf, replicate 2	bd_0_1_2_6_dr10	GSM3494513_ChIPseq_zebra_p63_24hpf_rep2_MACSpeaks.narrowPeak.gz
GSM3494512	Embryo_24hpf	NA	GSE123059		Whole embryo		 24hpf		p63	ChIP-Seq	GRCz10	Reads were aligned using Bowtie	ChIPseq of p63 in zebrafish wild type embryos at 24hpf, replicate 1	bd_0_1_2_6_dr10	GSM3494512_ChIPseq_zebra_p63_24hpf_rep1_MACSpeaks.narrowPeak.gz
GSM3494518	Embryo_24hpf	NA	GSE123059		Whole embryo		 24hpf		Sox3	ChIP-Seq	GRCz10	Reads were aligned using Bowtie	ChIPseq of Sox3 in zebrafish wild type embryos at 24hpf	bd_0_1_2_6_dr10	GSM3494518_ChIPseq_zebra_Sox3_24hpf_MACSpeaks.narrowPeak.gz
Embryo_24hpf	Embryo_24hpf	NA	GSE41458		 FACS sorted zic3 expressing cell from 24hpf embryo24hpf embryos		 24hpf embryos		Zic3	ChIP-Seq	zv9	Sequencing reads were mapped to the zebrafish genome assembly version July 2010 (Zv9), following which peak finding was performed using the QuEST algorithm (Valouev et al., 2008)	Zic3 24hrs sorted	bd_0_1_2_6_dr10	UsingSRR
GSM3396551	Embryo_24hpf	NA	GSE120238	 FACS-sorted embryo cells	FACS-sorted embryo cells		 24 hpf			ATAC-Seq	GRCz10	Nextera adapters removal was performed by using Trimmomatic (0.36) (Bolger et al. 2014)	wt_ATACseq_GFPpos_24hpf_rep2	bd_0_1_2_6_dr10	UsingSRR
GSM3396550	Embryo_24hpf	NA	GSE120238	 FACS-sorted embryo cells	FACS-sorted embryo cells		 24 hpf			ATAC-Seq	GRCz10	Nextera adapters removal was performed by using Trimmomatic (0.36) (Bolger et al. 2014)	wt_ATACseq_GFPpos_24hpf_rep1	bd_0_1_2_6_dr10	UsingSRR
GSM2935527	Embryo_24hpf	NA	GSE109219	 whole embryos; hindbrain	ATAC-seq in hindbrain samples from 24hpf zebrafish embryos		 24hpf			ATAC-Seq	danRer10	ATAC-seq:	ATAC-seq in hindbrain samples from 24hpf zebrafish embryos, replicate 2	bw_0_1_2_4_dr10	GSM2935527_ATAC_zebrafish_hindbrain_24hpf_rep2.bw
GSM2935526	Embryo_24hpf	NA	GSE109219	 whole embryos; hindbrain	ATAC-seq in hindbrain samples from 24hpf zebrafish embryos		 24hpf			ATAC-Seq	danRer10	ATAC-seq:	ATAC-seq in hindbrain samples from 24hpf zebrafish embryos, replicate 1	bw_0_1_2_4_dr10	GSM2935526_ATAC_zebrafish_hindbrain_24hpf_rep1.bw
GSM2560240	Embryo_24hpf	NA	GSE97257		 endothelial cells		 24 hours post fertilization	 Tg(fli1a:egfp)		ATAC-Seq	Zv9	basecalls were made with standard Illumina HiSeq 1000 pipeline to generate fastq files	GFPplus3_ATAC-seq	bd_0_1_2_6_dr7	GSM2560240_GFPplus3_peaks.2.narrowPeak.gz
GSM2560239	Embryo_24hpf	NA	GSE97257		 endothelial cells		 24 hours post fertilization	 Tg(fli1a:egfp)		ATAC-Seq	Zv9	basecalls were made with standard Illumina HiSeq 1000 pipeline to generate fastq files	GFPplus2_ATAC-seq	bd_0_1_2_6_dr7	GSM2560239_GFPplus2_peaks.2.narrowPeak.gz
GSM2560238	Embryo_24hpf	NA	GSE97257		 endothelial cells		 24 hours post fertilization	 Tg(fli1a:egfp)		ATAC-Seq	Zv9	basecalls were made with standard Illumina HiSeq 1000 pipeline to generate fastq files	GFPplus1_ATAC-seq	bd_0_1_2_6_dr7	GSM2560238_GFPplus1_peaks.2.narrowPeak.gz
GSM2560237	Embryo_24hpf	NA	GSE97257		 non-endothelial cells		 24 hours post fertilization	 Tg(fli1a:egfp)		ATAC-Seq	Zv9	basecalls were made with standard Illumina HiSeq 1000 pipeline to generate fastq files	GFPminus3_ATAC-seq	bd_0_1_2_6_dr7	GSM2560237_GFPminus3_peaks.2.narrowPeak.gz
GSM2560236	Embryo_24hpf	NA	GSE97257		 non-endothelial cells		 24 hours post fertilization	 Tg(fli1a:egfp)		ATAC-Seq	Zv9	basecalls were made with standard Illumina HiSeq 1000 pipeline to generate fastq files	GFPminus2_ATAC-seq	bd_0_1_2_6_dr7	GSM2560236_GFPminus2_peaks.2.narrowPeak.gz
GSM2560235	Embryo_24hpf	NA	GSE97257		 non-endothelial cells		 24 hours post fertilization	 Tg(fli1a:egfp)		ATAC-Seq	Zv9	basecalls were made with standard Illumina HiSeq 1000 pipeline to generate fastq files	GFPminus1_ATAC-seq	bd_0_1_2_6_dr7	GSM2560235_GFPminus1_peaks.2.narrowPeak.gz
GSM1496130	Embryo_24hpf	NA	GSE61065	 whole embryos	Zebrafish whole embryos		 24hpf			ATAC-Seq	danRer7	Library strategy: ATAC-seq	ATACseq in whole 24hpf zebrafish embryos	bw_0_1_2_4_dr7	GSM1496130_ATAC_zebra.bw