GSM915198	Embryo_epiboly_80	NA	GSE32483	 whole embryo	H3K27ac_80%epi, danRer7		 80% epiboly		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_80%epi, danRer7	bd_0_1_2_6_dr10	UsingSRR
GSM803831	Embryo_epiboly_80	NA	GSE32483	 whole embryo	H3K27ac_80%epi, danRer6		 80% epiboly		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_80%epi, danRer6	bd_0_1_2_6_dr10	UsingSRR
GSM915194	Embryo_epiboly_80	NA	GSE32483	 whole embryo	H3K4me1_80%epi, danRer7		 80% epiboly		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_80%epi, danRer7	bd_0_1_2_6_dr10	UsingSRR
GSM803827	Embryo_epiboly_80	NA	GSE32483	 whole embryo	H3K4me1_80%epi, danRer6		 80% epiboly		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_80%epi, danRer6	bd_0_1_2_6_dr10	UsingSRR
GSM3494517	Embryo_epiboly_80	NA	GSE123059		Whole embryo		 80% epiboly		p63	ChIP-Seq	GRCz10	Reads were aligned using Bowtie	ChIPseq of p63 in zebrafish wild type embryos at 80epi, replicate 2	bd_0_1_2_6_dr10	GSM3494517_ChIPseq_zebra_p63_80epi_rep2_MACSpeaks.narrowPeak.gz
GSM3494516	Embryo_epiboly_80	NA	GSE123059		Whole embryo		 80% epiboly		p63	ChIP-Seq	GRCz10	Reads were aligned using Bowtie	ChIPseq of p63 in zebrafish wild type embryos at 80epi, replicate 1	bd_0_1_2_6_dr10	GSM3494516_ChIPseq_zebra_p63_80epi_rep1_MACSpeaks.narrowPeak.gz
GSM3494523	Embryo_epiboly_80	NA	GSE123059		Whole embryo		 80% epiboly		Sox3	ChIP-Seq	GRCz10	Reads were aligned using Bowtie	ChIPseq of Sox3 in zebrafish wild type embryos at 80epi	bd_0_1_2_6_dr10	GSM3494523_ChIPseq_zebra_Sox3_80epi_MACSpeaks.narrowPeak.gz
GSM2242766	Embryo_epiboly_80	NA	GSE84619		whole zebrafish embryos		 75-85% epiboly	 AB	Ta_ChIP 	ChIP-Seq	Zv9	Reads were mapped to the Zv9 version of the genome with Bowtie using the following parameters: -y -m2 -k2 --best.	Ta_ChIP (2 replicates)	bd_0_1_2_6_dr10	UsingSRR
GSM2242767	Embryo_epiboly_80	NA	GSE84619		whole zebrafish embryos		 75-85% epiboly	 AB	Tbx16_ChIP 	ChIP-Seq	Zv9	Reads were mapped to the Zv9 version of the genome with Bowtie using the following parameters: -y -m2 -k2 --best.	Tbx16_ChIP (2 replicates)	bd_0_1_2_6_dr10	UsingSRR
GSM2845180	Embryo_epiboly_80	NA	GSE106676	 Citrine reporter and Cherry reporter expressing cells from 75% Epiboly stage embryos	Citrine reporter and Cherry reporter expressing cells from 75% Epiboly stage embryos		 75% Epiboly	 Gt(foxd3-citrine)ct110; Gt(foxd3-mCherry)ct110R		ATAC-Seq	danRer10	ChIP-seq, Biotin-ChIP-seq, and ATAC-seq reads were trimmed for quality using sickle (v 1.33) and mapped using bowtie (v.1.0.0). Smoothened bigWig files were generated using a enhanced Perl script courtesy of Jim Hughes.	ATACseq_Epiboly_Citrine-Cherry_2	bd_1_2_3_non_dr10	GSM2845180_Epi_CCB.bed.gz
GSM2845179	Embryo_epiboly_80	NA	GSE106676	 Citrine reporter and Cherry reporter expressing cells from 75% Epiboly stage embryos	Citrine reporter and Cherry reporter expressing cells from 75% Epiboly stage embryos		 75% Epiboly	 Gt(foxd3-citrine)ct110; Gt(foxd3-mCherry)ct110R		ATAC-Seq	danRer10	ChIP-seq, Biotin-ChIP-seq, and ATAC-seq reads were trimmed for quality using sickle (v 1.33) and mapped using bowtie (v.1.0.0). Smoothened bigWig files were generated using a enhanced Perl script courtesy of Jim Hughes.	ATACseq_Epiboly_Citrine-Cherry_1	bd_1_2_3_non_dr10	GSM2845179_Epi_CCA.bed.gz
GSM2845178	Embryo_epiboly_80	NA	GSE106676	 Citrine reporter expressing cells from 75% Epiboly stage embryos	Citrine reporter expressing cells from 75% Epiboly stage embryos		 75% Epiboly	 Gt(foxd3-citrine)ct110		ATAC-Seq	danRer10	ChIP-seq, Biotin-ChIP-seq, and ATAC-seq reads were trimmed for quality using sickle (v 1.33) and mapped using bowtie (v.1.0.0). Smoothened bigWig files were generated using a enhanced Perl script courtesy of Jim Hughes.	ATACseq_Epiboly_Citrine_2	bd_1_2_3_non_dr10	GSM2845178_Epi_CB.bed.gz
GSM2845177	Embryo_epiboly_80	NA	GSE106676	 Citrine reporter expressing cells from 75% Epiboly stage embryos	Citrine reporter expressing cells from 75% Epiboly stage embryos		 75% Epiboly	 Gt(foxd3-citrine)ct110		ATAC-Seq	danRer10	ChIP-seq, Biotin-ChIP-seq, and ATAC-seq reads were trimmed for quality using sickle (v 1.33) and mapped using bowtie (v.1.0.0). Smoothened bigWig files were generated using a enhanced Perl script courtesy of Jim Hughes.	ATACseq_Epiboly_Citrine_1	bd_1_2_3_non_dr10	GSM2845177_Epi_CA.bed.gz
GSM2837492	Embryo_epiboly_80	NA	GSE106431		whole embryo		 80% epiboly			ATAC-Seq	GRCz10	Alignment: reads were aligned against reference genome using Bowtie2 software.	ATACseq zebra 80% epiboly replicate 2	bd_0_1_2_6_dr10	UsingSRR
GSM2837491	Embryo_epiboly_80	NA	GSE106431		whole embryo		 80% epiboly			ATAC-Seq	GRCz10	Alignment: reads were aligned against reference genome using Bowtie2 software.	ATACseq zebra 80% epiboly replicate 1	bd_0_1_2_6_dr10	UsingSRR