Source Name	Comment [Sample_description]	Comment [Sample_source_name]	Comment [Sample_title]	Characteristics [chip antibody]	Characteristics [organism]	Term Source REF	Term Accession Number	Characteristics [organism part]	Characteristics [strain]	Protocol REF	Term Source REF	Protocol REF	Term Source REF	Protocol REF	Term Source REF	Extract Name	Comment [INSTRUMENT_MODEL]	Comment [LIBRARY_SELECTION]	Comment [LIBRARY_SOURCE]	Comment [LIBRARY_STRATEGY]	Material Type	Assay Name	Comment [ENA_EXPERIMENT]	Comment [Platform_title]	Technology Type	Derived Array Data File	Comment [Derived ArrayExpress FTP file]	FactorValue [CHIP ANTIBODY]
GSM1173385 1	Input	Bud stage embryo	Input sequencing in bud-stage embryo rep 3	Input	Danio rerio	EFO	http://purl.obolibrary.org/obo/NCBITaxon_7955	whole embryo	Tu	P-GSE48254-1	ArrayExpress	P-GSE48254-2	ArrayExpress	P-GSE48254-3	ArrayExpress	GSM1173385 extract 1	Illumina HiSeq 2000	ChIP	genomic	ChIP-Seq	genomic DNA	GSM1173385	SRX314764	Illumina HiSeq 2000 (Danio rerio)	sequencing assay	GSM1173385_Zon_Bud_Input_130612_s7-1.bw	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-48254/E-GEOD-48254.processed.1.zip	Input
GSM1173384 1	Input	Bud stage embryo	Input sequencing in bud-stage embryo rep 2	Input	Danio rerio	EFO	http://purl.obolibrary.org/obo/NCBITaxon_7955	whole embryo	Tu	P-GSE48254-1	ArrayExpress	P-GSE48254-2	ArrayExpress	P-GSE48254-3	ArrayExpress	GSM1173384 extract 1	Illumina HiSeq 2000	ChIP	genomic	ChIP-Seq	genomic DNA	GSM1173384	SRX314763	Illumina HiSeq 2000 (Danio rerio)	sequencing assay	GSM1173384_Zon_Bud_Input_120103_s5-1.bw	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-48254/E-GEOD-48254.processed.1.zip	Input
GSM1173383 1	Input	Bud stage embryo	Input sequencing in bud-stage embryo rep 1	Input	Danio rerio	EFO	http://purl.obolibrary.org/obo/NCBITaxon_7955	whole embryo	Tu	P-GSE48254-1	ArrayExpress	P-GSE48254-2	ArrayExpress	P-GSE48254-3	ArrayExpress	GSM1173383 extract 1	Illumina Genome Analyzer II	ChIP	genomic	ChIP-Seq	genomic DNA	GSM1173383	SRX314762	Illumina Genome Analyzer II (Danio rerio)	sequencing assay	GSM1173383_Zon_Bud_Input_110914_s1.bw	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-48254/E-GEOD-48254.processed.1.zip	Input
GSM1173382 1	Chromatin IP against H3K4me3	Bud stage embryo	ChIP-seq H3K4me3 in bud-stage embryo	Anti-Trimethyl-Histone H3 (Lys4) (Millipore 07-473)	Danio rerio	EFO	http://purl.obolibrary.org/obo/NCBITaxon_7955	whole embryo	Tu	P-GSE48254-1	ArrayExpress	P-GSE48254-2	ArrayExpress	P-GSE48254-3	ArrayExpress	GSM1173382 extract 1	Illumina HiSeq 2000	ChIP	genomic	ChIP-Seq	genomic DNA	GSM1173382	SRX314761	Illumina HiSeq 2000 (Danio rerio)	sequencing assay	GSM1173382_Zon_Bud_H3K4me3_120103_s4-1.bw	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-48254/E-GEOD-48254.processed.1.zip	Anti-Trimethyl-Histone H3 (Lys4) (Millipore 07-473)
GSM1173382 1	Chromatin IP against H3K4me3	Bud stage embryo	ChIP-seq H3K4me3 in bud-stage embryo	Anti-Trimethyl-Histone H3 (Lys4) (Millipore 07-473)	Danio rerio	EFO	http://purl.obolibrary.org/obo/NCBITaxon_7955	whole embryo	Tu	P-GSE48254-1	ArrayExpress	P-GSE48254-2	ArrayExpress	P-GSE48254-3	ArrayExpress	GSM1173382 extract 1	Illumina HiSeq 2000	ChIP	genomic	ChIP-Seq	genomic DNA	GSM1173382	SRX314761	Illumina HiSeq 2000 (Danio rerio)	sequencing assay	GSM1173382_Zon_Bud_H3K4me3.domains.bed	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-48254/E-GEOD-48254.processed.1.zip	Anti-Trimethyl-Histone H3 (Lys4) (Millipore 07-473)
GSM1173381 1	Chromatin IP against H3K27ac	Bud stage embryo	ChIP-seq H3K27ac in bud-stage embryo	Anti-Histone H3 (acetyl K27) (Abcam ab4729)	Danio rerio	EFO	http://purl.obolibrary.org/obo/NCBITaxon_7955	whole embryo	Tu	P-GSE48254-1	ArrayExpress	P-GSE48254-2	ArrayExpress	P-GSE48254-3	ArrayExpress	GSM1173381 extract 1	Illumina HiSeq 2000	ChIP	genomic	ChIP-Seq	genomic DNA	GSM1173381	SRX314760	Illumina HiSeq 2000 (Danio rerio)	sequencing assay	GSM1173381_Zon_Bud_H3K27ac_130612_s7-1.bw	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-48254/E-GEOD-48254.processed.2.zip	Anti-Histone H3 (acetyl K27) (Abcam ab4729)
GSM1173381 1	Chromatin IP against H3K27ac	Bud stage embryo	ChIP-seq H3K27ac in bud-stage embryo	Anti-Histone H3 (acetyl K27) (Abcam ab4729)	Danio rerio	EFO	http://purl.obolibrary.org/obo/NCBITaxon_7955	whole embryo	Tu	P-GSE48254-1	ArrayExpress	P-GSE48254-2	ArrayExpress	P-GSE48254-3	ArrayExpress	GSM1173381 extract 1	Illumina HiSeq 2000	ChIP	genomic	ChIP-Seq	genomic DNA	GSM1173381	SRX314760	Illumina HiSeq 2000 (Danio rerio)	sequencing assay	GSM1173381_Zon_Bud_H3K27ac.domains.bed	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-48254/E-GEOD-48254.processed.2.zip	Anti-Histone H3 (acetyl K27) (Abcam ab4729)
GSM1173380 1	Chromatin IP against myc-tagged Sall4	Bud stage embryo	ChIP-seq myc-tagged Sall4 in bud-stage embryo	Anti-Myc (Abcam ab9132)	Danio rerio	EFO	http://purl.obolibrary.org/obo/NCBITaxon_7955	whole embryo	Tu	P-GSE48254-1	ArrayExpress	P-GSE48254-2	ArrayExpress	P-GSE48254-3	ArrayExpress	GSM1173380 extract 1	Illumina Genome Analyzer II	ChIP	genomic	ChIP-Seq	genomic DNA	GSM1173380	SRX314759	Illumina Genome Analyzer II (Danio rerio)	sequencing assay	GSM1173380_Zon_Bud_Sall4_110914_s4.bw	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-48254/E-GEOD-48254.processed.2.zip	Anti-Myc (Abcam ab9132)
GSM1173380 1	Chromatin IP against myc-tagged Sall4	Bud stage embryo	ChIP-seq myc-tagged Sall4 in bud-stage embryo	Anti-Myc (Abcam ab9132)	Danio rerio	EFO	http://purl.obolibrary.org/obo/NCBITaxon_7955	whole embryo	Tu	P-GSE48254-1	ArrayExpress	P-GSE48254-2	ArrayExpress	P-GSE48254-3	ArrayExpress	GSM1173380 extract 1	Illumina Genome Analyzer II	ChIP	genomic	ChIP-Seq	genomic DNA	GSM1173380	SRX314759	Illumina Genome Analyzer II (Danio rerio)	sequencing assay	GSM1173380_Zon_Bud_Sall4.peaks.bed	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-48254/E-GEOD-48254.processed.2.zip	Anti-Myc (Abcam ab9132)
GSM1173379 1	Chromatin IP against myc-tagged Cdx4	Bud stage embryo	ChIP-seq myc-tagged Cdx4 in bud-stage embryo	Anti-Myc (Abcam ab9132)	Danio rerio	EFO	http://purl.obolibrary.org/obo/NCBITaxon_7955	whole embryo	Tu	P-GSE48254-1	ArrayExpress	P-GSE48254-2	ArrayExpress	P-GSE48254-3	ArrayExpress	GSM1173379 extract 1	Illumina Genome Analyzer II	ChIP	genomic	ChIP-Seq	genomic DNA	GSM1173379	SRX314758	Illumina Genome Analyzer II (Danio rerio)	sequencing assay	GSM1173379_Zon_Bud_Cdx4_110914_s3.bw	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-48254/E-GEOD-48254.processed.2.zip	Anti-Myc (Abcam ab9132)
GSM1173379 1	Chromatin IP against myc-tagged Cdx4	Bud stage embryo	ChIP-seq myc-tagged Cdx4 in bud-stage embryo	Anti-Myc (Abcam ab9132)	Danio rerio	EFO	http://purl.obolibrary.org/obo/NCBITaxon_7955	whole embryo	Tu	P-GSE48254-1	ArrayExpress	P-GSE48254-2	ArrayExpress	P-GSE48254-3	ArrayExpress	GSM1173379 extract 1	Illumina Genome Analyzer II	ChIP	genomic	ChIP-Seq	genomic DNA	GSM1173379	SRX314758	Illumina Genome Analyzer II (Danio rerio)	sequencing assay	GSM1173379_Zon_Bud_Cdx4.peaks.bed	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-48254/E-GEOD-48254.processed.2.zip	Anti-Myc (Abcam ab9132)