metadata: run_metadata: 1,388 rows where devstage_curation = "Pharyngula" and tissue

1,388 rows where devstage_curation = "Pharyngula" and tissue_curation = "Embryo Imprecise"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
11753	11753	ERR11758614	ERX11157721	ERS16172939	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	fli1tp1 24hpf	SAMEA114192246	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192246\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:fli1tp1 24hpf\|age:24\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:24 hpf\|genotype:fli1:DsRed tp1:eGFP\|geographic location country and/or sea:not collected\|immunophenotype:fli1:DsRed+ tp1:eGFP+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:fli1tp1 24hpf\|scientific name:Danio rerio\|strain:fli1:DsRed tp1:eGFP	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:fli1tp1 24hpf p	fli1tp1 24hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	FliTp124hpf_S25_L001_R1_001.fastq.gz FliTp124hpf_S25_L001_R2_001.fastq.gz	fastq fastq	226833768.0	1800268.0	E MTAB 13196:FliTp124hpf S25 L001	0:28 1:98	A:65319978;C:50920193;G:49999849;T:60474280;N:119468	28	98	65319978	50920193	49999849	60474280	119468	ERX11157721	ERS16172939	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00122	0.88236	0.00056	0.09684	0.9978	0.89309	0.424	0.44186	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
11754	11754	ERR11758619	ERX11157721	ERS16172939	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	fli1tp1 24hpf	SAMEA114192246	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192246\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:fli1tp1 24hpf\|age:24\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:24 hpf\|genotype:fli1:DsRed tp1:eGFP\|geographic location country and/or sea:not collected\|immunophenotype:fli1:DsRed+ tp1:eGFP+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:fli1tp1 24hpf\|scientific name:Danio rerio\|strain:fli1:DsRed tp1:eGFP	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:fli1tp1 24hpf p	fli1tp1 24hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	FliTp124hpf_S27_L001_R1_001.fastq.gz FliTp124hpf_S27_L001_R2_001.fastq.gz	fastq fastq	261098334.0	2072209.0	E MTAB 13196:FliTp124hpf S27 L001	0:28 1:98	A:76098436;C:58031830;G:57099955;T:69729759;N:138354	28	98	76098436	58031830	57099955	69729759	138354	ERX11157721	ERS16172939	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00109	0.87641	0.00062	0.0976	0.99837	0.90065	0.45555	0.48712	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
11755	11755	ERR11758589	ERX11157721	ERS16172939	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	fli1tp1 24hpf	SAMEA114192246	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192246\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:fli1tp1 24hpf\|age:24\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:24 hpf\|genotype:fli1:DsRed tp1:eGFP\|geographic location country and/or sea:not collected\|immunophenotype:fli1:DsRed+ tp1:eGFP+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:fli1tp1 24hpf\|scientific name:Danio rerio\|strain:fli1:DsRed tp1:eGFP	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:fli1tp1 24hpf p	fli1tp1 24hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	FliTp124hpf_S16_L005_R1_001.fastq.gz FliTp124hpf_S16_L005_R2_001.fastq.gz	fastq fastq	1168367130.0	9272755.0	E MTAB 13196:FliTp124hpf S16 L005	0:28 1:98	A:323651598;C:269884286;G:268030176;T:306695030;N:106040	28	98	323651598	269884286	268030176	306695030	106040	ERX11157721	ERS16172939	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00491	0.90853	0.00131	0.07851	0.99019	0.84331	0.41536	0.48076	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
11756	11756	ERR11758638	ERX11157721	ERS16172939	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	fli1tp1 24hpf	SAMEA114192246	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192246\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:fli1tp1 24hpf\|age:24\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:24 hpf\|genotype:fli1:DsRed tp1:eGFP\|geographic location country and/or sea:not collected\|immunophenotype:fli1:DsRed+ tp1:eGFP+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:fli1tp1 24hpf\|scientific name:Danio rerio\|strain:fli1:DsRed tp1:eGFP	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:fli1tp1 24hpf p	fli1tp1 24hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	FliTp124hpf_S22_L001_R1_001.fastq.gz FliTp124hpf_S22_L001_R2_001.fastq.gz	fastq fastq	864786636.0	6863386.0	E MTAB 13196:FliTp124hpf S22 L001	0:28 1:98	A:241767760;C:198370882;G:198049093;T:226508751;N:90150	28	98	241767760	198370882	198049093	226508751	90150	ERX11157721	ERS16172939	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00375	0.89002	0.00114	0.0769	0.99237	0.84563	0.41796	0.48995	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
11757	11757	ERR11758599	ERX11157721	ERS16172939	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	fli1tp1 24hpf	SAMEA114192246	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192246\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:fli1tp1 24hpf\|age:24\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:24 hpf\|genotype:fli1:DsRed tp1:eGFP\|geographic location country and/or sea:not collected\|immunophenotype:fli1:DsRed+ tp1:eGFP+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:fli1tp1 24hpf\|scientific name:Danio rerio\|strain:fli1:DsRed tp1:eGFP	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:fli1tp1 24hpf p	fli1tp1 24hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	FliTp124hpf_S15_L005_R1_001.fastq.gz FliTp124hpf_S15_L005_R2_001.fastq.gz	fastq fastq	1795799502.0	14252377.0	E MTAB 13196:FliTp124hpf S15 L005	0:28 1:98	A:500590460;C:413239086;G:410401125;T:471402890;N:165941	28	98	500590460	413239086	410401125	471402890	165941	ERX11157721	ERS16172939	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00492	0.91242	0.0012	0.08044	0.99007	0.84668	0.42778	0.49291	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
11758	11758	ERR11758601	ERX11157721	ERS16172939	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	fli1tp1 24hpf	SAMEA114192246	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192246\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:fli1tp1 24hpf\|age:24\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:24 hpf\|genotype:fli1:DsRed tp1:eGFP\|geographic location country and/or sea:not collected\|immunophenotype:fli1:DsRed+ tp1:eGFP+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:fli1tp1 24hpf\|scientific name:Danio rerio\|strain:fli1:DsRed tp1:eGFP	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:fli1tp1 24hpf p	fli1tp1 24hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	FliTp124hpf_S26_L001_R1_001.fastq.gz FliTp124hpf_S26_L001_R2_001.fastq.gz	fastq fastq	266141358.0	2112233.0	E MTAB 13196:FliTp124hpf S26 L001	0:28 1:98	A:76996100;C:59592346;G:58963461;T:70457732;N:131719	28	98	76996100	59592346	58963461	70457732	131719	ERX11157721	ERS16172939	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00106	0.88422	0.00046	0.09358	0.99782	0.89449	0.47826	0.48948	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
11759	11759	ERR11758630	ERX11157721	ERS16172939	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	fli1tp1 24hpf	SAMEA114192246	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192246\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:fli1tp1 24hpf\|age:24\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:24 hpf\|genotype:fli1:DsRed tp1:eGFP\|geographic location country and/or sea:not collected\|immunophenotype:fli1:DsRed+ tp1:eGFP+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:fli1tp1 24hpf\|scientific name:Danio rerio\|strain:fli1:DsRed tp1:eGFP	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:fli1tp1 24hpf p	fli1tp1 24hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	FliTp124hpf_S14_L005_R1_001.fastq.gz FliTp124hpf_S14_L005_R2_001.fastq.gz	fastq fastq	1812847428.0	14387678.0	E MTAB 13196:FliTp124hpf S14 L005	0:28 1:98	A:502956890;C:417865079;G:416595454;T:475266679;N:163326	28	98	502956890	417865079	416595454	475266679	163326	ERX11157721	ERS16172939	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00483	0.91317	0.00123	0.07918	0.99036	0.84143	0.40704	0.4819	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
11760	11760	ERR11758603	ERX11157721	ERS16172939	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	fli1tp1 24hpf	SAMEA114192246	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192246\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:fli1tp1 24hpf\|age:24\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:24 hpf\|genotype:fli1:DsRed tp1:eGFP\|geographic location country and/or sea:not collected\|immunophenotype:fli1:DsRed+ tp1:eGFP+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:fli1tp1 24hpf\|scientific name:Danio rerio\|strain:fli1:DsRed tp1:eGFP	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:fli1tp1 24hpf p	fli1tp1 24hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	FliTp124hpf_S13_L005_R1_001.fastq.gz FliTp124hpf_S13_L005_R2_001.fastq.gz	fastq fastq	1544281830.0	12256205.0	E MTAB 13196:FliTp124hpf S13 L005	0:28 1:98	A:428008915;C:356252081;G:354333187;T:405545992;N:141655	28	98	428008915	356252081	354333187	405545992	141655	ERX11157721	ERS16172939	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00507	0.91025	0.00138	0.07858	0.98987	0.84295	0.41793	0.4891	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
11761	11761	ERR11758613	ERX11157721	ERS16172939	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	fli1tp1 24hpf	SAMEA114192246	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192246\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:fli1tp1 24hpf\|age:24\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:24 hpf\|genotype:fli1:DsRed tp1:eGFP\|geographic location country and/or sea:not collected\|immunophenotype:fli1:DsRed+ tp1:eGFP+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:fli1tp1 24hpf\|scientific name:Danio rerio\|strain:fli1:DsRed tp1:eGFP	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:fli1tp1 24hpf p	fli1tp1 24hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	FliTp124hpf_S21_L001_R1_001.fastq.gz FliTp124hpf_S21_L001_R2_001.fastq.gz	fastq fastq	761441436.0	6043186.0	E MTAB 13196:FliTp124hpf S21 L001	0:28 1:98	A:212876877;C:174700212;G:174244892;T:199537401;N:82054	28	98	212876877	174700212	174244892	199537401	82054	ERX11157721	ERS16172939	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00334	0.88899	0.00106	0.07762	0.99322	0.84476	0.42792	0.48783	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
11762	11762	ERR11758645	ERX11157721	ERS16172939	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	fli1tp1 24hpf	SAMEA114192246	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192246\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:fli1tp1 24hpf\|age:24\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:24 hpf\|genotype:fli1:DsRed tp1:eGFP\|geographic location country and/or sea:not collected\|immunophenotype:fli1:DsRed+ tp1:eGFP+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:fli1tp1 24hpf\|scientific name:Danio rerio\|strain:fli1:DsRed tp1:eGFP	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:fli1tp1 24hpf p	fli1tp1 24hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	FliTp124hpf_S23_L001_R1_001.fastq.gz FliTp124hpf_S23_L001_R2_001.fastq.gz	fastq fastq	873938772.0	6936022.0	E MTAB 13196:FliTp124hpf S23 L001	0:28 1:98	A:245075115;C:199879929;G:199312177;T:229576663;N:94888	28	98	245075115	199879929	199312177	229576663	94888	ERX11157721	ERS16172939	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00361	0.88671	0.00104	0.07855	0.99255	0.84723	0.41141	0.4885	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
11763	11763	ERR11758598	ERX11157721	ERS16172939	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	fli1tp1 24hpf	SAMEA114192246	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192246\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:fli1tp1 24hpf\|age:24\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:24 hpf\|genotype:fli1:DsRed tp1:eGFP\|geographic location country and/or sea:not collected\|immunophenotype:fli1:DsRed+ tp1:eGFP+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:fli1tp1 24hpf\|scientific name:Danio rerio\|strain:fli1:DsRed tp1:eGFP	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:fli1tp1 24hpf p	fli1tp1 24hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	FliTp124hpf_S28_L001_R1_001.fastq.gz FliTp124hpf_S28_L001_R2_001.fastq.gz	fastq fastq	164465532.0	1305282.0	E MTAB 13196:FliTp124hpf S28 L001	0:28 1:98	A:47319366;C:37063279;G:36394680;T:43602586;N:85621	28	98	47319366	37063279	36394680	43602586	85621	ERX11157721	ERS16172939	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00117	0.88222	0.00058	0.09358	0.99799	0.89217	0.54867	0.48545	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
11764	11764	ERR11758593	ERX11157721	ERS16172939	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	fli1tp1 24hpf	SAMEA114192246	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192246\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:fli1tp1 24hpf\|age:24\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:24 hpf\|genotype:fli1:DsRed tp1:eGFP\|geographic location country and/or sea:not collected\|immunophenotype:fli1:DsRed+ tp1:eGFP+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:fli1tp1 24hpf\|scientific name:Danio rerio\|strain:fli1:DsRed tp1:eGFP	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:fli1tp1 24hpf p	fli1tp1 24hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	FliTp124hpf_S24_L001_R1_001.fastq.gz FliTp124hpf_S24_L001_R2_001.fastq.gz	fastq fastq	558365976.0	4431476.0	E MTAB 13196:FliTp124hpf S24 L001	0:28 1:98	A:156054630;C:128109738;G:127885708;T:146256146;N:59754	28	98	156054630	128109738	127885708	146256146	59754	ERX11157721	ERS16172939	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00345	0.8879	0.00104	0.07718	0.99322	0.84364	0.38266	0.49193	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
11765	11765	ERR11758635	ERX11157720	ERS16172938	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	etv2 wt 22hpf	SAMEA114192245	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192245\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:etv2 wt 22hpf\|age:24\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:24 hpf\|genotype:etv2:Kaede\|geographic location country and/or sea:not collected\|immunophenotype:etv2:Kaede+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:etv2 wt 22hpf\|scientific name:Danio rerio\|strain:etv2:Kaede	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:etv2 wt 22hpf p	etv2 wt 22hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Etv2Kaede_WT_S6_L001_R1_001.fastq.gz Etv2Kaede_WT_S6_L001_R2_001.fastq.gz	fastq fastq	1144014102.0	9079477.0	E MTAB 13196:Etv2Kaede WT S6 L001	0:28 1:98	A:316366230;C:260322813;G:259447166;T:307680623;N:197270	28	98	316366230	260322813	259447166	307680623	197270	ERX11157720	ERS16172938	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00336	0.89267	0.00137	0.13734	0.99545	0.81957	0.3734	0.53458	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
11766	11766	ERR11758622	ERX11157720	ERS16172938	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	etv2 wt 22hpf	SAMEA114192245	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192245\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:etv2 wt 22hpf\|age:24\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:24 hpf\|genotype:etv2:Kaede\|geographic location country and/or sea:not collected\|immunophenotype:etv2:Kaede+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:etv2 wt 22hpf\|scientific name:Danio rerio\|strain:etv2:Kaede	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:etv2 wt 22hpf p	etv2 wt 22hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Etv2Kaede_WT_S8_L001_R2_001.fastq.gz Etv2Kaede_WT_S8_L001_R1_001.fastq.gz	fastq fastq	919270926.0	7295801.0	E MTAB 13196:Etv2Kaede WT S8 L001	0:28 1:98	A:259787542;C:207541571;G:206711907;T:245072713;N:157193	28	98	259787542	207541571	206711907	245072713	157193	ERX11157720	ERS16172938	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00358	0.88757	0.00137	0.15368	0.99551	0.83378	0.36405	0.53733	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
11767	11767	ERR11758644	ERX11157720	ERS16172938	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	etv2 wt 22hpf	SAMEA114192245	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192245\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:etv2 wt 22hpf\|age:24\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:24 hpf\|genotype:etv2:Kaede\|geographic location country and/or sea:not collected\|immunophenotype:etv2:Kaede+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:etv2 wt 22hpf\|scientific name:Danio rerio\|strain:etv2:Kaede	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:etv2 wt 22hpf p	etv2 wt 22hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Etv2Kaede_WT_S5_L001_R2_001.fastq.gz Etv2Kaede_WT_S5_L001_R1_001.fastq.gz	fastq fastq	877658166.0	6965541.0	E MTAB 13196:Etv2Kaede WT S5 L001	0:28 1:98	A:243057461;C:199464116;G:198654377;T:236322700;N:159512	28	98	243057461	199464116	198654377	236322700	159512	ERX11157720	ERS16172938	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00328	0.88916	0.00127	0.13782	0.99559	0.81925	0.38227	0.53623	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
11768	11768	ERR11758628	ERX11157720	ERS16172938	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	etv2 wt 22hpf	SAMEA114192245	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192245\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:etv2 wt 22hpf\|age:24\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:24 hpf\|genotype:etv2:Kaede\|geographic location country and/or sea:not collected\|immunophenotype:etv2:Kaede+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:etv2 wt 22hpf\|scientific name:Danio rerio\|strain:etv2:Kaede	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:etv2 wt 22hpf p	etv2 wt 22hpf p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Etv2Kaede_WT_S7_L001_R1_001.fastq.gz Etv2Kaede_WT_S7_L001_R2_001.fastq.gz	fastq fastq	930443598.0	7384473.0	E MTAB 13196:Etv2Kaede WT S7 L001	0:28 1:98	A:258539610;C:211017108;G:209074684;T:251641766;N:170430	28	98	258539610	211017108	209074684	251641766	170430	ERX11157720	ERS16172938	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00355	0.88938	0.00148	0.14297	0.99569	0.83358	0.35626	0.53314	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15070	15070	ERR12476466	ERX11852287	ERS17743541	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1219 from a cross with a starved father	1219 Starved	1219S		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:193 277029	1219S	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1219S_S12_L003_R1_001.fastq.gz	fastq	97592891.0	1298822.0	ena RUN TAB 15 01 2024 21:42:36:193 277030	0:75.14	A:34708924;C:19086989;G:21325291;T:22442527;N:29160	75		34708924	19086989	21325291	22442527	29160	ERX11852287	ERS17743541	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15071	15071	ERR12476447	ERX11852268	ERS17743536	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1203 from a cross with a fed father	1203 Fed	1203F		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:179 276991	1203F	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1203F_S5_L004_R1_001.fastq.gz	fastq	92134036.0	1226106.0	ena RUN TAB 15 01 2024 21:42:36:179 276992	0:75.14	A:33032252;C:17497320;G:19713134;T:21873197;N:18133	75		33032252	17497320	19713134	21873197	18133	ERX11852268	ERS17743536	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15072	15072	ERR12476437	ERX11852258	ERS17743534	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1118 from a cross with a fed father	1118 Fed	1118F		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:172 276971	1118F	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1118F_S9_L002_R1_001.fastq.gz	fastq	98606332.0	1311676.0	ena RUN TAB 15 01 2024 21:42:36:172 276972	0:75.18	A:35097475;C:19013865;G:21072825;T:23400976;N:21191	75		35097475	19013865	21072825	23400976	21191	ERX11852258	ERS17743534	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15073	15073	ERR12476468	ERX11852289	ERS17743542	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1242 from a cross with a fed father	1242D Fed	1242FD		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:194 277033	1242FD	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1242FD_S13_L001_R1_001.fastq.gz	fastq	89342488.0	1186885.0	ena RUN TAB 15 01 2024 21:42:36:194 277034	0:75.27	A:31174342;C:17129181;G:18704493;T:22323017;N:11455	75		31174342	17129181	18704493	22323017	11455	ERX11852289	ERS17743542	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15074	15074	ERR12476438	ERX11852259	ERS17743534	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1118 from a cross with a fed father	1118 Fed	1118F		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:173 276973	1118F	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1118F_S9_L003_R1_001.fastq.gz	fastq	98443412.0	1309747.0	ena RUN TAB 15 01 2024 21:42:36:173 276974	0:75.16	A:35171021;C:18991511;G:20974950;T:23280285;N:25645	75		35171021	18991511	20974950	23280285	25645	ERX11852259	ERS17743534	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15075	15075	ERR12476442	ERX11852263	ERS17743535	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1118 from a cross with a starved father	1118 Starved	1118S		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:176 276981	1118S	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1118S_S10_L003_R1_001.fastq.gz	fastq	98865255.0	1315357.0	ena RUN TAB 15 01 2024 21:42:36:176 276982	0:75.16	A:34981471;C:19126822;G:21304286;T:23427226;N:25450	75		34981471	19126822	21304286	23427226	25450	ERX11852263	ERS17743535	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15076	15076	ERR12476467	ERX11852288	ERS17743541	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1219 from a cross with a starved father	1219 Starved	1219S		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:193 277031	1219S	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1219S_S12_L004_R1_001.fastq.gz	fastq	88230016.0	1174256.0	ena RUN TAB 15 01 2024 21:42:36:194 277032	0:75.14	A:31409300;C:17203675;G:19284478;T:20309174;N:23389	75		31409300	17203675	19284478	20309174	23389	ERX11852288	ERS17743541	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15077	15077	ERR12476470	ERX11852291	ERS17743542	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1242 from a cross with a fed father	1242D Fed	1242FD		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:195 277037	1242FD	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1242FD_S13_L003_R1_001.fastq.gz	fastq	93375090.0	1240903.0	ena RUN TAB 15 01 2024 21:42:36:196 277038	0:75.25	A:32510114;C:17950920;G:19575617;T:23324862;N:13577	75		32510114	17950920	19575617	23324862	13577	ERX11852291	ERS17743542	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15078	15078	ERR12476436	ERX11852257	ERS17743534	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1118 from a cross with a fed father	1118 Fed	1118F		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:171 276969	1118F	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1118F_S9_L001_R1_001.fastq.gz	fastq	94258948.0	1253428.0	ena RUN TAB 15 01 2024 21:42:36:171 276970	0:75.20	A:33713614;C:18157124;G:20086205;T:22277451;N:24554	75		33713614	18157124	20086205	22277451	24554	ERX11852257	ERS17743534	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15079	15079	ERR12476452	ERX11852273	ERS17743538	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1210 from a cross with a fed father	1210 Fed	1210F		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:183 277001	1210F	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1210F_S7_L001_R1_001.fastq.gz	fastq	96414625.0	1283672.0	ena RUN TAB 15 01 2024 21:42:36:183 277002	0:75.11	A:35605799;C:18366729;G:20807908;T:21594044;N:40145	75		35605799	18366729	20807908	21594044	40145	ERX11852273	ERS17743538	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15080	15080	ERR12476475	ERX11852296	ERS17743544	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1242 from a cross with a fed father	1242E Fed	1242FE		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:199 277047	1242FE	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1242FE_S15_L004_R1_001.fastq.gz	fastq	99581325.0	1325945.0	ena RUN TAB 15 01 2024 21:42:36:199 277048	0:75.10	A:36802442;C:18868511;G:20958294;T:22926783;N:25295	75		36802442	18868511	20958294	22926783	25295	ERX11852296	ERS17743544	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15081	15081	ERR12476478	ERX11852299	ERS17743543	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1242 from a cross with a starved father	1242D Starved	1242SD		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:201 277053	1242SD	1		RNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1242SD_S14_L003_R1_001.fastq.gz	fastq	95457398.0	1268859.0	ena RUN TAB 15 01 2024 21:42:36:202 277054	0:75.23	A:33339157;C:18598733;G:20350072;T:23148005;N:21431	75		33339157	18598733	20350072	23148005	21431	ERX11852299	ERS17743543	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15082	15082	ERR12476473	ERX11852294	ERS17743544	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1242 from a cross with a fed father	1242E Fed	1242FE		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:198 277043	1242FE	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1242FE_S15_L002_R1_001.fastq.gz	fastq	111191327.0	1479982.0	ena RUN TAB 15 01 2024 21:42:36:198 277044	0:75.13	A:40873794;C:21118758;G:23508088;T:25663516;N:27171	75		40873794	21118758	23508088	25663516	27171	ERX11852294	ERS17743544	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15083	15083	ERR12476472	ERX11852293	ERS17743544	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1242 from a cross with a fed father	1242E Fed	1242FE		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:197 277041	1242FE	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1242FE_S15_L001_R1_001.fastq.gz	fastq	105936834.0	1409443.0	ena RUN TAB 15 01 2024 21:42:36:197 277042	0:75.16	A:39084749;C:20103850;G:22336806;T:24384711;N:26718	75		39084749	20103850	22336806	24384711	26718	ERX11852293	ERS17743544	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15084	15084	ERR12476455	ERX11852276	ERS17743538	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1210 from a cross with a fed father	1210 Fed	1210F		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:185 277007	1210F	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1210F_S7_L004_R1_001.fastq.gz	fastq	91003627.0	1212716.0	ena RUN TAB 15 01 2024 21:42:36:185 277008	0:75.04	A:33677348;C:17299066;G:19585548;T:20403064;N:38601	75		33677348	17299066	19585548	20403064	38601	ERX11852276	ERS17743538	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15085	15085	ERR12476450	ERX11852271	ERS17743537	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1203 from a cross with a starved father	1203 Starved	1203S		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:181 276997	1203S	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1203S_S6_L003_R1_001.fastq.gz	fastq	93998632.0	1251284.0	ena RUN TAB 15 01 2024 21:42:36:182 276998	0:75.12	A:33959433;C:18143368;G:20041026;T:21824242;N:30563	75		33959433	18143368	20041026	21824242	30563	ERX11852271	ERS17743537	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15086	15086	ERR12476446	ERX11852267	ERS17743536	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1203 from a cross with a fed father	1203 Fed	1203F		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:178 276989	1203F	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1203F_S5_L003_R1_001.fastq.gz	fastq	102209965.0	1360067.0	ena RUN TAB 15 01 2024 21:42:36:179 276990	0:75.15	A:36554629;C:19466103;G:21890238;T:24276196;N:22799	75		36554629	19466103	21890238	24276196	22799	ERX11852267	ERS17743536	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15087	15087	ERR12476458	ERX11852279	ERS17743539	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1210 from a cross with a starved father	1210 Starved	1210S		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:187 277013	1210S	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1210S_S8_L003_R1_001.fastq.gz	fastq	109602092.0	1466517.0	ena RUN TAB 15 01 2024 21:42:36:187 277014	0:74.74	A:42677564;C:20838229;G:24413347;T:21498031;N:174921	74		42677564	20838229	24413347	21498031	174921	ERX11852279	ERS17743539	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15088	15088	ERR12476453	ERX11852274	ERS17743538	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1210 from a cross with a fed father	1210 Fed	1210F		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:183 277003	1210F	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1210F_S7_L002_R1_001.fastq.gz	fastq	100538748.0	1339248.0	ena RUN TAB 15 01 2024 21:42:36:184 277004	0:75.07	A:36966184;C:19156780;G:21758079;T:22618911;N:38794	75		36966184	19156780	21758079	22618911	38794	ERX11852274	ERS17743538	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15089	15089	ERR12476460	ERX11852281	ERS17743540	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1219 from a cross with a fed father	1219 Fed	1219F		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:188 277017	1219F	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1219F_S11_L001_R1_001.fastq.gz	fastq	102219114.0	1358650.0	ena RUN TAB 15 01 2024 21:42:36:189 277018	0:75.24	A:35886099;C:19931420;G:22057068;T:24325918;N:18609	75		35886099	19931420	22057068	24325918	18609	ERX11852281	ERS17743540	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15090	15090	ERR12476451	ERX11852272	ERS17743537	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1203 from a cross with a starved father	1203 Starved	1203S		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:182 276999	1203S	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1203S_S6_L004_R1_001.fastq.gz	fastq	84880221.0	1129985.0	ena RUN TAB 15 01 2024 21:42:36:182 277000	0:75.12	A:30708531;C:16338743;G:18094345;T:19712906;N:25696	75		30708531	16338743	18094345	19712906	25696	ERX11852272	ERS17743537	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15091	15091	ERR12476441	ERX11852262	ERS17743535	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1118 from a cross with a starved father	1118 Starved	1118S		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:175 276979	1118S	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1118S_S10_L002_R1_001.fastq.gz	fastq	99340604.0	1321436.0	ena RUN TAB 15 01 2024 21:42:36:175 276980	0:75.18	A:34996267;C:19218610;G:21486623;T:23616635;N:22469	75		34996267	19218610	21486623	23616635	22469	ERX11852262	ERS17743535	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15092	15092	ERR12476440	ERX11852261	ERS17743535	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1118 from a cross with a starved father	1118 Starved	1118S		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:174 276977	1118S	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1118S_S10_L001_R1_001.fastq.gz	fastq	94655454.0	1258724.0	ena RUN TAB 15 01 2024 21:42:36:175 276978	0:75.20	A:33514914;C:18282513;G:20410100;T:22427564;N:20363	75		33514914	18282513	20410100	22427564	20363	ERX11852261	ERS17743535	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15093	15093	ERR12476469	ERX11852290	ERS17743542	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1242 from a cross with a fed father	1242D Fed	1242FD		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:195 277035	1242FD	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1242FD_S13_L002_R1_001.fastq.gz	fastq	93346527.0	1240308.0	ena RUN TAB 15 01 2024 21:42:36:195 277036	0:75.26	A:32401771;C:17929540;G:19597511;T:23408465;N:9240	75		32401771	17929540	19597511	23408465	9240	ERX11852290	ERS17743542	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15094	15094	ERR12476462	ERX11852283	ERS17743540	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1219 from a cross with a fed father	1219 Fed	1219F		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:190 277021	1219F	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1219F_S11_L003_R1_001.fastq.gz	fastq	106745726.0	1419461.0	ena RUN TAB 15 01 2024 21:42:36:190 277022	0:75.20	A:37396946;C:20851140;G:23075114;T:25400364;N:22162	75		37396946	20851140	23075114	25400364	22162	ERX11852283	ERS17743540	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15095	15095	ERR12476479	ERX11852300	ERS17743543	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1242 from a cross with a starved father	1242D Starved	1242SD		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:202 277055	1242SD	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1242SD_S14_L004_R1_001.fastq.gz	fastq	85586412.0	1137781.0	ena RUN TAB 15 01 2024 21:42:36:202 277056	0:75.22	A:29963542;C:16621745;G:18219345;T:20761941;N:19839	75		29963542	16621745	18219345	20761941	19839	ERX11852300	ERS17743543	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15096	15096	ERR12476444	ERX11852265	ERS17743536	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1203 from a cross with a fed father	1203 Fed	1203F		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:177 276985	1203F	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1203F_S5_L001_R1_001.fastq.gz	fastq	97624173.0	1298240.0	ena RUN TAB 15 01 2024 21:42:36:177 276986	0:75.20	A:34935070;C:18569640;G:20912883;T:23188491;N:18089	75		34935070	18569640	20912883	23188491	18089	ERX11852265	ERS17743536	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15097	15097	ERR12476471	ERX11852292	ERS17743542	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1242 from a cross with a fed father	1242D Fed	1242FD		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:196 277039	1242FD	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1242FD_S13_L004_R1_001.fastq.gz	fastq	83383881.0	1108207.0	ena RUN TAB 15 01 2024 21:42:36:196 277040	0:75.24	A:29091135;C:15949002;G:17455499;T:20878004;N:10241	75		29091135	15949002	17455499	20878004	10241	ERX11852292	ERS17743542	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15098	15098	ERR12476439	ERX11852260	ERS17743534	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1118 from a cross with a fed father	1118 Fed	1118F		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:174 276975	1118F	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1118F_S9_L004_R1_001.fastq.gz	fastq	88439160.0	1176751.0	ena RUN TAB 15 01 2024 21:42:36:174 276976	0:75.16	A:31652556;C:16996499;G:18832233;T:20937970;N:19902	75		31652556	16996499	18832233	20937970	19902	ERX11852260	ERS17743534	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15099	15099	ERR12476449	ERX11852270	ERS17743537	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1203 from a cross with a starved father	1203 Starved	1203S		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:181 276995	1203S	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1203S_S6_L002_R1_001.fastq.gz	fastq	94525103.0	1257985.0	ena RUN TAB 15 01 2024 21:42:36:181 276996	0:75.14	A:34035341;C:18242921;G:20233155;T:21988512;N:25174	75		34035341	18242921	20233155	21988512	25174	ERX11852270	ERS17743537	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15100	15100	ERR12476465	ERX11852286	ERS17743541	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1219 from a cross with a starved father	1219 Starved	1219S		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:192 277027	1219S	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1219S_S12_L002_R1_001.fastq.gz	fastq	97087536.0	1291846.0	ena RUN TAB 15 01 2024 21:42:36:192 277028	0:75.15	A:34386434;C:18969192;G:21277103;T:22430566;N:24241	75		34386434	18969192	21277103	22430566	24241	ERX11852286	ERS17743541	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15101	15101	ERR12476482	ERX11852303	ERS17743545	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1242 from a cross with a starved father	1242E Starved	1242SE		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:204 277061	1242SE	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1242SE_S16_L003_R1_001.fastq.gz	fastq	119572581.0	1595036.0	ena RUN TAB 15 01 2024 21:42:36:204 277062	0:74.97	A:45069577;C:22967641;G:25483351;T:25959672;N:92340	74		45069577	22967641	25483351	25959672	92340	ERX11852303	ERS17743545	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15102	15102	ERR12476459	ERX11852280	ERS17743539	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1210 from a cross with a starved father	1210 Starved	1210S		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:188 277015	1210S	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1210S_S8_L004_R1_001.fastq.gz	fastq	100688924.0	1347280.0	ena RUN TAB 15 01 2024 21:42:36:188 277016	0:74.73	A:39242841;C:19105480;G:22424580;T:19763164;N:152859	74		39242841	19105480	22424580	19763164	152859	ERX11852280	ERS17743539	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15103	15103	ERR12476481	ERX11852302	ERS17743545	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1242 from a cross with a starved father	1242E Starved	1242SE		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:203 277059	1242SE	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1242SE_S16_L002_R1_001.fastq.gz	fastq	119860507.0	1598259.0	ena RUN TAB 15 01 2024 21:42:36:204 277060	0:74.99	A:44981934;C:23018661;G:25670723;T:26114916;N:74273	74		44981934	23018661	25670723	26114916	74273	ERX11852302	ERS17743545	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15104	15104	ERR12476483	ERX11852304	ERS17743545	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1242 from a cross with a starved father	1242E Starved	1242SE		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:205 277063	1242SE	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1242SE_S16_L004_R1_001.fastq.gz	fastq	108782281.0	1451206.0	ena RUN TAB 15 01 2024 21:42:36:205 277064	0:74.96	A:41041986;C:20859560;G:23168159;T:23635345;N:77231	74		41041986	20859560	23168159	23635345	77231	ERX11852304	ERS17743545	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15105	15105	ERR12476448	ERX11852269	ERS17743537	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1203 from a cross with a starved father	1203 Starved	1203S		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:180 276993	1203S	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1203S_S6_L001_R1_001.fastq.gz	fastq	89917861.0	1196172.0	ena RUN TAB 15 01 2024 21:42:36:180 276994	0:75.17	A:32511634;C:17340472;G:19179480;T:20857531;N:28744	75		32511634	17340472	19179480	20857531	28744	ERX11852269	ERS17743537	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15106	15106	ERR12476457	ERX11852278	ERS17743539	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1210 from a cross with a starved father	1210 Starved	1210S		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:186 277011	1210S	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1210S_S8_L002_R1_001.fastq.gz	fastq	110304194.0	1474848.0	ena RUN TAB 15 01 2024 21:42:36:187 277012	0:74.79	A:42702966;C:20952577;G:24773042;T:21724801;N:150808	74		42702966	20952577	24773042	21724801	150808	ERX11852278	ERS17743539	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15107	15107	ERR12476456	ERX11852277	ERS17743539	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1210 from a cross with a starved father	1210 Starved	1210S		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:185 277009	1210S	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1210S_S8_L001_R1_001.fastq.gz	fastq	106074722.0	1417003.0	ena RUN TAB 15 01 2024 21:42:36:186 277010	0:74.86	A:41208838;C:20151614;G:23770531;T:20792595;N:151144	74		41208838	20151614	23770531	20792595	151144	ERX11852277	ERS17743539	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15108	15108	ERR12476461	ERX11852282	ERS17743540	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1219 from a cross with a fed father	1219 Fed	1219F		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:189 277019	1219F	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1219F_S11_L002_R1_001.fastq.gz	fastq	106799888.0	1420026.0	ena RUN TAB 15 01 2024 21:42:36:189 277020	0:75.21	A:37294667;C:20842952;G:23154298;T:25488653;N:19318	75		37294667	20842952	23154298	25488653	19318	ERX11852282	ERS17743540	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15109	15109	ERR12476480	ERX11852301	ERS17743545	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1242 from a cross with a starved father	1242E Starved	1242SE		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:203 277057	1242SE	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1242SE_S16_L001_R1_001.fastq.gz	fastq	115150299.0	1534621.0	ena RUN TAB 15 01 2024 21:42:36:203 277058	0:75.04	A:43393516;C:22116575;G:24607338;T:24954423;N:78447	75		43393516	22116575	24607338	24954423	78447	ERX11852301	ERS17743545	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15110	15110	ERR12476464	ERX11852285	ERS17743541	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1219 from a cross with a starved father	1219 Starved	1219S		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:191 277025	1219S	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1219S_S12_L001_R1_001.fastq.gz	fastq	93625807.0	1245248.0	ena RUN TAB 15 01 2024 21:42:36:192 277026	0:75.19	A:33311180;C:18278250;G:20453262;T:21557661;N:25454	75		33311180	18278250	20453262	21557661	25454	ERX11852285	ERS17743541	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15111	15111	ERR12476474	ERX11852295	ERS17743544	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1242 from a cross with a fed father	1242E Fed	1242FE		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:198 277045	1242FE	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1242FE_S15_L003_R1_001.fastq.gz	fastq	110591461.0	1472278.0	ena RUN TAB 15 01 2024 21:42:36:199 277046	0:75.12	A:40767831;C:21026089;G:23298123;T:25470025;N:29393	75		40767831	21026089	23298123	25470025	29393	ERX11852295	ERS17743544	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15112	15112	ERR12476454	ERX11852275	ERS17743538	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1210 from a cross with a fed father	1210 Fed	1210F		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:184 277005	1210F	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1210F_S7_L003_R1_001.fastq.gz	fastq	100467804.0	1338769.0	ena RUN TAB 15 01 2024 21:42:36:184 277006	0:75.04	A:37096238;C:19156191;G:21628367;T:22539758;N:47250	75		37096238	19156191	21628367	22539758	47250	ERX11852275	ERS17743538	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15113	15113	ERR12476477	ERX11852298	ERS17743543	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1242 from a cross with a starved father	1242D Starved	1242SD		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:200 277051	1242SD	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1242SD_S14_L002_R1_001.fastq.gz	fastq	95483395.0	1269021.0	ena RUN TAB 15 01 2024 21:42:36:201 277052	0:75.24	A:33251808;C:18599068;G:20397415;T:23215065;N:20039	75		33251808	18599068	20397415	23215065	20039	ERX11852298	ERS17743543	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15114	15114	ERR12476443	ERX11852264	ERS17743535	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1118 from a cross with a starved father	1118 Starved	1118S		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:176 276983	1118S	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1118S_S10_L004_R1_001.fastq.gz	fastq	88773312.0	1181250.0	ena RUN TAB 15 01 2024 21:42:36:177 276984	0:75.15	A:31460448;C:17120679;G:19117608;T:21054486;N:20091	75		31460448	17120679	19117608	21054486	20091	ERX11852264	ERS17743535	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15115	15115	ERR12476476	ERX11852297	ERS17743543	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1242 from a cross with a starved father	1242D Starved	1242SD		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:200 277049	1242SD	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1242SD_S14_L001_R1_001.fastq.gz	fastq	91072875.0	1210121.0	ena RUN TAB 15 01 2024 21:42:36:200 277050	0:75.26	A:31859074;C:17724212;G:19393637;T:22075784;N:20168	75		31859074	17724212	19393637	22075784	20168	ERX11852297	ERS17743543	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15116	15116	ERR12476463	ERX11852284	ERS17743540	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1219 from a cross with a fed father	1219 Fed	1219F		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:190 277023	1219F	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1219F_S11_L004_R1_001.fastq.gz	fastq	96315015.0	1280935.0	ena RUN TAB 15 01 2024 21:42:36:191 277024	0:75.19	A:33841468;C:18744196;G:20803688;T:22906396;N:19267	75		33841468	18744196	20803688	22906396	19267	ERX11852284	ERS17743540	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
15117	15117	ERR12476445	ERX11852266	ERS17743536	ERP156655	PRJEB71869	Effects of paternal starvation in the offspring development of zebrafish	33b9d14c-4211-4249-aede-f0f021d197e6	Other	Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother.	ENA FIRST PUBLIC:2024 01 15\|ENA LAST UPDATE:2024 01 15	24 hpf embryo collected at 1203 from a cross with a fed father	1203 Fed	1203F		organism:Danio rerio\|collection date:2018 02 02\|scientific name:Danio rerio\|common name:zebrafish\|geographic location country and/or sea:Sweden	NextSeq 500 sequencing	ena EXPERIMENT TAB 15 01 2024 21:42:36:178 276987	1203F	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	ERP156655	NextSeq 500 sequencing	ENA FIRST PUBLIC:2024 01 22\|ENA LAST UPDATE:2024 01 22	1203F_S5_L002_R1_001.fastq.gz	fastq	102458617.0	1363028.0	ena RUN TAB 15 01 2024 21:42:36:178 276988	0:75.17	A:36510957;C:19511996;G:22025384;T:24392965;N:17315	75		36510957	19511996	22025384	24392965	17315	ERX11852266	ERS17743536	ERA27788968	University of Birmingham\|European Nucleotide Archive	University of Birmingham												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2024-01-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16526	16526	ERR667398	ERX622886	ERS463339	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548493	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:03Z\|ENA LAST UPDATE:2018 03 08T17:42:43Z\|External Id:SAMEA2548493\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:03Z\|INSDC last update:2018 03 08T17:42:43Z\|INSDC status:public\|Submitter Id:50Cyclop 0 1EtOH 24hpf control 4 sc 1972462\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 0.1% v/v ethanol.A 8 base indexing sequence TCAGGAGG is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:50Cyclop 0 1EtOH 24hpf control 4 sc 1972462\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#36	10517312	Illumina sequencing of library 10517312 constructed from sample accession ERS463339 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TCAGGAGG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#36.cram	cram	170828190.0	1314063.0	SC RUN 13256 1#36	0:55 1:75	A:44768263;C:34386047;G:35500778;T:56156162;N:16940	55	75	44768263	34386047	35500778	56156162	16940	ERX622886	ERS463339	ERA375333	SC	Wellcome Sanger Institute	2	0.13166	0.8204	0.06755	0.19006	0.95753	0.81655	0.76236	0.68533	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16527	16527	ERR667397	ERX622885	ERS463338	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548492	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:03Z\|ENA LAST UPDATE:2018 03 08T17:41:34Z\|External Id:SAMEA2548492\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:03Z\|INSDC last update:2018 03 08T17:41:34Z\|INSDC status:public\|Submitter Id:50Cyclop 0 1EtOH 24hpf control 3 sc 1972461\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 0.1% v/v ethanol.A 8 base indexing sequence TCTCACGG is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:50Cyclop 0 1EtOH 24hpf control 3 sc 1972461\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#35	10517311	Illumina sequencing of library 10517311 constructed from sample accession ERS463338 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TCTCACGG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#35.cram	cram	261820650.0	2014005.0	SC RUN 13256 1#35	0:55 1:75	A:72670470;C:50112031;G:54263310;T:84750983;N:23856	55	75	72670470	50112031	54263310	84750983	23856	ERX622885	ERS463338	ERA375333	SC	Wellcome Sanger Institute	2	0.17465	0.75166	0.11391	0.1792	0.95937	0.84238	0.73795	0.70275	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16528	16528	ERR667396	ERX622884	ERS463337	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548491	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:03Z\|ENA LAST UPDATE:2018 03 08T17:42:17Z\|External Id:SAMEA2548491\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:03Z\|INSDC last update:2018 03 08T17:42:17Z\|INSDC status:public\|Submitter Id:50Cyclop 0 1EtOH 24hpf control 2 sc 1972460\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 0.1% v/v ethanol.A 8 base indexing sequence TACTTCGG is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:50Cyclop 0 1EtOH 24hpf control 2 sc 1972460\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#34	10517310	Illumina sequencing of library 10517310 constructed from sample accession ERS463337 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TACTTCGG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#34.cram	cram	291378100.0	2241370.0	SC RUN 13256 1#34	0:55 1:75	A:80660045;C:56367784;G:60328044;T:93993547;N:28680	55	75	80660045	56367784	60328044	93993547	28680	ERX622884	ERS463337	ERA375333	SC	Wellcome Sanger Institute	2	0.16274	0.76681	0.10005	0.16164	0.95994	0.84228	0.77601	0.72125	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16529	16529	ERR667395	ERX622883	ERS463336	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548490	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:03Z\|ENA LAST UPDATE:2018 03 08T17:42:43Z\|External Id:SAMEA2548490\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:03Z\|INSDC last update:2018 03 08T17:42:43Z\|INSDC status:public\|Submitter Id:50Cyclop 0 1EtOH 24hpf treated 12 sc 1972459\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 50 micromolar cyclopamine in 0.1% v/v ethanol. A 8 base indexing sequence TGAACTGG is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:50Cyclop 0 1EtOH 24hpf treated 12 sc 1972459\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#33	10517309	Illumina sequencing of library 10517309 constructed from sample accession ERS463336 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TGAACTGG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#33.cram	cram	159495050.0	1226885.0	SC RUN 13256 1#33	0:55 1:75	A:44526945;C:31107840;G:32400438;T:51444629;N:15198	55	75	44526945	31107840	32400438	51444629	15198	ERX622883	ERS463336	ERA375333	SC	Wellcome Sanger Institute	2	0.14405	0.72387	0.09685	0.16934	0.96585	0.84476	0.75451	0.71348	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16530	16530	ERR667394	ERX622882	ERS463335	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548489	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:03Z\|ENA LAST UPDATE:2018 03 08T17:41:33Z\|External Id:SAMEA2548489\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:03Z\|INSDC last update:2018 03 08T17:41:33Z\|INSDC status:public\|Submitter Id:50Cyclop 0 1EtOH 24hpf treated 11 sc 1972458\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 50 micromolar cyclopamine in 0.1% v/v ethanol. A 8 base indexing sequence TTGGTATG is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:50Cyclop 0 1EtOH 24hpf treated 11 sc 1972458\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#32	10517308	Illumina sequencing of library 10517308 constructed from sample accession ERS463335 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TTGGTATG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#32.cram	cram	230733620.0	1774874.0	SC RUN 13256 1#32	0:55 1:75	A:65923552;C:43534910;G:44813128;T:76440148;N:21882	55	75	65923552	43534910	44813128	76440148	21882	ERX622882	ERS463335	ERA375333	SC	Wellcome Sanger Institute	2	0.16493	0.71702	0.10319	0.16046	0.96035	0.83364	0.7605	0.69357	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16531	16531	ERR667393	ERX622881	ERS463334	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548488	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:03Z\|ENA LAST UPDATE:2018 03 08T17:42:17Z\|External Id:SAMEA2548488\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:03Z\|INSDC last update:2018 03 08T17:42:17Z\|INSDC status:public\|Submitter Id:50Cyclop 0 1EtOH 24hpf treated 10 sc 1972457\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 50 micromolar cyclopamine in 0.1% v/v ethanol. A 8 base indexing sequence TAACGCTG is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:50Cyclop 0 1EtOH 24hpf treated 10 sc 1972457\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#31	10517307	Illumina sequencing of library 10517307 constructed from sample accession ERS463334 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TAACGCTG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#31.cram	cram	169693940.0	1305338.0	SC RUN 13256 1#31	0:55 1:75	A:47216999;C:32233282;G:34303404;T:55924495;N:15760	55	75	47216999	32233282	34303404	55924495	15760	ERX622881	ERS463334	ERA375333	SC	Wellcome Sanger Institute	2	0.15711	0.76441	0.09573	0.15362	0.96185	0.83625	0.78358	0.43248	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16532	16532	ERR667392	ERX622880	ERS463333	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548487	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:03Z\|ENA LAST UPDATE:2018 03 08T17:42:43Z\|External Id:SAMEA2548487\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:03Z\|INSDC last update:2018 03 08T17:42:43Z\|INSDC status:public\|Submitter Id:50Cyclop 0 1EtOH 24hpf treated 9 sc 1972456\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 50 micromolar cyclopamine in 0.1% v/v ethanol. A 8 base indexing sequence TCGAAGTG is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:50Cyclop 0 1EtOH 24hpf treated 9 sc 1972456\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#30	10517306	Illumina sequencing of library 10517306 constructed from sample accession ERS463333 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TCGAAGTG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#30.cram	cram	246126400.0	1893280.0	SC RUN 13256 1#30	0:55 1:75	A:64877434;C:48807745;G:51055789;T:81362490;N:22942	55	75	64877434	48807745	51055789	81362490	22942	ERX622880	ERS463333	ERA375333	SC	Wellcome Sanger Institute	2	0.13616	0.81131	0.0854	0.19973	0.96556	0.82757	0.74775	0.70258	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16533	16533	ERR667391	ERX622879	ERS463332	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548486	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:03Z\|ENA LAST UPDATE:2018 03 08T17:41:33Z\|External Id:SAMEA2548486\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:03Z\|INSDC last update:2018 03 08T17:41:33Z\|INSDC status:public\|Submitter Id:50Cyclop 0 1EtOH 24hpf treated 8 sc 1972455\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 50 micromolar cyclopamine in 0.1% v/v ethanol. A 8 base indexing sequence TTCCATTG is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:50Cyclop 0 1EtOH 24hpf treated 8 sc 1972455\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#29	10517305	Illumina sequencing of library 10517305 constructed from sample accession ERS463332 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TTCCATTG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#29.cram	cram	237043690.0	1823413.0	SC RUN 13256 1#29	0:55 1:75	A:68761865;C:43795810;G:47113828;T:77348945;N:23242	55	75	68761865	43795810	47113828	77348945	23242	ERX622879	ERS463332	ERA375333	SC	Wellcome Sanger Institute	2	0.13798	0.71442	0.08126	0.13596	0.95712	0.83751	0.72277	0.7226	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16534	16534	ERR667390	ERX622878	ERS463331	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548485	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:03Z\|ENA LAST UPDATE:2018 03 08T17:42:17Z\|External Id:SAMEA2548485\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:03Z\|INSDC last update:2018 03 08T17:42:17Z\|INSDC status:public\|Submitter Id:50Cyclop 0 1EtOH 24hpf treated 7 sc 1972454\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 50 micromolar cyclopamine in 0.1% v/v ethanol. A 8 base indexing sequence TAGTCTTG is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:50Cyclop 0 1EtOH 24hpf treated 7 sc 1972454\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#28	10517304	Illumina sequencing of library 10517304 constructed from sample accession ERS463331 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TAGTCTTG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#28.cram	cram	394343300.0	3033410.0	SC RUN 13256 1#28	0:55 1:75	A:111651222;C:75521035;G:80020655;T:127113022;N:37366	55	75	111651222	75521035	80020655	127113022	37366	ERX622878	ERS463331	ERA375333	SC	Wellcome Sanger Institute	2	0.13408	0.74717	0.07471	0.14051	0.95958	0.83467	0.75125	0.70647	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16535	16535	ERR667389	ERX622877	ERS463330	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548484	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:03Z\|ENA LAST UPDATE:2018 03 08T17:42:43Z\|External Id:SAMEA2548484\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:03Z\|INSDC last update:2018 03 08T17:42:43Z\|INSDC status:public\|Submitter Id:50Cyclop 0 1EtOH 24hpf treated 6 sc 1972453\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 50 micromolar cyclopamine in 0.1% v/v ethanol. A 8 base indexing sequence TGTGGTTG is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:50Cyclop 0 1EtOH 24hpf treated 6 sc 1972453\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#27	10517303	Illumina sequencing of library 10517303 constructed from sample accession ERS463330 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TGTGGTTG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#27.cram	cram	284205350.0	2186195.0	SC RUN 13256 1#27	0:55 1:75	A:81760893;C:54722204;G:55386801;T:92306336;N:29116	55	75	81760893	54722204	55386801	92306336	29116	ERX622877	ERS463330	ERA375333	SC	Wellcome Sanger Institute	2	0.15161	0.71556	0.08596	0.14319	0.95868	0.8392	0.77754	0.71796	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16536	16536	ERR667388	ERX622876	ERS463329	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548483	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:03Z\|ENA LAST UPDATE:2018 03 08T17:41:33Z\|External Id:SAMEA2548483\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:03Z\|INSDC last update:2018 03 08T17:41:33Z\|INSDC status:public\|Submitter Id:50Cyclop 0 1EtOH 24hpf treated 5 sc 1972452\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 50 micromolar cyclopamine in 0.1% v/v ethanol. A 8 base indexing sequence TCCTCAAT is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:50Cyclop 0 1EtOH 24hpf treated 5 sc 1972452\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#26	10517302	Illumina sequencing of library 10517302 constructed from sample accession ERS463329 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TCCTCAAT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#26.cram	cram	330810350.0	2544695.0	SC RUN 13256 1#26	0:55 1:75	A:93408226;C:61812207;G:69176898;T:106383919;N:29100	55	75	93408226	61812207	69176898	106383919	29100	ERX622876	ERS463329	ERA375333	SC	Wellcome Sanger Institute	2	0.13377	0.69577	0.07532	0.14875	0.95781	0.8383	0.72303	0.71175	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16537	16537	ERR667387	ERX622875	ERS463328	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548482	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:03Z\|ENA LAST UPDATE:2018 03 08T17:42:16Z\|External Id:SAMEA2548482\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:03Z\|INSDC last update:2018 03 08T17:42:16Z\|INSDC status:public\|Submitter Id:50Cyclop 0 1EtOH 24hpf treated 4 sc 1972451\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 50 micromolar cyclopamine in 0.1% v/v ethanol. A 8 base indexing sequence TACAGGAT is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:50Cyclop 0 1EtOH 24hpf treated 4 sc 1972451\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#25	10517301	Illumina sequencing of library 10517301 constructed from sample accession ERS463328 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TACAGGAT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#25.cram	cram	474507020.0	3650054.0	SC RUN 13256 1#25	0:55 1:75	A:131496123;C:90613341;G:97290951;T:155059153;N:47452	55	75	131496123	90613341	97290951	155059153	47452	ERX622875	ERS463328	ERA375333	SC	Wellcome Sanger Institute	2	0.13262	0.73888	0.07276	0.15006	0.96451	0.83479	0.78366	0.72049	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16550	16550	ERR667386	ERX622874	ERS463327	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548481	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:03Z\|ENA LAST UPDATE:2018 03 08T17:42:43Z\|External Id:SAMEA2548481\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:03Z\|INSDC last update:2018 03 08T17:42:43Z\|INSDC status:public\|Submitter Id:50Cyclop 0 1EtOH 24hpf treated 3 sc 1972450\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 50 micromolar cyclopamine in 0.1% v/v ethanol. A 8 base indexing sequence TAGTGACT is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:50Cyclop 0 1EtOH 24hpf treated 3 sc 1972450\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#24	10517300	Illumina sequencing of library 10517300 constructed from sample accession ERS463327 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TAGTGACT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#24.cram	cram	296075650.0	2277505.0	SC RUN 13256 1#24	0:55 1:75	A:82935889;C:56062979;G:59762388;T:97286073;N:28321	55	75	82935889	56062979	59762388	97286073	28321	ERX622874	ERS463327	ERA375333	SC	Wellcome Sanger Institute	2	0.1437	0.74103	0.08347	0.14393	0.96325	0.83684	0.81783	0.70771	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16551	16551	ERR667385	ERX622873	ERS463326	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548480	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:03Z\|ENA LAST UPDATE:2018 03 08T17:41:33Z\|External Id:SAMEA2548480\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:03Z\|INSDC last update:2018 03 08T17:41:33Z\|INSDC status:public\|Submitter Id:50Cyclop 0 1EtOH 24hpf treated 2 sc 1972449\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 50 micromolar cyclopamine in 0.1% v/v ethanol. A 8 base indexing sequence TTCCTGCT is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:50Cyclop 0 1EtOH 24hpf treated 2 sc 1972449\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#23	10517299	Illumina sequencing of library 10517299 constructed from sample accession ERS463326 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TTCCTGCT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#23.cram	cram	443750710.0	3413467.0	SC RUN 13256 1#23	0:55 1:75	A:124952195;C:85586617;G:94833109;T:138341796;N:36993	55	75	124952195	85586617	94833109	138341796	36993	ERX622873	ERS463326	ERA375333	SC	Wellcome Sanger Institute	2	0.15245	0.72135	0.07368	0.15151	0.95568	0.84449	0.77081	0.72424	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16552	16552	ERR667384	ERX622872	ERS463325	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548479	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:03Z\|ENA LAST UPDATE:2018 03 08T17:42:16Z\|External Id:SAMEA2548479\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:03Z\|INSDC last update:2018 03 08T17:42:16Z\|INSDC status:public\|Submitter Id:50Cyclop 0 1EtOH 24hpf treated 1 sc 1972448\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 50 micromolar cyclopamine in 0.1% v/v ethanol. A 8 base indexing sequence TGCGATCT is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:50Cyclop 0 1EtOH 24hpf treated 1 sc 1972448\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#22	10517298	Illumina sequencing of library 10517298 constructed from sample accession ERS463325 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TGCGATCT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#22.cram	cram	298785370.0	2298349.0	SC RUN 13256 1#22	0:55 1:75	A:82163853;C:59663280;G:63342361;T:93589112;N:26764	55	75	82163853	59663280	63342361	93589112	26764	ERX622872	ERS463325	ERA375333	SC	Wellcome Sanger Institute	2	0.13397	0.72614	0.07209	0.16108	0.96303	0.85188	0.78255	0.73973	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16553	16553	ERR667383	ERX622871	ERS463324	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548478	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:03Z\|ENA LAST UPDATE:2018 03 08T17:42:43Z\|External Id:SAMEA2548478\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:03Z\|INSDC last update:2018 03 08T17:42:43Z\|INSDC status:public\|Submitter Id:25Cyclop 05EtOH 24hpf control 12 sc 1972447\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 05% v/v ethanol.A 8 base indexing sequence TTGACTCT is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:25Cyclop 05EtOH 24hpf control 12 sc 1972447\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#21	10517297	Illumina sequencing of library 10517297 constructed from sample accession ERS463324 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TTGACTCT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#21.cram	cram	140774920.0	1082884.0	SC RUN 13256 1#21	0:55 1:75	A:39481115;C:27348433;G:30029240;T:43903005;N:13127	55	75	39481115	27348433	30029240	43903005	13127	ERX622871	ERS463324	ERA375333	SC	Wellcome Sanger Institute	2	0.14879	0.72247	0.08143	0.15522	0.96118	0.84867	0.78965	0.74254	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16554	16554	ERR667382	ERX622870	ERS463323	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548477	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:03Z\|ENA LAST UPDATE:2018 03 08T17:41:33Z\|External Id:SAMEA2548477\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:03Z\|INSDC last update:2018 03 08T17:41:33Z\|INSDC status:public\|Submitter Id:25Cyclop 05EtOH 24hpf control 11 sc 1972446\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 05% v/v ethanol.A 8 base indexing sequence TGCATAGT is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:25Cyclop 05EtOH 24hpf control 11 sc 1972446\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#20	10517296	Illumina sequencing of library 10517296 constructed from sample accession ERS463323 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TGCATAGT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#20.cram	cram	178794590.0	1375343.0	SC RUN 13256 1#20	0:55 1:75	A:50890564;C:34618169;G:37008888;T:56258907;N:18062	55	75	50890564	34618169	37008888	56258907	18062	ERX622870	ERS463323	ERA375333	SC	Wellcome Sanger Institute	2	0.15828	0.68013	0.10522	0.16411	0.96301	0.85147	0.77788	0.71946	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16555	16555	ERR667381	ERX622869	ERS463322	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548476	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:03Z\|ENA LAST UPDATE:2018 03 08T17:42:16Z\|External Id:SAMEA2548476\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:03Z\|INSDC last update:2018 03 08T17:42:16Z\|INSDC status:public\|Submitter Id:25Cyclop 05EtOH 24hpf control 10 sc 1972445\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 05% v/v ethanol.A 8 base indexing sequence TGATACGT is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:25Cyclop 05EtOH 24hpf control 10 sc 1972445\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#19	10517295	Illumina sequencing of library 10517295 constructed from sample accession ERS463322 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TGATACGT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#19.cram	cram	152796020.0	1175354.0	SC RUN 13256 1#19	0:55 1:75	A:43164178;C:28497500;G:30636978;T:50482443;N:14921	55	75	43164178	28497500	30636978	50482443	14921	ERX622869	ERS463322	ERA375333	SC	Wellcome Sanger Institute	2	0.17338	0.74214	0.11412	0.17188	0.95954	0.83475	0.77599	0.69646	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16556	16556	ERR667380	ERX622868	ERS463321	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548475	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:03Z\|ENA LAST UPDATE:2018 03 08T17:42:43Z\|External Id:SAMEA2548475\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:03Z\|INSDC last update:2018 03 08T17:42:43Z\|INSDC status:public\|Submitter Id:25Cyclop 05EtOH 24hpf control 9 sc 1972444\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 05% v/v ethanol.A 8 base indexing sequence TCGAGCGT is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:25Cyclop 05EtOH 24hpf control 9 sc 1972444\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#18	10517294	Illumina sequencing of library 10517294 constructed from sample accession ERS463321 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TCGAGCGT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#18.cram	cram	246614290.0	1897033.0	SC RUN 13256 1#18	0:55 1:75	A:65847226;C:48649826;G:51891861;T:80201978;N:23399	55	75	65847226	48649826	51891861	80201978	23399	ERX622868	ERS463321	ERA375333	SC	Wellcome Sanger Institute	2	0.12616	0.80609	0.07386	0.19379	0.96566	0.82942	0.80786	0.70582	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16557	16557	ERR667379	ERX622867	ERS463320	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548474	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:03Z\|ENA LAST UPDATE:2018 03 08T17:41:33Z\|External Id:SAMEA2548474\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:03Z\|INSDC last update:2018 03 08T17:41:33Z\|INSDC status:public\|Submitter Id:25Cyclop 05EtOH 24hpf control 8 sc 1972443\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 05% v/v ethanol.A 8 base indexing sequence TTGGAGGT is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:25Cyclop 05EtOH 24hpf control 8 sc 1972443\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#17	10517293	Illumina sequencing of library 10517293 constructed from sample accession ERS463320 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TTGGAGGT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#17.cram	cram	192037820.0	1477214.0	SC RUN 13256 1#17	0:55 1:75	A:52262399;C:38034317;G:39394465;T:62328424;N:18215	55	75	52262399	38034317	39394465	62328424	18215	ERX622867	ERS463320	ERA375333	SC	Wellcome Sanger Institute	2	0.13419	0.77104	0.06619	0.15595	0.96234	0.83431	0.80856	0.7337	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16558	16558	ERR667378	ERX622866	ERS463319	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548473	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:03Z\|ENA LAST UPDATE:2018 03 08T17:42:16Z\|External Id:SAMEA2548473\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:03Z\|INSDC last update:2018 03 08T17:42:16Z\|INSDC status:public\|Submitter Id:25Cyclop 05EtOH 24hpf control 7 sc 1972442\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 05% v/v ethanol.A 8 base indexing sequence TCTGCTGT is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:25Cyclop 05EtOH 24hpf control 7 sc 1972442\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#16	10517292	Illumina sequencing of library 10517292 constructed from sample accession ERS463319 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TCTGCTGT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#16.cram	cram	131783210.0	1013717.0	SC RUN 13256 1#16	0:55 1:75	A:36740307;C:25906782;G:28184476;T:40940400;N:11245	55	75	36740307	25906782	28184476	40940400	11245	ERX622866	ERS463319	ERA375333	SC	Wellcome Sanger Institute	2	0.1814	0.75096	0.0779	0.15257	0.94408	0.83615	0.73999	0.70358	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16559	16559	ERR667377	ERX622865	ERS463318	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548472	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:03Z\|ENA LAST UPDATE:2018 03 08T17:42:43Z\|External Id:SAMEA2548472\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:03Z\|INSDC last update:2018 03 08T17:42:43Z\|INSDC status:public\|Submitter Id:25Cyclop 05EtOH 24hpf control 6 sc 1972441\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 05% v/v ethanol.A 8 base indexing sequence TTCTGTGT is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:25Cyclop 05EtOH 24hpf control 6 sc 1972441\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#15	10517291	Illumina sequencing of library 10517291 constructed from sample accession ERS463318 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TTCTGTGT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#15.cram	cram	297275420.0	2286734.0	SC RUN 13256 1#15	0:55 1:75	A:80591742;C:58460335;G:62097495;T:96099260;N:26588	55	75	80591742	58460335	62097495	96099260	26588	ERX622865	ERS463318	ERA375333	SC	Wellcome Sanger Institute	2	0.14856	0.79328	0.08045	0.18298	0.95388	0.82524	0.74068	0.69319	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16560	16560	ERR667376	ERX622864	ERS463317	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548471	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:03Z\|ENA LAST UPDATE:2018 03 08T17:41:33Z\|External Id:SAMEA2548471\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:03Z\|INSDC last update:2018 03 08T17:41:33Z\|INSDC status:public\|Submitter Id:25Cyclop 05EtOH 24hpf control 5 sc 1972440\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 05% v/v ethanol.A 8 base indexing sequence TGTACCTT is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:25Cyclop 05EtOH 24hpf control 5 sc 1972440\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#14	10517290	Illumina sequencing of library 10517290 constructed from sample accession ERS463317 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TGTACCTT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#14.cram	cram	242173750.0	1862875.0	SC RUN 13256 1#14	0:55 1:75	A:72439393;C:44966903;G:51788847;T:72956754;N:21853	55	75	72439393	44966903	51788847	72956754	21853	ERX622864	ERS463317	ERA375333	SC	Wellcome Sanger Institute	2	0.13638	0.61957	0.09812	0.16019	0.97009	0.87127	0.57527	0.73119	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16561	16561	ERR667375	ERX622863	ERS463316	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548470	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:03Z\|ENA LAST UPDATE:2018 03 08T17:42:16Z\|External Id:SAMEA2548470\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:03Z\|INSDC last update:2018 03 08T17:42:16Z\|INSDC status:public\|Submitter Id:25Cyclop 05EtOH 24hpf control 4 sc 1972439\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 05% v/v ethanol.A 8 base indexing sequence TCCGTCTT is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:25Cyclop 05EtOH 24hpf control 4 sc 1972439\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#13	10517289	Illumina sequencing of library 10517289 constructed from sample accession ERS463316 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TCCGTCTT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#13.cram	cram	236289560.0	1817612.0	SC RUN 13256 1#13	0:55 1:75	A:65497839;C:45569980;G:50614556;T:74585065;N:22120	55	75	65497839	45569980	50614556	74585065	22120	ERX622863	ERS463316	ERA375333	SC	Wellcome Sanger Institute	2	0.16763	0.7428	0.08432	0.16616	0.95217	0.83857	0.73569	0.69906	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16574	16574	ERR667374	ERX622862	ERS463315	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548469	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:03Z\|ENA LAST UPDATE:2018 03 08T17:42:43Z\|External Id:SAMEA2548469\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:03Z\|INSDC last update:2018 03 08T17:42:43Z\|INSDC status:public\|Submitter Id:25Cyclop 05EtOH 24hpf control 3 sc 1972438\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 05% v/v ethanol.A 8 base indexing sequence TAAGCGTT is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:25Cyclop 05EtOH 24hpf control 3 sc 1972438\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#12	10517288	Illumina sequencing of library 10517288 constructed from sample accession ERS463315 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TAAGCGTT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#12.cram	cram	381482400.0	2934480.0	SC RUN 13256 1#12	0:55 1:75	A:108129259;C:71762350;G:76804777;T:124748024;N:37990	55	75	108129259	71762350	76804777	124748024	37990	ERX622862	ERS463315	ERA375333	SC	Wellcome Sanger Institute	2	0.15494	0.73749	0.08887	0.16382	0.95747	0.83211	0.76336	0.69077	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16575	16575	ERR667373	ERX622861	ERS463314	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548468	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:03Z\|ENA LAST UPDATE:2018 03 08T17:41:33Z\|External Id:SAMEA2548468\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:03Z\|INSDC last update:2018 03 08T17:41:33Z\|INSDC status:public\|Submitter Id:25Cyclop 05EtOH 24hpf control 2 sc 1972437\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 05% v/v ethanol.A 8 base indexing sequence TCTCGGTT is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:25Cyclop 05EtOH 24hpf control 2 sc 1972437\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#11	10517287	Illumina sequencing of library 10517287 constructed from sample accession ERS463314 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TCTCGGTT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#11.cram	cram	219975210.0	1692117.0	SC RUN 13256 1#11	0:55 1:75	A:62730862;C:43360964;G:45653286;T:68211390;N:18708	55	75	62730862	43360964	45653286	68211390	18708	ERX622861	ERS463314	ERA375333	SC	Wellcome Sanger Institute	2	0.1335	0.67379	0.05402	0.14367	0.96319	0.84877	0.81344	0.7263	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16576	16576	ERR667372	ERX622860	ERS463313	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548467	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:03Z\|ENA LAST UPDATE:2018 03 08T17:42:05Z\|External Id:SAMEA2548467\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:03Z\|INSDC last update:2018 03 08T17:42:05Z\|INSDC status:public\|Submitter Id:25Cyclop 05EtOH 24hpf control 1 sc 1972436\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 05% v/v ethanol.A 8 base indexing sequence TGGTTGTT is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:25Cyclop 05EtOH 24hpf control 1 sc 1972436\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#10	10517286	Illumina sequencing of library 10517286 constructed from sample accession ERS463313 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TGGTTGTT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#10.cram	cram	289606330.0	2227741.0	SC RUN 13256 1#10	0:55 1:75	A:83619693;C:55715592;G:57603582;T:92639222;N:28241	55	75	83619693	55715592	57603582	92639222	28241	ERX622860	ERS463313	ERA375333	SC	Wellcome Sanger Institute	2	0.14312	0.69479	0.08173	0.15101	0.96185	0.84439	0.78182	0.7265	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16577	16577	ERR667371	ERX622859	ERS463312	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548466	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:03Z\|ENA LAST UPDATE:2018 03 08T17:42:43Z\|External Id:SAMEA2548466\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:03Z\|INSDC last update:2018 03 08T17:42:43Z\|INSDC status:public\|Submitter Id:25Cyclop 05EtOH 24hpf treated 12 sc 1972435\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 25 micromolar cyclopamine in 05% v/v ethanol. A 8 base indexing sequence GATCAGCG is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:25Cyclop 05EtOH 24hpf treated 12 sc 1972435\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#9	10517285	Illumina sequencing of library 10517285 constructed from sample accession ERS463312 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence GATCAGCG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#9.cram	cram	179568740.0	1381298.0	SC RUN 13256 1#9	0:55 1:75	A:48952176;C:34402129;G:36985871;T:59212722;N:15842	55	75	48952176	34402129	36985871	59212722	15842	ERX622859	ERS463312	ERA375333	SC	Wellcome Sanger Institute	2	0.16345	0.77594	0.10069	0.16964	0.95864	0.83045	0.78521	0.7004	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16578	16578	ERR667370	ERX622858	ERS463311	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548465	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:04Z\|ENA LAST UPDATE:2018 03 08T17:41:33Z\|External Id:SAMEA2548465\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:04Z\|INSDC last update:2018 03 08T17:41:33Z\|INSDC status:public\|Submitter Id:25Cyclop 05EtOH 24hpf treated 11 sc 1972434\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 25 micromolar cyclopamine in 05% v/v ethanol. A 8 base indexing sequence ACTTGATG is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:25Cyclop 05EtOH 24hpf treated 11 sc 1972434\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#8	10517284	Illumina sequencing of library 10517284 constructed from sample accession ERS463311 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence ACTTGATG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#8.cram	cram	137020910.0	1054007.0	SC RUN 13256 1#8	0:55 1:75	A:38049625;C:26414574;G:28139253;T:44406481;N:10977	55	75	38049625	26414574	28139253	44406481	10977	ERX622858	ERS463311	ERA375333	SC	Wellcome Sanger Institute	2	0.1402	0.74335	0.08322	0.1663	0.96268	0.84043	0.77733	0.71859	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16579	16579	ERR667369	ERX622857	ERS463310	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548464	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:03Z\|ENA LAST UPDATE:2018 03 08T17:42:05Z\|External Id:SAMEA2548464\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:03Z\|INSDC last update:2018 03 08T17:42:05Z\|INSDC status:public\|Submitter Id:25Cyclop 05EtOH 24hpf treated 10 sc 1972433\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 25 micromolar cyclopamine in 05% v/v ethanol. A 8 base indexing sequence CAGATCTG is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:25Cyclop 05EtOH 24hpf treated 10 sc 1972433\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#7	10517283	Illumina sequencing of library 10517283 constructed from sample accession ERS463310 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence CAGATCTG.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#7.cram	cram	198153410.0	1524257.0	SC RUN 13256 1#7	0:55 1:75	A:52670252;C:39254438;G:42385338;T:63824260;N:19122	55	75	52670252	39254438	42385338	63824260	19122	ERX622857	ERS463310	ERA375333	SC	Wellcome Sanger Institute	2	0.12556	0.78468	0.07074	0.18847	0.964	0.83526	0.78795	0.71023	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16580	16580	ERR667368	ERX622856	ERS463309	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548463	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:03Z\|ENA LAST UPDATE:2018 03 08T17:42:43Z\|External Id:SAMEA2548463\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:03Z\|INSDC last update:2018 03 08T17:42:43Z\|INSDC status:public\|Submitter Id:25Cyclop 05EtOH 24hpf treated 9 sc 1972432\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 25 micromolar cyclopamine in 05% v/v ethanol. A 8 base indexing sequence GCCAATGT is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:25Cyclop 05EtOH 24hpf treated 9 sc 1972432\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#6	10517282	Illumina sequencing of library 10517282 constructed from sample accession ERS463309 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence GCCAATGT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#6.cram	cram	311861420.0	2398934.0	SC RUN 13256 1#6	0:55 1:75	A:83917355;C:60106233;G:64499135;T:103308448;N:30249	55	75	83917355	60106233	64499135	103308448	30249	ERX622856	ERS463309	ERA375333	SC	Wellcome Sanger Institute	2	0.12297	0.80619	0.0593	0.15961	0.96234	0.82248	0.79929	0.70162	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16581	16581	ERR667367	ERX622855	ERS463308	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548462	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:03Z\|ENA LAST UPDATE:2018 03 08T17:41:33Z\|External Id:SAMEA2548462\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:03Z\|INSDC last update:2018 03 08T17:41:33Z\|INSDC status:public\|Submitter Id:25Cyclop 05EtOH 24hpf treated 8 sc 1972431\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 25 micromolar cyclopamine in 05% v/v ethanol. A 8 base indexing sequence ACAGTGGT is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:25Cyclop 05EtOH 24hpf treated 8 sc 1972431\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#5	10517281	Illumina sequencing of library 10517281 constructed from sample accession ERS463308 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence ACAGTGGT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#5.cram	cram	319355660.0	2456582.0	SC RUN 13256 1#5	0:55 1:75	A:84900314;C:64205253;G:67464229;T:102759467;N:26397	55	75	84900314	64205253	67464229	102759467	26397	ERX622855	ERS463308	ERA375333	SC	Wellcome Sanger Institute	2	0.11383	0.78215	0.05838	0.17935	0.96619	0.83727	0.7861	0.72598	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16582	16582	ERR667366	ERX622854	ERS463307	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548461	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:03Z\|ENA LAST UPDATE:2018 03 08T17:42:05Z\|External Id:SAMEA2548461\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:03Z\|INSDC last update:2018 03 08T17:42:05Z\|INSDC status:public\|Submitter Id:25Cyclop 05EtOH 24hpf treated 7 sc 1972430\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 25 micromolar cyclopamine in 05% v/v ethanol. A 8 base indexing sequence TGACCACT is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:25Cyclop 05EtOH 24hpf treated 7 sc 1972430\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#4	10517280	Illumina sequencing of library 10517280 constructed from sample accession ERS463307 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TGACCACT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#4.cram	cram	354540160.0	2727232.0	SC RUN 13256 1#4	0:55 1:75	A:97757414;C:68003475;G:75993436;T:112753315;N:32520	55	75	97757414	68003475	75993436	112753315	32520	ERX622854	ERS463307	ERA375333	SC	Wellcome Sanger Institute	2	0.12969	0.72947	0.07042	0.14757	0.9614	0.84017	0.78018	0.71871	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16583	16583	ERR667365	ERX622853	ERS463306	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548460	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:03Z\|ENA LAST UPDATE:2018 03 08T17:42:43Z\|External Id:SAMEA2548460\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:03Z\|INSDC last update:2018 03 08T17:42:43Z\|INSDC status:public\|Submitter Id:25Cyclop 05EtOH 24hpf treated 6 sc 1972429\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 25 micromolar cyclopamine in 05% v/v ethanol. A 8 base indexing sequence TTAGGCAT is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:25Cyclop 05EtOH 24hpf treated 6 sc 1972429\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#3	10517279	Illumina sequencing of library 10517279 constructed from sample accession ERS463306 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence TTAGGCAT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#3.cram	cram	602820270.0	4637079.0	SC RUN 13256 1#3	0:55 1:75	A:165474925;C:115590273;G:123825630;T:197870518;N:58924	55	75	165474925	115590273	123825630	197870518	58924	ERX622853	ERS463306	ERA375333	SC	Wellcome Sanger Institute	2	0.141	0.74407	0.08834	0.15443	0.96475	0.83958	0.78331	0.7194	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16584	16584	ERR667364	ERX622852	ERS463305	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548459	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:03Z\|ENA LAST UPDATE:2018 03 08T17:41:33Z\|External Id:SAMEA2548459\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:03Z\|INSDC last update:2018 03 08T17:41:33Z\|INSDC status:public\|Submitter Id:25Cyclop 05EtOH 24hpf treated 4 sc 1972428\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 25 micromolar cyclopamine in 05% v/v ethanol. A 8 base indexing sequence CGATGTTT is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:25Cyclop 05EtOH 24hpf treated 4 sc 1972428\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#2	10517278	Illumina sequencing of library 10517278 constructed from sample accession ERS463305 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence CGATGTTT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#2.cram	cram	192840440.0	1483388.0	SC RUN 13256 1#2	0:55 1:75	A:53469380;C:37747264;G:40238127;T:61365974;N:19695	55	75	53469380	37747264	40238127	61365974	19695	ERX622852	ERS463305	ERA375333	SC	Wellcome Sanger Institute	2	0.14229	0.74015	0.07887	0.16243	0.96357	0.84687	0.7426	0.72806	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
16585	16585	ERR667363	ERX622851	ERS463304	ERP008536	PRJEB7614	Screening zebrafish embryos treated with small molecules by transcriptome profiling	Screening_zebrafish_embryos_treated_with_small_molecules_by_transcriptome_profiling-sc-3143	Transcriptome Analysis	Paired end sequence data from the Illumina HiSeq was prepared from RNA of zebrafish embryos treated with small molecules and their corresponding solvent treated and untreated controls.				SAMEA2548458	SC	ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 11 04T16:19:04Z\|ENA LAST UPDATE:2018 03 08T17:42:05Z\|External Id:SAMEA2548458\|INSDC center name:SC\|INSDC first public:2014 11 04T16:19:04Z\|INSDC last update:2018 03 08T17:42:05Z\|INSDC status:public\|Submitter Id:25Cyclop 05EtOH 24hpf treated 3 sc 1972427\|common name:zebrafish\|sample description:3 prime end enriched mRNA from single wild type 24hpf embryo treated with 25 micromolar cyclopamine in 05% v/v ethanol. A 8 base indexing sequence ATCACGTT is bases 13 to 20 of read 1 followed by CG and polyT.\|sample name:25Cyclop 05EtOH 24hpf treated 3 sc 1972427\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 paired end sequencing	SC EXP 13256 1#1	10517277	Illumina sequencing of library 10517277 constructed from sample accession ERS463304 for study accession ERP008536. This is part of an Illumina multiplexed sequencing run 13256 1. This submission includes reads tagged with the sequence ATCACGTT.	qPCR only	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP008536	Illumina HiSeq 2500 paired end sequencing	ENA FIRST PUBLIC:2014 11 04\|ENA LAST UPDATE:2018 11 16	13256_1#1.cram	cram	160035720.0	1231044.0	SC RUN 13256 1#1	0:55 1:75	A:44435310;C:30672417;G:33442253;T:51472358;N:13382	55	75	44435310	30672417	33442253	51472358	13382	ERX622851	ERS463304	ERA375333	SC	Wellcome Sanger Institute	2	0.13712	0.73194	0.08578	0.14534	0.96617	0.8465	0.77185	0.72507	55	75	T	B	mate1 technical by mapping diff	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2014-11-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures

Advanced export

JSON shape: default, array, newline-delimited

CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;