metadata: run_metadata: 64 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "CAGE" and technology = "unknown"

64 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "CAGE" and technology = "unknown"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	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
9803	9803	ERR3909553	ERX3918377	ERS4309135	ERP120006	PRJEB36776	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E-MTAB-8795	Transcriptome Analysis	The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics.	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 13		Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Total3	SAMEA6544760	UNIVERSITY OF BIRMINGHAM	ENA FIRST PUBLIC:2020 06 19T17:05:18Z\|ENA LAST UPDATE:2020 02 13T15:36:56Z\|External Id:SAMEA6544760\|INSDC center name:UNIVERSITY OF BIRMINGHAM\|INSDC first public:2020 06 19T17:05:18Z\|INSDC last update:2020 02 13T15:36:56Z\|INSDC status:public\|Submitter Id:E MTAB 8795:Total3\|age:14\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo\|fraction:unsorted whole organism\|organism part:whole organism\|sample name:E MTAB 8795:Total3\|scientific name:Danio rerio\|sex:not available\|strain:Dual FUCCI							Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E MTAB 8795:Total3 s	Total3 s	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Experimental Factor: fraction:unsorted whole organism	OTHER	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP120006	Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 25	14SomiteTotal3_TCGACG_L003_R1_001.fastq.gz	fastq	652379310.0	14497318.0	E MTAB 8795:Total3	0:45 1:0	A:150840591;C:135992123;G:240098326;T:125390188;N:58082	45	0	150840591	135992123	240098326	125390188	58082	ERX3918377	ERS4309135	ERA2381432	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	1	0.00539	0.00111	0.99582	0.74079	45	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	United Kingdom	2020-02-13	Segmentation	Embryo	Whole Organism	All anatomical structures
9804	9804	ERR3909552	ERX3918376	ERS4309134	ERP120006	PRJEB36776	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E-MTAB-8795	Transcriptome Analysis	The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics.	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 13		Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Total2	SAMEA6544759	UNIVERSITY OF BIRMINGHAM	ENA FIRST PUBLIC:2020 06 19T17:05:18Z\|ENA LAST UPDATE:2020 02 13T15:36:56Z\|External Id:SAMEA6544759\|INSDC center name:UNIVERSITY OF BIRMINGHAM\|INSDC first public:2020 06 19T17:05:18Z\|INSDC last update:2020 02 13T15:36:56Z\|INSDC status:public\|Submitter Id:E MTAB 8795:Total2\|age:14\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo\|fraction:unsorted whole organism\|organism part:whole organism\|sample name:E MTAB 8795:Total2\|scientific name:Danio rerio\|sex:not available\|strain:Dual FUCCI							Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E MTAB 8795:Total2 s	Total2 s	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Experimental Factor: fraction:unsorted whole organism	OTHER	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP120006	Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 25	14SomiteTotal2_TATAGC_L003_R1_001.fastq.gz	fastq	457981740.0	10177372.0	E MTAB 8795:Total2	0:45 1:0	A:108846441;C:95327665;G:163111561;T:90654528;N:41545	45	0	108846441	95327665	163111561	90654528	41545	ERX3918376	ERS4309134	ERA2381432	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	1	0.00612	0.00144	0.99387	0.66666	45	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	United Kingdom	2020-02-13	Segmentation	Embryo	Whole Organism	All anatomical structures
9805	9805	ERR3909551	ERX3918375	ERS4309133	ERP120006	PRJEB36776	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E-MTAB-8795	Transcriptome Analysis	The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics.	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 13		Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Total1	SAMEA6544758	UNIVERSITY OF BIRMINGHAM	ENA FIRST PUBLIC:2020 06 19T17:05:18Z\|ENA LAST UPDATE:2020 02 13T15:36:56Z\|External Id:SAMEA6544758\|INSDC center name:UNIVERSITY OF BIRMINGHAM\|INSDC first public:2020 06 19T17:05:18Z\|INSDC last update:2020 02 13T15:36:56Z\|INSDC status:public\|Submitter Id:E MTAB 8795:Total1\|age:14\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo\|fraction:unsorted whole organism\|organism part:whole organism\|sample name:E MTAB 8795:Total1\|scientific name:Danio rerio\|sex:not available\|strain:Dual FUCCI							Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E MTAB 8795:Total1 s	Total1 s	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Experimental Factor: fraction:unsorted whole organism	OTHER	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP120006	Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 25	14SomiteTotal1_GTATAC_L003_R1_001.fastq.gz	fastq	778934655.0	17309659.0	E MTAB 8795:Total1	0:45 1:0	A:175694794;C:165046556;G:285795545;T:152324198;N:73562	45	0	175694794	165046556	285795545	152324198	73562	ERX3918375	ERS4309133	ERA2381432	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	1	0.0048	0.00098	0.99492	0.69892	45	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	United Kingdom	2020-02-13	Segmentation	Embryo	Whole Organism	All anatomical structures
9806	9806	ERR3909550	ERX3918374	ERS4309132	ERP120006	PRJEB36776	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E-MTAB-8795	Transcriptome Analysis	The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics.	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 13		Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Red3	SAMEA6544757	UNIVERSITY OF BIRMINGHAM	ENA FIRST PUBLIC:2020 06 19T17:05:18Z\|ENA LAST UPDATE:2020 02 13T15:36:56Z\|External Id:SAMEA6544757\|INSDC center name:UNIVERSITY OF BIRMINGHAM\|INSDC first public:2020 06 19T17:05:18Z\|INSDC last update:2020 02 13T15:36:56Z\|INSDC status:public\|Submitter Id:E MTAB 8795:Red3\|age:14\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo\|fraction:G1 slow cycling\|organism part:whole organism\|sample name:E MTAB 8795:Red3\|scientific name:Danio rerio\|sex:not available\|strain:Dual FUCCI							Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E MTAB 8795:Red3 s	Red3 s	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Experimental Factor: fraction:G1 slow cycling	OTHER	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP120006	Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 25	14SomiteRed3_CACGAT_L003_R1_001.fastq.gz	fastq	980271990.0	21783822.0	E MTAB 8795:Red3	0:45 1:0	A:231772782;C:201265416;G:341867307;T:205267905;N:98580	45	0	231772782	201265416	341867307	205267905	98580	ERX3918374	ERS4309132	ERA2381432	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	1	0.0047	0.00138	0.99366	0.64343	45	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	United Kingdom	2020-02-13	Segmentation	Embryo	Whole Organism	All anatomical structures
9807	9807	ERR3909549	ERX3918373	ERS4309131	ERP120006	PRJEB36776	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E-MTAB-8795	Transcriptome Analysis	The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics.	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 13		Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Red2	SAMEA6544756	UNIVERSITY OF BIRMINGHAM	ENA FIRST PUBLIC:2020 06 19T17:05:18Z\|ENA LAST UPDATE:2020 02 13T15:36:56Z\|External Id:SAMEA6544756\|INSDC center name:UNIVERSITY OF BIRMINGHAM\|INSDC first public:2020 06 19T17:05:18Z\|INSDC last update:2020 02 13T15:36:56Z\|INSDC status:public\|Submitter Id:E MTAB 8795:Red2\|age:14\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo\|fraction:G1 slow cycling\|organism part:whole organism\|sample name:E MTAB 8795:Red2\|scientific name:Danio rerio\|sex:not available\|strain:Dual FUCCI							Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E MTAB 8795:Red2 s	Red2 s	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Experimental Factor: fraction:G1 slow cycling	OTHER	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP120006	Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 25	14SomiteRed2_ATCGTG_L003_R1_001.fastq.gz	fastq	755095185.0	16779893.0	E MTAB 8795:Red2	0:45 1:0	A:173488674;C:161696782;G:267896203;T:151943387;N:70139	45	0	173488674	161696782	267896203	151943387	70139	ERX3918373	ERS4309131	ERA2381432	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	1	0.00548	0.00113	0.99415	0.65826	45	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	United Kingdom	2020-02-13	Segmentation	Embryo	Whole Organism	All anatomical structures
9808	9808	ERR3909548	ERX3918372	ERS4309130	ERP120006	PRJEB36776	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E-MTAB-8795	Transcriptome Analysis	The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics.	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 13		Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Red1	SAMEA6544755	UNIVERSITY OF BIRMINGHAM	ENA FIRST PUBLIC:2020 06 19T17:05:18Z\|ENA LAST UPDATE:2020 02 13T15:36:56Z\|External Id:SAMEA6544755\|INSDC center name:UNIVERSITY OF BIRMINGHAM\|INSDC first public:2020 06 19T17:05:18Z\|INSDC last update:2020 02 13T15:36:56Z\|INSDC status:public\|Submitter Id:E MTAB 8795:Red1\|age:14\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo\|fraction:G1 slow cycling\|organism part:whole organism\|sample name:E MTAB 8795:Red1\|scientific name:Danio rerio\|sex:not available\|strain:Dual FUCCI							Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E MTAB 8795:Red1 s	Red1 s	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Experimental Factor: fraction:G1 slow cycling	OTHER	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP120006	Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 25	14SomiteRed1_ACAGAT_L003_R1_001.fastq.gz	fastq	755180370.0	16781786.0	E MTAB 8795:Red1	0:45 1:0	A:179369537;C:157573419;G:260889303;T:157277751;N:70360	45	0	179369537	157573419	260889303	157277751	70360	ERX3918372	ERS4309130	ERA2381432	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	1	0.00451	0.00099	0.99314	0.66248	45	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	United Kingdom	2020-02-13	Segmentation	Embryo	Whole Organism	All anatomical structures
9809	9809	ERR3909547	ERX3918371	ERS4309129	ERP120006	PRJEB36776	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E-MTAB-8795	Transcriptome Analysis	The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics.	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 13		Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Green3	SAMEA6544754	UNIVERSITY OF BIRMINGHAM	ENA FIRST PUBLIC:2020 06 19T17:05:18Z\|ENA LAST UPDATE:2020 02 13T15:36:56Z\|External Id:SAMEA6544754\|INSDC center name:UNIVERSITY OF BIRMINGHAM\|INSDC first public:2020 06 19T17:05:18Z\|INSDC last update:2020 02 13T15:36:56Z\|INSDC status:public\|Submitter Id:E MTAB 8795:Green3\|age:14\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo\|fraction:S/G2/M rapid cycling\|organism part:whole organism\|sample name:E MTAB 8795:Green3\|scientific name:Danio rerio\|sex:not available\|strain:Dual FUCCI							Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E MTAB 8795:Green3 s	Green3 s	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Experimental Factor: fraction:S/G2/M rapid cycling	OTHER	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP120006	Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 25	14SomiteGreen3_GAGTGA_L003_R1_001.fastq.gz	fastq	819288855.0	18206419.0	E MTAB 8795:Green3	0:45 1:0	A:189173618;C:170597494;G:286250625;T:173188944;N:78174	45	0	189173618	170597494	286250625	173188944	78174	ERX3918371	ERS4309129	ERA2381432	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	1	0.00439	0.001	0.99377	0.68367	45	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	United Kingdom	2020-02-13	Segmentation	Embryo	Whole Organism	All anatomical structures
9810	9810	ERR3909546	ERX3918370	ERS4309128	ERP120006	PRJEB36776	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E-MTAB-8795	Transcriptome Analysis	The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics.	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 13		Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Green2	SAMEA6544753	UNIVERSITY OF BIRMINGHAM	ENA FIRST PUBLIC:2020 06 19T17:05:18Z\|ENA LAST UPDATE:2020 02 13T15:36:56Z\|External Id:SAMEA6544753\|INSDC center name:UNIVERSITY OF BIRMINGHAM\|INSDC first public:2020 06 19T17:05:18Z\|INSDC last update:2020 02 13T15:36:56Z\|INSDC status:public\|Submitter Id:E MTAB 8795:Green2\|age:14\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo\|fraction:S/G2/M rapid cycling\|organism part:whole organism\|sample name:E MTAB 8795:Green2\|scientific name:Danio rerio\|sex:not available\|strain:Dual FUCCI							Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E MTAB 8795:Green2 s	Green2 s	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Experimental Factor: fraction:S/G2/M rapid cycling	OTHER	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP120006	Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 25	14SomiteGreen2_CTGACG_L003_R1_001.fastq.gz	fastq	697971375.0	15510475.0	E MTAB 8795:Green2	0:45 1:0	A:160028926;C:147075253;G:245773112;T:145025474;N:68610	45	0	160028926	147075253	245773112	145025474	68610	ERX3918370	ERS4309128	ERA2381432	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	1	0.00489	0.00085	0.99586	0.80163	45	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	United Kingdom	2020-02-13	Segmentation	Embryo	Whole Organism	All anatomical structures
9811	9811	ERR3909545	ERX3918369	ERS4309127	ERP120006	PRJEB36776	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E-MTAB-8795	Transcriptome Analysis	The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics.	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 13		Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Green1	SAMEA6544752	UNIVERSITY OF BIRMINGHAM	ENA FIRST PUBLIC:2020 06 19T17:05:18Z\|ENA LAST UPDATE:2020 02 13T15:36:56Z\|External Id:SAMEA6544752\|INSDC center name:UNIVERSITY OF BIRMINGHAM\|INSDC first public:2020 06 19T17:05:18Z\|INSDC last update:2020 02 13T15:36:56Z\|INSDC status:public\|Submitter Id:E MTAB 8795:Green1\|age:14\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo\|fraction:S/G2/M rapid cycling\|organism part:whole organism\|sample name:E MTAB 8795:Green1\|scientific name:Danio rerio\|sex:not available\|strain:Dual FUCCI							Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	E MTAB 8795:Green1 s	Green1 s	CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.	Experimental Factor: fraction:S/G2/M rapid cycling	OTHER	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP120006	Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red	ENA FIRST PUBLIC:2020 06 19\|ENA LAST UPDATE:2020 02 25	14SomiteGreen1_CACTGA_L003_R1_001.fastq.gz	fastq	826595640.0	18368792.0	E MTAB 8795:Green1	0:45 1:0	A:193728088;C:171605661;G:287824557;T:173352680;N:84654	45	0	193728088	171605661	287824557	173352680	84654	ERX3918369	ERS4309127	ERA2381432	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	UNIVERSITY OF BIRMINGHAM\|European Nucleotide Archive	1	0.00505	0.00101	0.99287	0.58198	45	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	United Kingdom	2020-02-13	Segmentation	Embryo	Whole Organism	All anatomical structures
36409	36409	SRR516560	SRX156356	SRS347213	SRP013950	PRJNA169500	Danio rerio embryonic promoterome	PRJNA169500	Transcriptome Analysis	Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.		pubmed:24531765	Zebrafish wild type AB strain embryo prim20 stage	D. rerio prim20 embryo	D. rerio prim20 embryo									CAGE D. rerio prim20 embryo	CAGE D. rerio prim20 embryo run2	D. rerio prim20 embryo	1			OTHER	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP013950			CAGE_prim20_run1.fastq	fastq	76770666.0	2843358.0	CAGE D. rerio prim20 embryo run1	0:27	A:19320047;C:17585086;G:22511175;T:17354358;N:0	27		19320047	17585086	22511175	17354358	0	SRX156356	SRS347213	SRA055273	University of Bergen	ZEPROME consortium	1	0.56472	0.10044	0.77469	0.74192	27	B	usable mapping rate	illumina	early_illumina	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2012-06-28	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
36410	36410	SRR516561	SRX156356	SRS347213	SRP013950	PRJNA169500	Danio rerio embryonic promoterome	PRJNA169500	Transcriptome Analysis	Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.		pubmed:24531765	Zebrafish wild type AB strain embryo prim20 stage	D. rerio prim20 embryo	D. rerio prim20 embryo									CAGE D. rerio prim20 embryo	CAGE D. rerio prim20 embryo run2	D. rerio prim20 embryo	1			OTHER	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP013950			CAGE_prim20_run2.fastq	fastq	163254906.0	6046478.0	CAGE D. rerio prim20 embryo run2	0:27	A:40211042;C:36959797;G:46866669;T:39217398;N:0	27		40211042	36959797	46866669	39217398	0	SRX156356	SRS347213	SRA055273	University of Bergen	ZEPROME consortium	1	0.47475	0.06947	0.78409	0.78014	27	B	usable mapping rate	illumina	early_illumina	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2013-08-31	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
36411	36411	SRR516559	SRX156355	SRS347212	SRP013950	PRJNA169500	Danio rerio embryonic promoterome	PRJNA169500	Transcriptome Analysis	Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.		pubmed:24531765	Zebrafish wild type AB strain embryo prim6 stage	D. rerio prim6 embryo	D. rerio prim6 embryo									CAGE D. rerio prim6 embryo	CAGE D. rerio prim6 embryo	D. rerio prim6 embryo	1			OTHER	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP013950			CAGE_prim6.fastq	fastq	283414275.0	10496825.0	CAGE D. rerio prim6 embryo	0:27	A:70974303;C:66202040;G:80064124;T:66173808;N:0	27		70974303	66202040	80064124	66173808	0	SRX156355	SRS347212	SRA055273	University of Bergen	ZEPROME consortium	1	0.53395	0.07806	0.78255	0.77575	27	B	usable mapping rate	illumina	early_illumina	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2013-08-31	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
36412	36412	SRR516557	SRX156352	SRS347211	SRP013950	PRJNA169500	Danio rerio embryonic promoterome	PRJNA169500	Transcriptome Analysis	Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.		pubmed:24531765	Zebrafish wild type AB strain embryo 14 somites stage	D. rerio 14 somites embryo	D. rerio 14 somites embryo									CAGE D. rerio 14 somites embryo	CAGE D. rerio 14 somites embryo run2	D. rerio 14 somites embryo	1			OTHER	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP013950					73689048.0	2729224.0	CAGE D. rerio 14 somites embryo run1	0:27	A:19506796;C:16238588;G:21636330;T:16307334;N:0	27		19506796	16238588	21636330	16307334	0	SRX156352	SRS347211	SRA055273	University of Bergen	ZEPROME consortium	1	0.63348	0.09461	0.76199	0.68697	27	B	usable mapping rate	illumina	early_illumina	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2012-06-28	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
36413	36413	SRR516558	SRX156352	SRS347211	SRP013950	PRJNA169500	Danio rerio embryonic promoterome	PRJNA169500	Transcriptome Analysis	Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.		pubmed:24531765	Zebrafish wild type AB strain embryo 14 somites stage	D. rerio 14 somites embryo	D. rerio 14 somites embryo									CAGE D. rerio 14 somites embryo	CAGE D. rerio 14 somites embryo run2	D. rerio 14 somites embryo	1			OTHER	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP013950			CAGE_14somites_run2.fastq	fastq	212381811.0	7865993.0	CAGE D. rerio 14 somites embryo run2	0:27	A:53780820;C:47467464;G:59893810;T:51239717;N:0	27		53780820	47467464	59893810	51239717	0	SRX156352	SRS347211	SRA055273	University of Bergen	ZEPROME consortium	1	0.5278	0.0806	0.77589	0.72881	27	B	usable mapping rate	illumina	early_illumina	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2012-06-28	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
36414	36414	SRR516555	SRX156350	SRS347210	SRP013950	PRJNA169500	Danio rerio embryonic promoterome	PRJNA169500	Transcriptome Analysis	Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.		pubmed:24531765	Zebrafish wild type AB strain embryo shield stage	D. rerio shield embryo	D. rerio shield embryo									CAGE D. rerio shield embryo	CAGE D. rerio shield embryo run2	D. rerio shield embryo	1			OTHER	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP013950					81086886.0	3003218.0	CAGE D. rerio shield embryo run1	0:27	A:20800196;C:18582826;G:23491216;T:18212648;N:0	27		20800196	18582826	23491216	18212648	0	SRX156350	SRS347210	SRA055273	University of Bergen	ZEPROME consortium	1	0.60434	0.09948	0.80432	0.72631	27	B	usable mapping rate	illumina	early_illumina	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2012-06-28	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
36415	36415	SRR516556	SRX156350	SRS347210	SRP013950	PRJNA169500	Danio rerio embryonic promoterome	PRJNA169500	Transcriptome Analysis	Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.		pubmed:24531765	Zebrafish wild type AB strain embryo shield stage	D. rerio shield embryo	D. rerio shield embryo									CAGE D. rerio shield embryo	CAGE D. rerio shield embryo run2	D. rerio shield embryo	1			OTHER	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP013950			CAGE_shield_run2.fastq	fastq	81675891.0	3025033.0	CAGE D. rerio shield embryo run2	0:27	A:21590166;C:17662459;G:22692127;T:19731139;N:0	27		21590166	17662459	22692127	19731139	0	SRX156350	SRS347210	SRA055273	University of Bergen	ZEPROME consortium	1	0.52624	0.08062	0.81793	0.76291	27	B	usable mapping rate	illumina	early_illumina	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2012-06-28	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
36416	36416	SRR516554	SRX156349	SRS347209	SRP013950	PRJNA169500	Danio rerio embryonic promoterome	PRJNA169500	Transcriptome Analysis	Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.		pubmed:24531765	Zebrafish wild type AB strain embryo dome/zfs:0000015 stage	D. rerio dome/zfs:0000015 embryo	D. rerio dome/zfs:0000015 embryo									CAGE D. rerio dome/zfs:0000015 embryo	CAGE D. rerio dome/zfs:0000015 embryo	D. rerio dome/zfs:0000015 embryo	1			OTHER	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP013950			CAGE_30p_dome.fastq	fastq	165690819.0	6136697.0	CAGE D. rerio dome/zfs:0000015 embryo	0:27	A:42721293;C:36492232;G:46154926;T:40322368;N:0	27		42721293	36492232	46154926	40322368	0	SRX156349	SRS347209	SRA055273	University of Bergen	ZEPROME consortium	1	0.50236	0.0905	0.81824	0.8156	27	B	usable mapping rate	illumina	early_illumina	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2012-06-28	Blastula	Embryo	Embryo Imprecise	All anatomical structures
36417	36417	SRR516552	SRX156347	SRS347208	SRP013950	PRJNA169500	Danio rerio embryonic promoterome	PRJNA169500	Transcriptome Analysis	Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.		pubmed:24531765	Zebrafish wild type AB strain embryo sphere/dome stage	D. rerio sphere/dome embryo	D. rerio sphere/dome embryo									CAGE D. rerio sphere/dome embryo	CAGE D. rerio sphere/dome embryo run2	D. rerio sphere/dome embryo	1			OTHER	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP013950			CAGE_sphere_dome_run1.fastq	fastq	78937740.0	2923620.0	CAGE D. rerio sphere/dome embryo run1	0:27	A:20705496;C:17020957;G:22237043;T:18974244;N:0	27		20705496	17020957	22237043	18974244	0	SRX156347	SRS347208	SRA055273	University of Bergen	ZEPROME consortium	1	0.50917	0.09193	0.81523	0.8084	27	B	usable mapping rate	illumina	early_illumina	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2012-06-28	Blastula	Embryo	Embryo Imprecise	All anatomical structures
36418	36418	SRR516553	SRX156347	SRS347208	SRP013950	PRJNA169500	Danio rerio embryonic promoterome	PRJNA169500	Transcriptome Analysis	Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.		pubmed:24531765	Zebrafish wild type AB strain embryo sphere/dome stage	D. rerio sphere/dome embryo	D. rerio sphere/dome embryo									CAGE D. rerio sphere/dome embryo	CAGE D. rerio sphere/dome embryo run2	D. rerio sphere/dome embryo	1			OTHER	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP013950			CAGE_sphere_dome_run2.fastq	fastq	82071009.0	3039667.0	CAGE D. rerio sphere/dome embryo run2	0:27	A:20823133;C:17914934;G:22973465;T:20359477;N:0	27		20823133	17914934	22973465	20359477	0	SRX156347	SRS347208	SRA055273	University of Bergen	ZEPROME consortium	1	0.47213	0.07583	0.82384	0.8313	27	B	usable mapping rate	illumina	early_illumina	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2012-06-28	Blastula	Embryo	Embryo Imprecise	All anatomical structures
36419	36419	SRR516551	SRX156338	SRS347207	SRP013950	PRJNA169500	Danio rerio embryonic promoterome	PRJNA169500	Transcriptome Analysis	Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.		pubmed:24531765	Zebrafish wild type AB strain embryo oblong stage	D. rerio oblong embryo	D. rerio oblong embryo									CAGE D. rerio oblong embryo	CAGE D. rerio oblong embryo	D. rerio oblong embryo	1			OTHER	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP013950					135892080.0	5033040.0	CAGE D. rerio oblong embryo	0:27	A:34565898;C:30442218;G:38967845;T:31916119;N:0	27		34565898	30442218	38967845	31916119	0	SRX156338	SRS347207	SRA055273	University of Bergen	ZEPROME consortium	1	0.56265	0.09335	0.80068	0.70759	27	B	usable mapping rate	illumina	early_illumina	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2012-06-28	Blastula	Embryo	Embryo Imprecise	All anatomical structures
36420	36420	SRR516550	SRX156337	SRS347206	SRP013950	PRJNA169500	Danio rerio embryonic promoterome	PRJNA169500	Transcriptome Analysis	Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.		pubmed:24531765	Zebrafish wild type AB strain embryo high stage	D. rerio high embryo	D. rerio high embryo									CAGE D. rerio high embryo	CAGE D. rerio high embryo	D. rerio high embryo	1			OTHER	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP013950			CAGE_high.fastq	fastq	128592846.0	4762698.0	CAGE D. rerio high embryo	0:27	A:33693838;C:27629256;G:36692263;T:30577489;N:0	27		33693838	27629256	36692263	30577489	0	SRX156337	SRS347206	SRA055273	University of Bergen	ZEPROME consortium	1	0.53282	0.08323	0.80854	0.77395	27	B	usable mapping rate	illumina	early_illumina	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2013-08-31	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
36421	36421	SRR516549	SRX156336	SRS347204	SRP013950	PRJNA169500	Danio rerio embryonic promoterome	PRJNA169500	Transcriptome Analysis	Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.		pubmed:24531765	Zebrafish wild type AB strain embryo 512 cells stage	D. rerio 512 cells embryo	D. rerio 512 cells embyo									CAGE D. rerio 512 cells embryo	CAGE D. rerio 512 cells embryo	D. rerio 512 cells embryo	1			OTHER	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP013950			CAGE_512cells.fastq	fastq	150228810.0	5564030.0	CAGE D. rerio 512 cells embryo	0:27	A:37826960;C:33838922;G:43403014;T:35159914;N:0	27		37826960	33838922	43403014	35159914	0	SRX156336	SRS347204	SRA055273	University of Bergen	ZEPROME consortium	1	0.57925	0.08753	0.79933	0.72579	27	B	usable mapping rate	illumina	early_illumina	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2012-06-28	Blastula	Embryo	Embryo Imprecise	All anatomical structures
36422	36422	SRR516548	SRX156334	SRS347202	SRP013950	PRJNA169500	Danio rerio embryonic promoterome	PRJNA169500	Transcriptome Analysis	Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.		pubmed:24531765	Zebrafish wild type AB strain embryo 64 cells stage	D. rerio 64 cells embryo	D. rerio 64 cells embryo									CAGE D. rerio 64 cells embryo	CAGE D. rerio 64 cells embryo	D. rerio 64 cells embryo	1			OTHER	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP013950			CAGE_64cells.fastq	fastq	162784188.0	6029044.0	CAGE D. rerio 64 cells embryo	0:27	A:41192860;C:36547869;G:46848833;T:38194626;N:0	27		41192860	36547869	46848833	38194626	0	SRX156334	SRS347202	SRA055273	University of Bergen	ZEPROME consortium							B	usable mapping rate	illumina	early_illumina	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2013-08-31	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
36423	36423	SRR516547	SRX156325	SRS347201	SRP013950	PRJNA169500	Danio rerio embryonic promoterome	PRJNA169500	Transcriptome Analysis	Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.		pubmed:24531765	Zebrafish wild type AB strain fertilized egg	D. rerio fertilized egg	D. rerio fertilized egg									CAGE D. rerio fertilized egg	CAGE D. rerio fertilized egg	D. rerio fertilized egg	1			OTHER	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP013950			CAGE_fertilized_egg.fastq	fastq	160948350.0	5961050.0	CAGE D. rerio fertilized egg	0:27	A:42030009;C:34700589;G:45399755;T:38817997;N:0	27		42030009	34700589	45399755	38817997	0	SRX156325	SRS347201	SRA055273	University of Bergen	ZEPROME consortium	1	0.49394	0.07554	0.81684	0.79759	27	B	usable mapping rate	illumina	early_illumina	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2012-06-28	Undetermined	Embryo	Undetermined	Embryo Imprecise
36424	36424	SRR516545	SRX156307	SRS347187	SRP013950	PRJNA169500	Danio rerio embryonic promoterome	PRJNA169500	Transcriptome Analysis	Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.		pubmed:24531765	Zebrafish wild type AB strain unfertilized egg	D. rerio unfertilized egg	D. rerio unfertilized egg									CAGE D. rerio unfertilized egg	CAGE D. rerio unfertilized egg run2	D. rerio unfertilized egg	1			OTHER	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP013950					115273233.0	4269379.0	CAGE D. rerio unfertilized egg run1	0:27	A:29909511;C:24823784;G:32519899;T:28020039;N:0	27		29909511	24823784	32519899	28020039	0	SRX156307	SRS347187	SRA055273	University of Bergen	ZEPROME consortium	1	0.49872	0.07655	0.81673	0.80445	27	B	usable mapping rate	illumina	early_illumina	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2012-06-28	Zygote	Embryo	Oocyte	Reproductive System
36425	36425	SRR516546	SRX156307	SRS347187	SRP013950	PRJNA169500	Danio rerio embryonic promoterome	PRJNA169500	Transcriptome Analysis	Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.		pubmed:24531765	Zebrafish wild type AB strain unfertilized egg	D. rerio unfertilized egg	D. rerio unfertilized egg									CAGE D. rerio unfertilized egg	CAGE D. rerio unfertilized egg run2	D. rerio unfertilized egg	1			OTHER	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP013950					112673943.0	4173109.0	CAGE D. rerio unfertilized egg run2	0:27	A:28315221;C:24199098;G:32599482;T:27560142;N:0	27		28315221	24199098	32599482	27560142	0	SRX156307	SRS347187	SRA055273	University of Bergen	ZEPROME consortium	1	0.46201	0.06422	0.82118	0.82184	27	B	usable mapping rate	illumina	early_illumina	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2012-06-28	Zygote	Embryo	Oocyte	Reproductive System
48305	48305	SRR10368285	SRX7076279	SRS5592164	SRP145615	PRJNA471311	Gene expression analysis of jam3b mutant embryos	GSE114416	Transcriptome Analysis	Junctional adhesion molecule 3 Jam3 is a cell adhesion molecule that is involved in cell cell interaction cell migration and cell polarization in many tissue including the epithelium endothelium and hematopoietic cells. Although Jam3 is functionally relevant for both hematopoietic and vascular endothelial cells the role of Jam3 in hematopoietic or vascular development is still unknown. In this study a zebrafish jam3b mutant line jam3b sa37 was used for the cap analysis gene expression CAGE sequencing to identify genes that are involved in hematopoietic and/or vascular development in the zebrafish embryo. Overall design: Whole embryos mRNA profiles of wild type or jam3b sa37 embryos at 12 or 16 hpf were generated by CAGE sequencing using Illumina NextSeq500.				sa37 16hpf 2	GSM4144779		source name:whole embryo\|tissue:whole embryo\|age:16 hpf sa37	sa37 16hpf 2	Illumina RTA software was used for base calling. Sequenced CAGE tags were mapped to the full genome sequences for Danio rerio danRer10 using the Burrows Wheeler Aligner BWA and HiSAT2 software. Tags per million TPM were calculated using the CAGEr package of Bioconductor in R ver. 3.3.3 with the minimum TPM value of 0.5. Genome build: danRer10 Supplementary files format and content: Tab delimited text files include tags per million TPM values for each sample.	whole embryo	Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2?g of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit DNAFORM. five primecaps of RNAs are biotinylated post reverse transcription. RNA cDNA hybirds were then captured by streptavidin conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5? linker which includes the three nucleotide barcodes followed by 3? linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer creating the final double stranded DNA product. Cap analysis gene expression CAGE sequencing	tissue:whole embryo\|age:16 hpf sa37	GSM4144779	GSM4144779: sa37 16hpf 2; Danio rerio; RNA Seq	GSM4144779		1	Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2?g of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit DNAFORM. five primecaps of RNAs are biotinylated post reverse transcription. RNA cDNA hybirds were then captured by streptavidin conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5? linker which includes the three nucleotide barcodes followed by 3? linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer creating the final double stranded DNA product. Cap analysis gene expression CAGE sequencing	GEO Accession:GSM4144779	RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	NextSeq 500		SRP145615			S04.fastq.gz	fastq	2166354993.0	28701604.0	GSM4144779 r1	0:75.48 1:0	A:566482594;C:525711117;G:579970160;T:493751194;N:439928	75	0	566482594	525711117	579970160	493751194	439928	SRX7076279	SRS5592164	SRA703389	GEO	Kanazawa University	1	0.92378	0.09905	0.74479	0.52368	75	B	usable mapping rate	illumina	nextseq	unknown	cage	unknown	bulk	unknown	unknown	Japan	2019-10-30	Segmentation	Embryo	Whole Organism	All anatomical structures
48306	48306	SRR10368284	SRX7076278	SRS5592163	SRP145615	PRJNA471311	Gene expression analysis of jam3b mutant embryos	GSE114416	Transcriptome Analysis	Junctional adhesion molecule 3 Jam3 is a cell adhesion molecule that is involved in cell cell interaction cell migration and cell polarization in many tissue including the epithelium endothelium and hematopoietic cells. Although Jam3 is functionally relevant for both hematopoietic and vascular endothelial cells the role of Jam3 in hematopoietic or vascular development is still unknown. In this study a zebrafish jam3b mutant line jam3b sa37 was used for the cap analysis gene expression CAGE sequencing to identify genes that are involved in hematopoietic and/or vascular development in the zebrafish embryo. Overall design: Whole embryos mRNA profiles of wild type or jam3b sa37 embryos at 12 or 16 hpf were generated by CAGE sequencing using Illumina NextSeq500.				sa37 12hpf 2	GSM4144778		source name:whole embryo\|tissue:whole embryo\|age:12 hpf sa37	sa37 12hpf 2	Illumina RTA software was used for base calling. Sequenced CAGE tags were mapped to the full genome sequences for Danio rerio danRer10 using the Burrows Wheeler Aligner BWA and HiSAT2 software. Tags per million TPM were calculated using the CAGEr package of Bioconductor in R ver. 3.3.3 with the minimum TPM value of 0.5. Genome build: danRer10 Supplementary files format and content: Tab delimited text files include tags per million TPM values for each sample.	whole embryo	Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2?g of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit DNAFORM. five primecaps of RNAs are biotinylated post reverse transcription. RNA cDNA hybirds were then captured by streptavidin conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5? linker which includes the three nucleotide barcodes followed by 3? linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer creating the final double stranded DNA product. Cap analysis gene expression CAGE sequencing	tissue:whole embryo\|age:12 hpf sa37	GSM4144778	GSM4144778: sa37 12hpf 2; Danio rerio; RNA Seq	GSM4144778		1	Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2?g of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit DNAFORM. five primecaps of RNAs are biotinylated post reverse transcription. RNA cDNA hybirds were then captured by streptavidin conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5? linker which includes the three nucleotide barcodes followed by 3? linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer creating the final double stranded DNA product. Cap analysis gene expression CAGE sequencing	GEO Accession:GSM4144778	RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	NextSeq 500		SRP145615			S03.fastq.gz	fastq	1653073372.0	21903605.0	GSM4144778 r1	0:75.47 1:0	A:433206792;C:402537379;G:446761303;T:370161548;N:406350	75	0	433206792	402537379	446761303	370161548	406350	SRX7076278	SRS5592163	SRA703389	GEO	Kanazawa University	1	0.91778	0.12219	0.76684	0.54487	76	B	usable mapping rate	illumina	nextseq	unknown	cage	unknown	bulk	unknown	unknown	Japan	2019-10-30	Segmentation	Embryo	Whole Organism	All anatomical structures
48307	48307	SRR10368283	SRX7076277	SRS5592162	SRP145615	PRJNA471311	Gene expression analysis of jam3b mutant embryos	GSE114416	Transcriptome Analysis	Junctional adhesion molecule 3 Jam3 is a cell adhesion molecule that is involved in cell cell interaction cell migration and cell polarization in many tissue including the epithelium endothelium and hematopoietic cells. Although Jam3 is functionally relevant for both hematopoietic and vascular endothelial cells the role of Jam3 in hematopoietic or vascular development is still unknown. In this study a zebrafish jam3b mutant line jam3b sa37 was used for the cap analysis gene expression CAGE sequencing to identify genes that are involved in hematopoietic and/or vascular development in the zebrafish embryo. Overall design: Whole embryos mRNA profiles of wild type or jam3b sa37 embryos at 12 or 16 hpf were generated by CAGE sequencing using Illumina NextSeq500.				WT 16hpf 2	GSM4144777		source name:whole embryo\|tissue:whole embryo\|age:16 hpf type	WT 16hpf 2	Illumina RTA software was used for base calling. Sequenced CAGE tags were mapped to the full genome sequences for Danio rerio danRer10 using the Burrows Wheeler Aligner BWA and HiSAT2 software. Tags per million TPM were calculated using the CAGEr package of Bioconductor in R ver. 3.3.3 with the minimum TPM value of 0.5. Genome build: danRer10 Supplementary files format and content: Tab delimited text files include tags per million TPM values for each sample.	whole embryo	Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2?g of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit DNAFORM. five primecaps of RNAs are biotinylated post reverse transcription. RNA cDNA hybirds were then captured by streptavidin conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5? linker which includes the three nucleotide barcodes followed by 3? linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer creating the final double stranded DNA product. Cap analysis gene expression CAGE sequencing	tissue:whole embryo\|age:16 hpf type	GSM4144777	GSM4144777: WT 16hpf 2; Danio rerio; RNA Seq	GSM4144777		1	Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2?g of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit DNAFORM. five primecaps of RNAs are biotinylated post reverse transcription. RNA cDNA hybirds were then captured by streptavidin conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5? linker which includes the three nucleotide barcodes followed by 3? linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer creating the final double stranded DNA product. Cap analysis gene expression CAGE sequencing	GEO Accession:GSM4144777	RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	NextSeq 500		SRP145615			S02.fastq.gz	fastq	2178611783.0	28900952.0	GSM4144777 r1	0:75.38 1:0	A:566689783;C:530433539;G:590611812;T:488215395;N:2661254	75	0	566689783	530433539	590611812	488215395	2661254	SRX7076277	SRS5592162	SRA703389	GEO	Kanazawa University	1	0.93637	0.10293	0.7542	0.53437	76	B	usable mapping rate	illumina	nextseq	unknown	cage	unknown	bulk	unknown	unknown	Japan	2019-10-30	Segmentation	Embryo	Whole Organism	All anatomical structures
48308	48308	SRR10368282	SRX7076276	SRS5592161	SRP145615	PRJNA471311	Gene expression analysis of jam3b mutant embryos	GSE114416	Transcriptome Analysis	Junctional adhesion molecule 3 Jam3 is a cell adhesion molecule that is involved in cell cell interaction cell migration and cell polarization in many tissue including the epithelium endothelium and hematopoietic cells. Although Jam3 is functionally relevant for both hematopoietic and vascular endothelial cells the role of Jam3 in hematopoietic or vascular development is still unknown. In this study a zebrafish jam3b mutant line jam3b sa37 was used for the cap analysis gene expression CAGE sequencing to identify genes that are involved in hematopoietic and/or vascular development in the zebrafish embryo. Overall design: Whole embryos mRNA profiles of wild type or jam3b sa37 embryos at 12 or 16 hpf were generated by CAGE sequencing using Illumina NextSeq500.				WT 12hpf 2	GSM4144776		source name:whole embryo\|tissue:whole embryo\|age:12 hpf type	WT 12hpf 2	Illumina RTA software was used for base calling. Sequenced CAGE tags were mapped to the full genome sequences for Danio rerio danRer10 using the Burrows Wheeler Aligner BWA and HiSAT2 software. Tags per million TPM were calculated using the CAGEr package of Bioconductor in R ver. 3.3.3 with the minimum TPM value of 0.5. Genome build: danRer10 Supplementary files format and content: Tab delimited text files include tags per million TPM values for each sample.	whole embryo	Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2?g of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit DNAFORM. five primecaps of RNAs are biotinylated post reverse transcription. RNA cDNA hybirds were then captured by streptavidin conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5? linker which includes the three nucleotide barcodes followed by 3? linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer creating the final double stranded DNA product. Cap analysis gene expression CAGE sequencing	tissue:whole embryo\|age:12 hpf type	GSM4144776	GSM4144776: WT 12hpf 2; Danio rerio; RNA Seq	GSM4144776		1	Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2?g of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit DNAFORM. five primecaps of RNAs are biotinylated post reverse transcription. RNA cDNA hybirds were then captured by streptavidin conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5? linker which includes the three nucleotide barcodes followed by 3? linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer creating the final double stranded DNA product. Cap analysis gene expression CAGE sequencing	GEO Accession:GSM4144776	RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	NextSeq 500		SRP145615			S01.fastq.gz	fastq	2235469804.0	29611055.0	GSM4144776 r1	0:75.49 1:0	A:582276989;C:546056334;G:609905170;T:497018748;N:212563	75	0	582276989	546056334	609905170	497018748	212563	SRX7076276	SRS5592161	SRA703389	GEO	Kanazawa University	1	0.9362	0.12401	0.76857	0.48408	76	B	usable mapping rate	illumina	nextseq	unknown	cage	unknown	bulk	unknown	unknown	Japan	2019-10-30	Segmentation	Embryo	Whole Organism	All anatomical structures
48309	48309	SRR7162665	SRX4080963	SRS3298238	SRP145615	PRJNA471311	Gene expression analysis of jam3b mutant embryos	GSE114416	Transcriptome Analysis	Junctional adhesion molecule 3 Jam3 is a cell adhesion molecule that is involved in cell cell interaction cell migration and cell polarization in many tissue including the epithelium endothelium and hematopoietic cells. Although Jam3 is functionally relevant for both hematopoietic and vascular endothelial cells the role of Jam3 in hematopoietic or vascular development is still unknown. In this study a zebrafish jam3b mutant line jam3b sa37 was used for the cap analysis gene expression CAGE sequencing to identify genes that are involved in hematopoietic and/or vascular development in the zebrafish embryo. Overall design: Whole embryos mRNA profiles of wild type or jam3b sa37 embryos at 12 or 16 hpf were generated by CAGE sequencing using Illumina NextSeq500.				sa37 16hpf	GSM3141418		source name:whole embryo\|tissue:whole embryo\|age:16 hpf sa37	sa37 16hpf	Illumina RTA software was used for base calling. Sequenced CAGE tags were mapped to the full genome sequences for Danio rerio danRer10 using the Burrows Wheeler Aligner BWA and HiSAT2 software. Tags per million TPM were calculated using the CAGEr package of Bioconductor in R ver. 3.3.3 with the minimum TPM value of 0.5. Genome build: danRer10 Supplementary files format and content: Tab delimited text files include tags per million TPM values for each sample.	whole embryo	Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2μg of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit DNAFORM. five primecaps of RNAs are biotinylated post reverse transcription. RNA cDNA hybirds were then captured by streptavidin conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5′ linker which includes the three nucleotide barcodes followed by 3′ linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer creating the final double stranded DNA product. Cap analysis gene expression CAGE sequencing	tissue:whole embryo\|age:16 hpf sa37	GSM3141418	GSM3141418: sa37 16hpf; Danio rerio; RNA Seq	GSM3141418		1	Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2μg of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit DNAFORM. five primecaps of RNAs are biotinylated post reverse transcription. RNA cDNA hybirds were then captured by streptavidin conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5′ linker which includes the three nucleotide barcodes followed by 3′ linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer creating the final double stranded DNA product. Cap analysis gene expression CAGE sequencing	GEO Accession:GSM3141418	RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	NextSeq 500		SRP145615			KB4.fastq.gz	fastq	1534816794.0	20351965.0	GSM3141418 r1	0:75.41 1:0	A:406883394;C:371384442;G:408553824;T:347148313;N:846821	75	0	406883394	371384442	408553824	347148313	846821	SRX4080963	SRS3298238	SRA703389	GEO	Kanazawa University	1	0.90303	0.11364	0.7726	0.54943	76	B	usable mapping rate	illumina	nextseq	unknown	cage	unknown	bulk	unknown	unknown	Japan	2018-05-14	Segmentation	Embryo	Whole Organism	All anatomical structures
48310	48310	SRR7162664	SRX4080962	SRS3298237	SRP145615	PRJNA471311	Gene expression analysis of jam3b mutant embryos	GSE114416	Transcriptome Analysis	Junctional adhesion molecule 3 Jam3 is a cell adhesion molecule that is involved in cell cell interaction cell migration and cell polarization in many tissue including the epithelium endothelium and hematopoietic cells. Although Jam3 is functionally relevant for both hematopoietic and vascular endothelial cells the role of Jam3 in hematopoietic or vascular development is still unknown. In this study a zebrafish jam3b mutant line jam3b sa37 was used for the cap analysis gene expression CAGE sequencing to identify genes that are involved in hematopoietic and/or vascular development in the zebrafish embryo. Overall design: Whole embryos mRNA profiles of wild type or jam3b sa37 embryos at 12 or 16 hpf were generated by CAGE sequencing using Illumina NextSeq500.				sa37 12hpf	GSM3141417		source name:whole embryo\|tissue:whole embryo\|age:12 hpf sa37	sa37 12hpf	Illumina RTA software was used for base calling. Sequenced CAGE tags were mapped to the full genome sequences for Danio rerio danRer10 using the Burrows Wheeler Aligner BWA and HiSAT2 software. Tags per million TPM were calculated using the CAGEr package of Bioconductor in R ver. 3.3.3 with the minimum TPM value of 0.5. Genome build: danRer10 Supplementary files format and content: Tab delimited text files include tags per million TPM values for each sample.	whole embryo	Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2μg of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit DNAFORM. five primecaps of RNAs are biotinylated post reverse transcription. RNA cDNA hybirds were then captured by streptavidin conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5′ linker which includes the three nucleotide barcodes followed by 3′ linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer creating the final double stranded DNA product. Cap analysis gene expression CAGE sequencing	tissue:whole embryo\|age:12 hpf sa37	GSM3141417	GSM3141417: sa37 12hpf; Danio rerio; RNA Seq	GSM3141417		1	Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2μg of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit DNAFORM. five primecaps of RNAs are biotinylated post reverse transcription. RNA cDNA hybirds were then captured by streptavidin conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5′ linker which includes the three nucleotide barcodes followed by 3′ linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer creating the final double stranded DNA product. Cap analysis gene expression CAGE sequencing	GEO Accession:GSM3141417	RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	NextSeq 500		SRP145615			KB3.fastq.gz	fastq	1102623174.0	14620872.0	GSM3141417 r1	0:75.41 1:0	A:294837961;C:265832591;G:295010626;T:246478308;N:463688	75	0	294837961	265832591	295010626	246478308	463688	SRX4080962	SRS3298237	SRA703389	GEO	Kanazawa University	1	0.89407	0.145	0.79299	0.58846	76	B	usable mapping rate	illumina	nextseq	unknown	cage	unknown	bulk	unknown	unknown	Japan	2018-05-14	Segmentation	Embryo	Whole Organism	All anatomical structures
48311	48311	SRR7162663	SRX4080961	SRS3298236	SRP145615	PRJNA471311	Gene expression analysis of jam3b mutant embryos	GSE114416	Transcriptome Analysis	Junctional adhesion molecule 3 Jam3 is a cell adhesion molecule that is involved in cell cell interaction cell migration and cell polarization in many tissue including the epithelium endothelium and hematopoietic cells. Although Jam3 is functionally relevant for both hematopoietic and vascular endothelial cells the role of Jam3 in hematopoietic or vascular development is still unknown. In this study a zebrafish jam3b mutant line jam3b sa37 was used for the cap analysis gene expression CAGE sequencing to identify genes that are involved in hematopoietic and/or vascular development in the zebrafish embryo. Overall design: Whole embryos mRNA profiles of wild type or jam3b sa37 embryos at 12 or 16 hpf were generated by CAGE sequencing using Illumina NextSeq500.				WT 16hpf	GSM3141416		source name:whole embryo\|tissue:whole embryo\|age:16 hpf type	WT 16hpf	Illumina RTA software was used for base calling. Sequenced CAGE tags were mapped to the full genome sequences for Danio rerio danRer10 using the Burrows Wheeler Aligner BWA and HiSAT2 software. Tags per million TPM were calculated using the CAGEr package of Bioconductor in R ver. 3.3.3 with the minimum TPM value of 0.5. Genome build: danRer10 Supplementary files format and content: Tab delimited text files include tags per million TPM values for each sample.	whole embryo	Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2μg of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit DNAFORM. five primecaps of RNAs are biotinylated post reverse transcription. RNA cDNA hybirds were then captured by streptavidin conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5′ linker which includes the three nucleotide barcodes followed by 3′ linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer creating the final double stranded DNA product. Cap analysis gene expression CAGE sequencing	tissue:whole embryo\|age:16 hpf type	GSM3141416	GSM3141416: WT 16hpf; Danio rerio; RNA Seq	GSM3141416		1	Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2μg of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit DNAFORM. five primecaps of RNAs are biotinylated post reverse transcription. RNA cDNA hybirds were then captured by streptavidin conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5′ linker which includes the three nucleotide barcodes followed by 3′ linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer creating the final double stranded DNA product. Cap analysis gene expression CAGE sequencing	GEO Accession:GSM3141416	RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	NextSeq 500		SRP145615			KB2.fastq.gz	fastq	1436366901.0	19049708.0	GSM3141416 r1	0:75.40 1:0	A:385845952;C:344690132;G:380040548;T:324881238;N:909031	75	0	385845952	344690132	380040548	324881238	909031	SRX4080961	SRS3298236	SRA703389	GEO	Kanazawa University	1	0.90003	0.11916	0.77579	0.54897	75	B	usable mapping rate	illumina	nextseq	unknown	cage	unknown	bulk	unknown	unknown	Japan	2018-05-14	Segmentation	Embryo	Whole Organism	All anatomical structures
48312	48312	SRR7162662	SRX4080960	SRS3298235	SRP145615	PRJNA471311	Gene expression analysis of jam3b mutant embryos	GSE114416	Transcriptome Analysis	Junctional adhesion molecule 3 Jam3 is a cell adhesion molecule that is involved in cell cell interaction cell migration and cell polarization in many tissue including the epithelium endothelium and hematopoietic cells. Although Jam3 is functionally relevant for both hematopoietic and vascular endothelial cells the role of Jam3 in hematopoietic or vascular development is still unknown. In this study a zebrafish jam3b mutant line jam3b sa37 was used for the cap analysis gene expression CAGE sequencing to identify genes that are involved in hematopoietic and/or vascular development in the zebrafish embryo. Overall design: Whole embryos mRNA profiles of wild type or jam3b sa37 embryos at 12 or 16 hpf were generated by CAGE sequencing using Illumina NextSeq500.				WT 12hpf	GSM3141415		source name:whole embryo\|tissue:whole embryo\|age:12 hpf type	WT 12hpf	Illumina RTA software was used for base calling. Sequenced CAGE tags were mapped to the full genome sequences for Danio rerio danRer10 using the Burrows Wheeler Aligner BWA and HiSAT2 software. Tags per million TPM were calculated using the CAGEr package of Bioconductor in R ver. 3.3.3 with the minimum TPM value of 0.5. Genome build: danRer10 Supplementary files format and content: Tab delimited text files include tags per million TPM values for each sample.	whole embryo	Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2μg of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit DNAFORM. five primecaps of RNAs are biotinylated post reverse transcription. RNA cDNA hybirds were then captured by streptavidin conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5′ linker which includes the three nucleotide barcodes followed by 3′ linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer creating the final double stranded DNA product. Cap analysis gene expression CAGE sequencing	tissue:whole embryo\|age:12 hpf type	GSM3141415	GSM3141415: WT 12hpf; Danio rerio; RNA Seq	GSM3141415		1	Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2μg of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit DNAFORM. five primecaps of RNAs are biotinylated post reverse transcription. RNA cDNA hybirds were then captured by streptavidin conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5′ linker which includes the three nucleotide barcodes followed by 3′ linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer creating the final double stranded DNA product. Cap analysis gene expression CAGE sequencing	GEO Accession:GSM3141415	RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	NextSeq 500		SRP145615			KB1.fastq.gz	fastq	1207735359.0	16013304.0	GSM3141415 r1	0:75.42 1:0	A:319723192;C:291608829;G:328515002;T:267246909;N:641427	75	0	319723192	291608829	328515002	267246909	641427	SRX4080960	SRS3298235	SRA703389	GEO	Kanazawa University	1	0.90112	0.14655	0.79762	0.52207	76	B	usable mapping rate	illumina	nextseq	unknown	cage	unknown	bulk	unknown	unknown	Japan	2018-05-14	Segmentation	Embryo	Whole Organism	All anatomical structures
55266	55266	SRR10418684	SRX7116713	SRS5465204	SRP223930	PRJNA575342	CAGE /CappedRNA sequencig	PRJNA575342	Other	CAGE and full length capped RNA sequencing for identification of transcription start TSS utilisation during Zebrafish Danio rerio embryonic development					S06 Prim5		strain:AB\|dev stage:Prim 5\|sex:N/A\|tissue:whole embryo\|BioSampleModel:Model organism or animal							CAGE seq of Danio rerio whole embryo Prim 5 stage Cycloheximide treated for 2 hours	Prim5 tagCAGE CHX	Prim5 tagCAGE CHX	Tagging CAGE			RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx		SRP223930			S06_Prim5_tagCAGE-CHX.fastq.gz	fastq	272077515.0	10076945.0	S06 Prim5 tagCAGE CHX.fastq.gz	0:27	A:67002738;C:62164745;G:73707100;T:69202932;N:0	27		67002738	62164745	73707100	69202932	0	SRX7116713	SRS5465204	SRA993027	University of Birmingham\|Cancer and Genomic Sciences	University of Birmingham	1	0.44237	0.05018	0.80296	0.84125	27	B	usable mapping rate	illumina	early_illumina	full_length	cage	unknown	bulk	unknown	unknown	United Kingdom	2019-11-08	Pharyngula	Embryo	Whole Organism	All anatomical structures
55267	55267	SRR10418685	SRX7116712	SRS5465204	SRP223930	PRJNA575342	CAGE /CappedRNA sequencig	PRJNA575342	Other	CAGE and full length capped RNA sequencing for identification of transcription start TSS utilisation during Zebrafish Danio rerio embryonic development					S06 Prim5		strain:AB\|dev stage:Prim 5\|sex:N/A\|tissue:whole embryo\|BioSampleModel:Model organism or animal							CAGE seq of Danio rerio whole embryo Prim 5 stage DMSO control	Prim5 tagCAGE DMSO	Prim5 tagCAGE DMSO	Tagging CAGE			RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx		SRP223930			S06_Prim5_tagCAGE-DMSO.fastq.gz	fastq	339322419.0	12567497.0	S06 Prim5 tagCAGE DMSO.fastq.gz	0:27	A:81884992;C:78138597;G:89012923;T:90285907;N:0	27		81884992	78138597	89012923	90285907	0	SRX7116712	SRS5465204	SRA993027	University of Birmingham\|Cancer and Genomic Sciences	University of Birmingham	1	0.43876	0.05032	0.82404	0.85765	27	B	usable mapping rate	illumina	early_illumina	full_length	cage	unknown	bulk	unknown	unknown	United Kingdom	2019-11-08	Pharyngula	Embryo	Whole Organism	All anatomical structures
55269	55269	SRR10215485	SRX6935170	SRS5465205	SRP223930	PRJNA575342	CAGE /CappedRNA sequencig	PRJNA575342	Other	CAGE and full length capped RNA sequencing for identification of transcription start TSS utilisation during Zebrafish Danio rerio embryonic development					S07 LongPec		strain:AB\|dev stage:Long pec\|sex:N/A\|tissue:whole embryo\|BioSampleModel:Model organism or animal							CAGE seq of Danio rerio whole embryo Long pec stage	LongPec nAnTiCAGE	LongPec nAnTiCAGE	nAnTiCAGE			RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	NextSeq 500		SRP223930			S07_LongPec_nAnTiCAGE.fastq.gz	fastq	1326115656.0	18418273.0	S07 LongPec nAnTiCAGE.fastq.gz	0:72 1:0	A:355337919;C:317217156;G:362577018;T:290983563;N:0	72	0	355337919	317217156	362577018	290983563	0	SRX6935170	SRS5465205	SRA971223	University of Birmingham\|Cancer and Genomic Sciences	University of Birmingham	1	0.94675	0.13499	0.77512	0.56663	72	B	usable mapping rate	illumina	nextseq	full_length	cage	unknown	bulk	unknown	unknown	United Kingdom	2019-10-02	Hatching	Embryo	Whole Organism	All anatomical structures
55272	55272	SRR10215488	SRX6935167	SRS5465202	SRP223930	PRJNA575342	CAGE /CappedRNA sequencig	PRJNA575342	Other	CAGE and full length capped RNA sequencing for identification of transcription start TSS utilisation during Zebrafish Danio rerio embryonic development					S04 30Epi		strain:AB\|dev stage:zfs:0000015\|sex:N/A\|tissue:whole embryo\|BioSampleModel:Model organism or animal							CAGE seq of Danio rerio whole embryo zfs:0000015 stage	zfs:0000015 nAnTiCAGE	zfs:0000015 nAnTiCAGE	nAnTiCAGE			RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP223930			S04_30pEpib_nAnTiCAGE.fastq.gz	fastq	629440272.0	13113339.0	S04 30pEpib nAnTiCAGE.fastq.gz	0:48 1:0	A:170201862;C:150343558;G:166046900;T:141987430;N:860522	48	0	170201862	150343558	166046900	141987430	860522	SRX6935167	SRS5465202	SRA971223	University of Birmingham\|Cancer and Genomic Sciences	University of Birmingham	1	0.83843	0.15935	0.81499	0.71304	48	B	usable mapping rate	illumina	hiseq_era	full_length	cage	unknown	bulk	unknown	unknown	United Kingdom	2019-10-02	Blastula	Embryo	Whole Organism	All anatomical structures
55273	55273	SRR10215489	SRX6935166	SRS5465201	SRP223930	PRJNA575342	CAGE /CappedRNA sequencig	PRJNA575342	Other	CAGE and full length capped RNA sequencing for identification of transcription start TSS utilisation during Zebrafish Danio rerio embryonic development					S03 512Cells		strain:AB\|dev stage:512 cell\|sex:N/A\|tissue:whole embryo\|BioSampleModel:Model organism or animal							CAGE seq of Danio rerio whole embryo 512 cell stage	512Cells nAnTiCAGE	512Cells nAnTiCAGE	nAnTiCAGE			RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP223930			S03_512Cells_nAnTiCAGE.fastq.gz	fastq	725783040.0	15120480.0	S03 512Cells nAnTiCAGE.fastq.gz	0:48 1:0	A:196224130;C:171017037;G:189882541;T:167660445;N:998887	48	0	196224130	171017037	189882541	167660445	998887	SRX6935166	SRS5465201	SRA971223	University of Birmingham\|Cancer and Genomic Sciences	University of Birmingham	1	0.85441	0.14832	0.79659	0.68016	48	B	usable mapping rate	illumina	hiseq_era	full_length	cage	unknown	bulk	unknown	unknown	United Kingdom	2019-10-02	Blastula	Embryo	Whole Organism	All anatomical structures
55274	55274	SRR10215490	SRX6935165	SRS5465200	SRP223930	PRJNA575342	CAGE /CappedRNA sequencig	PRJNA575342	Other	CAGE and full length capped RNA sequencing for identification of transcription start TSS utilisation during Zebrafish Danio rerio embryonic development					S02 128Cells		strain:AB\|dev stage:128 cell\|sex:N/A\|tissue:whole embryo\|BioSampleModel:Model organism or animal							CAGE seq of Danio rerio whole embryo 128 cell stage	128Cells nAnTiCAGE	128Cells nAnTiCAGE	nAnTiCAGE			RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP223930			S02_128Cells_nAnTiCAGE.fastq.gz	fastq	510549408.0	10636446.0	S02 128Cells nAnTiCAGE.fastq.gz	0:48 1:0	A:135389960;C:121538362;G:140642547;T:112273195;N:705344	48	0	135389960	121538362	140642547	112273195	705344	SRX6935165	SRS5465200	SRA971223	University of Birmingham\|Cancer and Genomic Sciences	University of Birmingham	1	0.84843	0.14523	0.79845	0.68592	48	B	usable mapping rate	illumina	hiseq_era	full_length	cage	unknown	bulk	unknown	unknown	United Kingdom	2019-10-02	Blastula	Embryo	Whole Organism	All anatomical structures
69378	69378	SRR18516702	SRX14647801	SRS12413210	SRP366491	PRJNA821088	Enhancer calling in early stages	PRJNA821088	Other	CAGE seq for enhancer calling in early stages for the DANIO CODE project.					DCD007475BS		strain:WT\|age:4.7hpf\|dev stage:zfs:0000015\|sex:not applicable\|tissue:early embryonic cell\|biomaterial provider:Mueller lab University of Birmingham\|replicate:2\|BioSampleModel:Model organism or animal							CAGE seq zfs:0000015 Whole cell CAGE	DCD003740SQ	DCD003740SQ	max read length:50			RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP366491			CAGE-seq_Mueller_lab_0013AS.DCD003740SQ.USERdanio-user.R1.fastq.gz	fastq	57981552.0	1207949.0	CAGE seq Mueller lab 0013AS.DCD003740SQ.USERdanio user.R1.fastq.gz	0:48 1:0	A:13228227;C:15492921;G:15505739;T:13750626;N:4039	48	0	13228227	15492921	15505739	13750626	4039	SRX14647801	SRS12413210	SRA1393740	DANIO-CODE\|Department for Biosciences and Nutrition	DANIO-CODE DANIO-CODE	1	0.18388	0.02619	0.85811	0.52264	48	B	usable mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2022-03-29	Blastula	Embryo	Embryo Imprecise	All anatomical structures
69379	69379	SRR18516703	SRX14647800	SRS12413216	SRP366491	PRJNA821088	Enhancer calling in early stages	PRJNA821088	Other	CAGE seq for enhancer calling in early stages for the DANIO CODE project.					DCD007476BS		strain:WT\|age:24hpf\|dev stage:Prim 5\|sex:not applicable\|tissue:early embryonic cell\|biomaterial provider:Mueller lab University of Birmingham\|replicate:1\|BioSampleModel:Model organism or animal							CAGE seq Prim Nuclear CAGE	DCD003719SQ	DCD003719SQ	max read length:50			RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP366491			CAGE-seq_Mueller_lab_0014AS.DCD003719SQ.USERdanio-user.R1.fastq.gz	fastq	585510192.0	12198129.0	CAGE seq Mueller lab 0014AS.DCD003719SQ.USERdanio user.R1.fastq.gz	0:48 1:0	A:129885703;C:153766182;G:160138903;T:141666883;N:52521	48	0	129885703	153766182	160138903	141666883	52521	SRX14647800	SRS12413216	SRA1393740	DANIO-CODE\|Department for Biosciences and Nutrition	DANIO-CODE DANIO-CODE	1	0.20391	0.04196	0.83453	0.4979	48	B	usable mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2022-03-29	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
69380	69380	SRR18516704	SRX14647799	SRS12413216	SRP366491	PRJNA821088	Enhancer calling in early stages	PRJNA821088	Other	CAGE seq for enhancer calling in early stages for the DANIO CODE project.					DCD007476BS		strain:WT\|age:24hpf\|dev stage:Prim 5\|sex:not applicable\|tissue:early embryonic cell\|biomaterial provider:Mueller lab University of Birmingham\|replicate:1\|BioSampleModel:Model organism or animal							CAGE seq Prim Nuclear CAGE	DCD003718SQ	DCD003718SQ	max read length:50			RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP366491			CAGE-seq_Mueller_lab_0014AS.DCD003718SQ.USERdanio-user.R1.fastq.gz	fastq	593136528.0	12357011.0	CAGE seq Mueller lab 0014AS.DCD003718SQ.USERdanio user.R1.fastq.gz	0:48 1:0	A:130366174;C:156810351;G:159219365;T:146691922;N:48716	48	0	130366174	156810351	159219365	146691922	48716	SRX14647799	SRS12413216	SRA1393740	DANIO-CODE\|Department for Biosciences and Nutrition	DANIO-CODE DANIO-CODE	1	0.14873	0.03239	0.86557	0.49634	48	B	usable mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2022-03-29	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
69381	69381	SRR18516705	SRX14647798	SRS12413216	SRP366491	PRJNA821088	Enhancer calling in early stages	PRJNA821088	Other	CAGE seq for enhancer calling in early stages for the DANIO CODE project.					DCD007476BS		strain:WT\|age:24hpf\|dev stage:Prim 5\|sex:not applicable\|tissue:early embryonic cell\|biomaterial provider:Mueller lab University of Birmingham\|replicate:1\|BioSampleModel:Model organism or animal							CAGE seq Prim Nuclear CAGE	DCD003723SQ	DCD003723SQ	max read length:50			RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP366491			CAGE-seq_Mueller_lab_0014AS.DCD003723SQ.USERdanio-user.R1.fastq.gz	fastq	422696256.0	8806172.0	CAGE seq Mueller lab 0014AS.DCD003723SQ.USERdanio user.R1.fastq.gz	0:48 1:0	A:92712632;C:111696999;G:115145846;T:103105611;N:35168	48	0	92712632	111696999	115145846	103105611	35168	SRX14647798	SRS12413216	SRA1393740	DANIO-CODE\|Department for Biosciences and Nutrition	DANIO-CODE DANIO-CODE	1	0.1594	0.02997	0.85591	0.48496	48	B	usable mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2022-03-29	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
69382	69382	SRR18516706	SRX14647797	SRS12413215	SRP366491	PRJNA821088	Enhancer calling in early stages	PRJNA821088	Other	CAGE seq for enhancer calling in early stages for the DANIO CODE project.					DCD007477BS		strain:WT\|age:42hpf\|dev stage:High pec\|sex:not applicable\|tissue:early embryonic cell\|biomaterial provider:Mueller lab University of Birmingham\|replicate:1\|BioSampleModel:Model organism or animal							CAGE seq High pec Nuclear CAGE	DCD003737SQ	DCD003737SQ	max read length:50			RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP366491			CAGE-seq_Mueller_lab_0014AS.DCD003737SQ.USERdanio-user.R1.fastq.gz	fastq	1041108672.0	21689764.0	CAGE seq Mueller lab 0014AS.DCD003737SQ.USERdanio user.R1.fastq.gz	0:48 1:0	A:233996885;C:276232291;G:275987771;T:254800016;N:91709	48	0	233996885	276232291	275987771	254800016	91709	SRX14647797	SRS12413215	SRA1393740	DANIO-CODE\|Department for Biosciences and Nutrition	DANIO-CODE DANIO-CODE	1	0.19665	0.0423	0.84271	0.49525	48	B	usable mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2022-03-29	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
69383	69383	SRR18516707	SRX14647796	SRS12413215	SRP366491	PRJNA821088	Enhancer calling in early stages	PRJNA821088	Other	CAGE seq for enhancer calling in early stages for the DANIO CODE project.					DCD007477BS		strain:WT\|age:42hpf\|dev stage:High pec\|sex:not applicable\|tissue:early embryonic cell\|biomaterial provider:Mueller lab University of Birmingham\|replicate:1\|BioSampleModel:Model organism or animal							CAGE seq High pec Nuclear CAGE	DCD003729SQ	DCD003729SQ	max read length:50			RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP366491			CAGE-seq_Mueller_lab_0014AS.DCD003729SQ.USERdanio-user.R1.fastq.gz	fastq	383268528.0	7984761.0	CAGE seq Mueller lab 0014AS.DCD003729SQ.USERdanio user.R1.fastq.gz	0:48 1:0	A:83789437;C:103371728;G:102876480;T:93198236;N:32647	48	0	83789437	103371728	102876480	93198236	32647	SRX14647796	SRS12413215	SRA1393740	DANIO-CODE\|Department for Biosciences and Nutrition	DANIO-CODE DANIO-CODE	1	0.15605	0.03059	0.86951	0.50369	48	B	usable mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2022-03-29	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
69384	69384	SRR18516708	SRX14647795	SRS12413215	SRP366491	PRJNA821088	Enhancer calling in early stages	PRJNA821088	Other	CAGE seq for enhancer calling in early stages for the DANIO CODE project.					DCD007477BS		strain:WT\|age:42hpf\|dev stage:High pec\|sex:not applicable\|tissue:early embryonic cell\|biomaterial provider:Mueller lab University of Birmingham\|replicate:1\|BioSampleModel:Model organism or animal							CAGE seq High pec Nuclear CAGE	DCD003734SQ	DCD003734SQ	max read length:50			RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP366491			CAGE-seq_Mueller_lab_0014AS.DCD003734SQ.USERdanio-user.R1.fastq.gz	fastq	560665392.0	11680529.0	CAGE seq Mueller lab 0014AS.DCD003734SQ.USERdanio user.R1.fastq.gz	0:48 1:0	A:123278501;C:149059346;G:152514412;T:135763704;N:49429	48	0	123278501	149059346	152514412	135763704	49429	SRX14647795	SRS12413215	SRA1393740	DANIO-CODE\|Department for Biosciences and Nutrition	DANIO-CODE DANIO-CODE	1	0.16518	0.02906	0.85283	0.47924	48	B	usable mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2022-03-29	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
69385	69385	SRR18516709	SRX14647794	SRS12413214	SRP366491	PRJNA821088	Enhancer calling in early stages	PRJNA821088	Other	CAGE seq for enhancer calling in early stages for the DANIO CODE project.					DCD007471BS		strain:WT\|age:42hpf\|dev stage:High pec\|sex:not applicable\|tissue:early embryonic cell\|biomaterial provider:Mueller lab University of Birmingham\|replicate:2\|BioSampleModel:Model organism or animal							CAGE seq High pec Whole cell CAGE	DCD003731SQ	DCD003731SQ	max read length:50			RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP366491			CAGE-seq_Mueller_lab_0013AS.DCD003731SQ.USERdanio-user.R1.fastq.gz	fastq	534745104.0	11140523.0	CAGE seq Mueller lab 0013AS.DCD003731SQ.USERdanio user.R1.fastq.gz	0:48 1:0	A:122900964;C:145291239;G:142314928;T:124199394;N:38579	48	0	122900964	145291239	142314928	124199394	38579	SRX14647794	SRS12413214	SRA1393740	DANIO-CODE\|Department for Biosciences and Nutrition	DANIO-CODE DANIO-CODE	1	0.21193	0.03662	0.8576	0.51061	48	B	usable mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2022-03-29	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
69386	69386	SRR18516710	SRX14647793	SRS12413214	SRP366491	PRJNA821088	Enhancer calling in early stages	PRJNA821088	Other	CAGE seq for enhancer calling in early stages for the DANIO CODE project.					DCD007471BS		strain:WT\|age:42hpf\|dev stage:High pec\|sex:not applicable\|tissue:early embryonic cell\|biomaterial provider:Mueller lab University of Birmingham\|replicate:2\|BioSampleModel:Model organism or animal							CAGE seq High pec Whole cell CAGE	DCD003733SQ	DCD003733SQ	max read length:50			RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP366491			CAGE-seq_Mueller_lab_0013AS.DCD003733SQ.USERdanio-user.R1.fastq.gz	fastq	1106623152.0	23054649.0	CAGE seq Mueller lab 0013AS.DCD003733SQ.USERdanio user.R1.fastq.gz	0:48 1:0	A:244437769;C:302018709;G:293780395;T:266329857;N:56422	48	0	244437769	302018709	293780395	266329857	56422	SRX14647793	SRS12413214	SRA1393740	DANIO-CODE\|Department for Biosciences and Nutrition	DANIO-CODE DANIO-CODE	1	0.25973	0.02959	0.84778	0.50948	48	B	usable mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2022-03-29	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
69387	69387	SRR18516711	SRX14647792	SRS12413214	SRP366491	PRJNA821088	Enhancer calling in early stages	PRJNA821088	Other	CAGE seq for enhancer calling in early stages for the DANIO CODE project.					DCD007471BS		strain:WT\|age:42hpf\|dev stage:High pec\|sex:not applicable\|tissue:early embryonic cell\|biomaterial provider:Mueller lab University of Birmingham\|replicate:2\|BioSampleModel:Model organism or animal							CAGE seq High pec Whole cell CAGE	DCD003735SQ	DCD003735SQ	max read length:50			RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP366491			CAGE-seq_Mueller_lab_0013AS.DCD003735SQ.USERdanio-user.R1.fastq.gz	fastq	829987920.0	17291415.0	CAGE seq Mueller lab 0013AS.DCD003735SQ.USERdanio user.R1.fastq.gz	0:48 1:0	A:189638839;C:226118233;G:218991435;T:195178858;N:60555	48	0	189638839	226118233	218991435	195178858	60555	SRX14647792	SRS12413214	SRA1393740	DANIO-CODE\|Department for Biosciences and Nutrition	DANIO-CODE DANIO-CODE	1	0.20953	0.03562	0.85285	0.52927	48	B	usable mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2022-03-29	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
69388	69388	SRR18516712	SRX14647791	SRS12413213	SRP366491	PRJNA821088	Enhancer calling in early stages	PRJNA821088	Other	CAGE seq for enhancer calling in early stages for the DANIO CODE project.					DCD007472BS		strain:WT\|age:14hpf\|dev stage:5 9 somites\|sex:not applicable\|tissue:early embryonic cell\|biomaterial provider:Mueller lab University of Birmingham\|replicate:2\|BioSampleModel:Model organism or animal							CAGE seq 5 9 somites Whole cell CAGE	DCD003730SQ	DCD003730SQ	max read length:50			RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP366491			CAGE-seq_Mueller_lab_0013AS.DCD003730SQ.USERdanio-user.R1.fastq.gz	fastq	358730736.0	7473557.0	CAGE seq Mueller lab 0013AS.DCD003730SQ.USERdanio user.R1.fastq.gz	0:48 1:0	A:82114871;C:96481695;G:97889447;T:82217691;N:27032	48	0	82114871	96481695	97889447	82217691	27032	SRX14647791	SRS12413213	SRA1393740	DANIO-CODE\|Department for Biosciences and Nutrition	DANIO-CODE DANIO-CODE	1	0.22955	0.03488	0.84719	0.51204	48	B	usable mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2022-03-29	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
69389	69389	SRR18516713	SRX14647790	SRS12413209	SRP366491	PRJNA821088	Enhancer calling in early stages	PRJNA821088	Other	CAGE seq for enhancer calling in early stages for the DANIO CODE project.					DCD007478BS		strain:WT\|age:4.7hpf\|dev stage:zfs:0000015\|sex:not applicable\|tissue:early embryonic cell\|biomaterial provider:Mueller lab University of Birmingham\|replicate:1\|BioSampleModel:Model organism or animal							CAGE seq zfs:0000015 Nuclear CAGE	DCD003732SQ	DCD003732SQ	max read length:50			RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP366491			CAGE-seq_Mueller_lab_0014AS.DCD003732SQ.USERdanio-user.R1.fastq.gz	fastq	833831760.0	17371495.0	CAGE seq Mueller lab 0014AS.DCD003732SQ.USERdanio user.R1.fastq.gz	0:48 1:0	A:184529953;C:221676233;G:220734592;T:206820467;N:70515	48	0	184529953	221676233	220734592	206820467	70515	SRX14647790	SRS12413209	SRA1393740	DANIO-CODE\|Department for Biosciences and Nutrition	DANIO-CODE DANIO-CODE	1	0.16336	0.03655	0.88633	0.47894	48	B	usable mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2022-03-29	Blastula	Embryo	Embryo Imprecise	All anatomical structures
69390	69390	SRR18516714	SRX14647789	SRS12413213	SRP366491	PRJNA821088	Enhancer calling in early stages	PRJNA821088	Other	CAGE seq for enhancer calling in early stages for the DANIO CODE project.					DCD007472BS		strain:WT\|age:14hpf\|dev stage:5 9 somites\|sex:not applicable\|tissue:early embryonic cell\|biomaterial provider:Mueller lab University of Birmingham\|replicate:2\|BioSampleModel:Model organism or animal							CAGE seq 5 9 somites Whole cell CAGE	DCD003738SQ	DCD003738SQ	max read length:50			RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP366491			CAGE-seq_Mueller_lab_0013AS.DCD003738SQ.USERdanio-user.R1.fastq.gz	fastq	1160622288.0	24179631.0	CAGE seq Mueller lab 0013AS.DCD003738SQ.USERdanio user.R1.fastq.gz	0:48 1:0	A:261568282;C:313737609;G:310169539;T:275088632;N:58226	48	0	261568282	313737609	310169539	275088632	58226	SRX14647789	SRS12413213	SRA1393740	DANIO-CODE\|Department for Biosciences and Nutrition	DANIO-CODE DANIO-CODE	1	0.27025	0.0344	0.86505	0.50961	48	B	usable mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2022-03-29	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
69391	69391	SRR18516715	SRX14647788	SRS12413213	SRP366491	PRJNA821088	Enhancer calling in early stages	PRJNA821088	Other	CAGE seq for enhancer calling in early stages for the DANIO CODE project.					DCD007472BS		strain:WT\|age:14hpf\|dev stage:5 9 somites\|sex:not applicable\|tissue:early embryonic cell\|biomaterial provider:Mueller lab University of Birmingham\|replicate:2\|BioSampleModel:Model organism or animal							CAGE seq 5 9 somites Whole cell CAGE	DCD003722SQ	DCD003722SQ	max read length:50			RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP366491			CAGE-seq_Mueller_lab_0013AS.DCD003722SQ.USERdanio-user.R1.fastq.gz	fastq	666656256.0	13888672.0	CAGE seq Mueller lab 0013AS.DCD003722SQ.USERdanio user.R1.fastq.gz	0:48 1:0	A:149770159;C:178068662;G:177661463;T:161122864;N:33108	48	0	149770159	178068662	177661463	161122864	33108	SRX14647788	SRS12413213	SRA1393740	DANIO-CODE\|Department for Biosciences and Nutrition	DANIO-CODE DANIO-CODE	1	0.25511	0.02671	0.86436	0.50531	48	B	usable mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2022-03-29	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
69392	69392	SRR18516716	SRX14647787	SRS12413212	SRP366491	PRJNA821088	Enhancer calling in early stages	PRJNA821088	Other	CAGE seq for enhancer calling in early stages for the DANIO CODE project.					DCD007473BS		strain:WT\|age:24hpf\|dev stage:Prim 5\|sex:not applicable\|tissue:early embryonic cell\|biomaterial provider:Mueller lab University of Birmingham\|replicate:2\|BioSampleModel:Model organism or animal							CAGE seq Prim Whole cell CAGE	DCD003727SQ	DCD003727SQ	max read length:50			RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP366491			CAGE-seq_Mueller_lab_0013AS.DCD003727SQ.USERdanio-user.R1.fastq.gz	fastq	924879888.0	19268331.0	CAGE seq Mueller lab 0013AS.DCD003727SQ.USERdanio user.R1.fastq.gz	0:48 1:0	A:214005056;C:251321459;G:244648845;T:214835794;N:68734	48	0	214005056	251321459	244648845	214835794	68734	SRX14647787	SRS12413212	SRA1393740	DANIO-CODE\|Department for Biosciences and Nutrition	DANIO-CODE DANIO-CODE	1	0.2165	0.03701	0.84768	0.54102	48	B	usable mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2022-03-29	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
69393	69393	SRR18516717	SRX14647786	SRS12413212	SRP366491	PRJNA821088	Enhancer calling in early stages	PRJNA821088	Other	CAGE seq for enhancer calling in early stages for the DANIO CODE project.					DCD007473BS		strain:WT\|age:24hpf\|dev stage:Prim 5\|sex:not applicable\|tissue:early embryonic cell\|biomaterial provider:Mueller lab University of Birmingham\|replicate:2\|BioSampleModel:Model organism or animal							CAGE seq Prim Whole cell CAGE	DCD003717SQ	DCD003717SQ	max read length:50			RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP366491			CAGE-seq_Mueller_lab_0013AS.DCD003717SQ.USERdanio-user.R1.fastq.gz	fastq	1485845376.0	30955112.0	CAGE seq Mueller lab 0013AS.DCD003717SQ.USERdanio user.R1.fastq.gz	0:48 1:0	A:329122121;C:402514173;G:390388645;T:363745867;N:74570	48	0	329122121	402514173	390388645	363745867	74570	SRX14647786	SRS12413212	SRA1393740	DANIO-CODE\|Department for Biosciences and Nutrition	DANIO-CODE DANIO-CODE	1	0.23893	0.0248	0.86125	0.50849	48	B	usable mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2022-03-29	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
69394	69394	SRR18516718	SRX14647785	SRS12413212	SRP366491	PRJNA821088	Enhancer calling in early stages	PRJNA821088	Other	CAGE seq for enhancer calling in early stages for the DANIO CODE project.					DCD007473BS		strain:WT\|age:24hpf\|dev stage:Prim 5\|sex:not applicable\|tissue:early embryonic cell\|biomaterial provider:Mueller lab University of Birmingham\|replicate:2\|BioSampleModel:Model organism or animal							CAGE seq Prim Whole cell CAGE	DCD003739SQ	DCD003739SQ	max read length:50			RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP366491			CAGE-seq_Mueller_lab_0013AS.DCD003739SQ.USERdanio-user.R1.fastq.gz	fastq	1372622736.0	28596307.0	CAGE seq Mueller lab 0013AS.DCD003739SQ.USERdanio user.R1.fastq.gz	0:48 1:0	A:306709302;C:373224967;G:360990874;T:331626639;N:70954	48	0	306709302	373224967	360990874	331626639	70954	SRX14647785	SRS12413212	SRA1393740	DANIO-CODE\|Department for Biosciences and Nutrition	DANIO-CODE DANIO-CODE	1	0.26574	0.02914	0.85113	0.52147	48	B	usable mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2022-03-29	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
69395	69395	SRR18516719	SRX14647784	SRS12413211	SRP366491	PRJNA821088	Enhancer calling in early stages	PRJNA821088	Other	CAGE seq for enhancer calling in early stages for the DANIO CODE project.					DCD007474BS		strain:WT\|age:14hpf\|dev stage:5 9 somites\|sex:not applicable\|tissue:early embryonic cell\|biomaterial provider:Mueller lab University of Birmingham\|replicate:1\|BioSampleModel:Model organism or animal							CAGE seq 5 9 somites Nuclear CAGE	DCD003721SQ	DCD003721SQ	max read length:50			RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP366491			CAGE-seq_Mueller_lab_0014AS.DCD003721SQ.USERdanio-user.R1.fastq.gz	fastq	425483904.0	8864248.0	CAGE seq Mueller lab 0014AS.DCD003721SQ.USERdanio user.R1.fastq.gz	0:48 1:0	A:98642418;C:114264552;G:114112965;T:98433833;N:30136	48	0	98642418	114264552	114112965	98433833	30136	SRX14647784	SRS12413211	SRA1393740	DANIO-CODE\|Department for Biosciences and Nutrition	DANIO-CODE DANIO-CODE	1	0.21658	0.03797	0.85226	0.48604	48	B	usable mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2022-03-29	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
69396	69396	SRR18516720	SRX14647783	SRS12413211	SRP366491	PRJNA821088	Enhancer calling in early stages	PRJNA821088	Other	CAGE seq for enhancer calling in early stages for the DANIO CODE project.					DCD007474BS		strain:WT\|age:14hpf\|dev stage:5 9 somites\|sex:not applicable\|tissue:early embryonic cell\|biomaterial provider:Mueller lab University of Birmingham\|replicate:1\|BioSampleModel:Model organism or animal							CAGE seq 5 9 somites Nuclear CAGE	DCD003736SQ	DCD003736SQ	max read length:50			RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP366491			CAGE-seq_Mueller_lab_0014AS.DCD003736SQ.USERdanio-user.R1.fastq.gz	fastq	533681088.0	11118356.0	CAGE seq Mueller lab 0014AS.DCD003736SQ.USERdanio user.R1.fastq.gz	0:48 1:0	A:115850766;C:142773032;G:143794343;T:131220159;N:42788	48	0	115850766	142773032	143794343	131220159	42788	SRX14647783	SRS12413211	SRA1393740	DANIO-CODE\|Department for Biosciences and Nutrition	DANIO-CODE DANIO-CODE	1	0.15054	0.0279	0.87434	0.4867	48	B	usable mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2022-03-29	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
69397	69397	SRR18516721	SRX14647782	SRS12413211	SRP366491	PRJNA821088	Enhancer calling in early stages	PRJNA821088	Other	CAGE seq for enhancer calling in early stages for the DANIO CODE project.					DCD007474BS		strain:WT\|age:14hpf\|dev stage:5 9 somites\|sex:not applicable\|tissue:early embryonic cell\|biomaterial provider:Mueller lab University of Birmingham\|replicate:1\|BioSampleModel:Model organism or animal							CAGE seq 5 9 somites Nuclear CAGE	DCD003726SQ	DCD003726SQ	max read length:50			RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP366491			CAGE-seq_Mueller_lab_0014AS.DCD003726SQ.USERdanio-user.R1.fastq.gz	fastq	250307520.0	5214740.0	CAGE seq Mueller lab 0014AS.DCD003726SQ.USERdanio user.R1.fastq.gz	0:48 1:0	A:55705158;C:65429159;G:68119770;T:61031856;N:21577	48	0	55705158	65429159	68119770	61031856	21577	SRX14647782	SRS12413211	SRA1393740	DANIO-CODE\|Department for Biosciences and Nutrition	DANIO-CODE DANIO-CODE	1	0.19864	0.04157	0.85279	0.48786	48	B	usable mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2022-03-29	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
69398	69398	SRR18516722	SRX14647781	SRS12413210	SRP366491	PRJNA821088	Enhancer calling in early stages	PRJNA821088	Other	CAGE seq for enhancer calling in early stages for the DANIO CODE project.					DCD007475BS		strain:WT\|age:4.7hpf\|dev stage:zfs:0000015\|sex:not applicable\|tissue:early embryonic cell\|biomaterial provider:Mueller lab University of Birmingham\|replicate:2\|BioSampleModel:Model organism or animal							CAGE seq zfs:0000015 Whole cell CAGE	DCD003720SQ	DCD003720SQ	max read length:50			RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP366491			CAGE-seq_Mueller_lab_0013AS.DCD003720SQ.USERdanio-user.R1.fastq.gz	fastq	536292432.0	11172759.0	CAGE seq Mueller lab 0013AS.DCD003720SQ.USERdanio user.R1.fastq.gz	0:48 1:0	A:122756671;C:142850582;G:140364671;T:130293257;N:27251	48	0	122756671	142850582	140364671	130293257	27251	SRX14647781	SRS12413210	SRA1393740	DANIO-CODE\|Department for Biosciences and Nutrition	DANIO-CODE DANIO-CODE	1	0.23072	0.04674	0.89572	0.59187	48	B	usable mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2022-03-29	Blastula	Embryo	Embryo Imprecise	All anatomical structures
69399	69399	SRR18516723	SRX14647780	SRS12413210	SRP366491	PRJNA821088	Enhancer calling in early stages	PRJNA821088	Other	CAGE seq for enhancer calling in early stages for the DANIO CODE project.					DCD007475BS		strain:WT\|age:4.7hpf\|dev stage:zfs:0000015\|sex:not applicable\|tissue:early embryonic cell\|biomaterial provider:Mueller lab University of Birmingham\|replicate:2\|BioSampleModel:Model organism or animal							CAGE seq zfs:0000015 Whole cell CAGE	DCD003725SQ	DCD003725SQ	max read length:50			RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP366491			CAGE-seq_Mueller_lab_0013AS.DCD003725SQ.USERdanio-user.R1.fastq.gz	fastq	1839979776.0	38332912.0	CAGE seq Mueller lab 0013AS.DCD003725SQ.USERdanio user.R1.fastq.gz	0:48 1:0	A:422772310;C:484519947;G:479159876;T:453437875;N:89768	48	0	422772310	484519947	479159876	453437875	89768	SRX14647780	SRS12413210	SRA1393740	DANIO-CODE\|Department for Biosciences and Nutrition	DANIO-CODE DANIO-CODE	1	0.22646	0.03978	0.88574	0.556	48	B	usable mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2022-03-29	Blastula	Embryo	Embryo Imprecise	All anatomical structures
69400	69400	SRR18516724	SRX14647779	SRS12413209	SRP366491	PRJNA821088	Enhancer calling in early stages	PRJNA821088	Other	CAGE seq for enhancer calling in early stages for the DANIO CODE project.					DCD007478BS		strain:WT\|age:4.7hpf\|dev stage:zfs:0000015\|sex:not applicable\|tissue:early embryonic cell\|biomaterial provider:Mueller lab University of Birmingham\|replicate:1\|BioSampleModel:Model organism or animal							CAGE seq zfs:0000015 Nuclear CAGE	DCD003728SQ	DCD003728SQ	max read length:50			RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP366491			CAGE-seq_Mueller_lab_0014AS.DCD003728SQ.USERdanio-user.R1.fastq.gz	fastq	778510272.0	16218964.0	CAGE seq Mueller lab 0014AS.DCD003728SQ.USERdanio user.R1.fastq.gz	0:48 1:0	A:170505572;C:207531743;G:206655879;T:193751108;N:65970	48	0	170505572	207531743	206655879	193751108	65970	SRX14647779	SRS12413209	SRA1393740	DANIO-CODE\|Department for Biosciences and Nutrition	DANIO-CODE DANIO-CODE	1	0.1419	0.02783	0.8954	0.49693	48	B	usable mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2022-03-29	Blastula	Embryo	Embryo Imprecise	All anatomical structures
69401	69401	SRR18516725	SRX14647778	SRS12413209	SRP366491	PRJNA821088	Enhancer calling in early stages	PRJNA821088	Other	CAGE seq for enhancer calling in early stages for the DANIO CODE project.					DCD007478BS		strain:WT\|age:4.7hpf\|dev stage:zfs:0000015\|sex:not applicable\|tissue:early embryonic cell\|biomaterial provider:Mueller lab University of Birmingham\|replicate:1\|BioSampleModel:Model organism or animal							CAGE seq zfs:0000015 Nuclear CAGE	DCD003724SQ	DCD003724SQ	max read length:50			RNA-Seq	TRANSCRIPTOMIC	CAGE	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP366491			CAGE-seq_Mueller_lab_0014AS.DCD003724SQ.USERdanio-user.R1.fastq.gz	fastq	641108496.0	13356427.0	CAGE seq Mueller lab 0014AS.DCD003724SQ.USERdanio user.R1.fastq.gz	0:48 1:0	A:143927298;C:167543966;G:171107575;T:158473503;N:56154	48	0	143927298	167543966	171107575	158473503	56154	SRX14647778	SRS12413209	SRA1393740	DANIO-CODE\|Department for Biosciences and Nutrition	DANIO-CODE DANIO-CODE	1	0.20203	0.0454	0.87091	0.51364	48	B	usable mapping rate	illumina	hiseq_era	unknown	cage	unknown	bulk	unknown	unknown	Unknown	2022-03-29	Blastula	Embryo	Embryo Imprecise	All anatomical structures

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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");;