metadata: run_metadata: 23 rows where experiment.library_selection = "CAGE", experiment.library_strategy = "OTHER" and tissue_curation

23 rows where experiment.library_selection = "CAGE", experiment.library_strategy = "OTHER" and tissue_curation_coarse = "All anatomical structures"

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	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

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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");;