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89 rows where experiment.library_selection = "CAGE" and experiment.library_source = "TRANSCRIPTOMIC"

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tissue_curation 6

experiment.library_strategy 2

experiment.library_layout 2

devstage_curation_coarse 2

technology 1

experiment.platform 1

experiment.library_source 1

  • TRANSCRIPTOMIC · 89 ✖

experiment.library_selection 1

  • CAGE · 89 ✖
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.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol 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.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant 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
37185 37185 SRR1010334 SRX363385 SRS490049 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio MUTL7F transgenic line   strain:AB strain MUTL7F line|development stage:high 3.3 hpf                 D. rerio MUTL7F transgenic line single locus CAGE mutated sf3a2:mCherry transgene D. rerio MUTL7F transgenic line single locus CAGE mutated sf3a2:mCherry transgene 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     MUTL7F_transgene_R1.fastq MUTL7F_transgene_R2.fastq fastq fastq 30678849.0 444621.0 D. rerio MUTL7F transgenic line single locus CAGE mutated sf3a2:mCherry transgene 0:34 1:35 A:5994534;C:7452275;G:9596502;T:7623459;N:12079 34 35     5994534 7452275 9596502 7623459 12079 SRX363385 SRS490049 SRA104816 University of Bergen ZEPROME consortium 2 0.38487 0.37445 0.0013 9e-05 0.99841 0.99991 0.00309 0.00012 34 35 B B biological fallback assumption illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37186 37186 SRR1010333 SRX363384 SRS490049 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio MUTL7F transgenic line   strain:AB strain MUTL7F line|development stage:high 3.3 hpf                 D. rerio MUTL7F transgenic line single locus CAGE endogeneous sf3a2 D. rerio MUTL7F transgenic line single locus CAGE endogeneous sf3a2 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     MUTL7F_endogenous_R2.fastq MUTL7F_endogenous_R1.fastq fastq fastq 78367233.0 1135757.0 D. rerio MUTL7F transgenic line single locus CAGE endogeneous sf3a2 0:34 1:35 A:21010895;C:20506800;G:21883789;T:14935556;N:30193 34 35     21010895 20506800 21883789 14935556 30193 SRX363384 SRS490049 SRA104816 University of Bergen ZEPROME consortium 2 0.56643 0.02972 6e-05 0.00056 0.99965 0.99995 0.00017 0.05769 34 35 B T mate2 technical by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37187 37187 SRR1010332 SRX363383 SRS490048 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio MUTL6F transgenic line   strain:AB strain MUTL6F line|development stage:high 3.3 hpf                 D. rerio MUTL6F transgenic line single locus CAGE mutated sf3a2:mCherry transgene D. rerio MUTL6F transgenic line single locus CAGE mutated sf3a2:mCherry transgene 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     MUTL6F_transgene_R2.fastq MUTL6F_transgene_R1.fastq fastq fastq 36838272.0 533888.0 D. rerio MUTL6F transgenic line single locus CAGE mutated sf3a2:mCherry transgene 0:34 1:35 A:7267891;C:8939911;G:11513757;T:9101861;N:14852 34 35     7267891 8939911 11513757 9101861 14852 SRX363383 SRS490048 SRA104816 University of Bergen ZEPROME consortium 2 0.35237 0.20738 0.00196 4e-05 0.9991 0.99987 0.00131 0.00022 34 35 B B mate2-mate1 similar by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37188 37188 SRR1010331 SRX363382 SRS490048 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio MUTL6F transgenic line   strain:AB strain MUTL6F line|development stage:high 3.3 hpf                 D. rerio MUTL6F transgenic line single locus CAGE endogeneous sf3a2 D. rerio MUTL6F transgenic line single locus CAGE endogeneous sf3a2 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     MUTL6F_endogenous_R1.fastq MUTL6F_endogenous_R2.fastq fastq fastq 67887582.0 983878.0 D. rerio MUTL6F transgenic line single locus CAGE endogeneous sf3a2 0:34 1:35 A:18224546;C:17687428;G:19119778;T:12829091;N:26739 34 35     18224546 17687428 19119778 12829091 26739 SRX363382 SRS490048 SRA104816 University of Bergen ZEPROME consortium 2 0.57761 0.02201 0.0001 0.00048 0.99975 0.99991 0.00011 0.02247 34 35 B T mate2 technical by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37189 37189 SRR1010330 SRX363381 SRS490047 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio MUTL5F transgenic line   strain:AB strain MUTL5F line|development stage:high 3.3 hpf                 D. rerio MUTL5F transgenic line single locus CAGE mutated sf3a2:mCherry transgene D. rerio MUTL5F transgenic line single locus CAGE mutated sf3a2:mCherry transgene 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     MUTL5F_transgene_R1.fastq MUTL5F_transgene_R2.fastq fastq fastq 48750708.0 706532.0 D. rerio MUTL5F transgenic line single locus CAGE mutated sf3a2:mCherry transgene 0:34 1:35 A:9468865;C:11866504;G:15193605;T:12203213;N:18521 34 35     9468865 11866504 15193605 12203213 18521 SRX363381 SRS490047 SRA104816 University of Bergen ZEPROME consortium 2 0.37677 0.39423 0.0018 0.00013 0.99801 0.99989 0.00295 0.00011 34 35 B B biological fallback assumption illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37190 37190 SRR1010329 SRX363380 SRS490047 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio MUTL5F transgenic line   strain:AB strain MUTL5F line|development stage:high 3.3 hpf                 D. rerio MUTL5F transgenic line single locus CAGE endogeneous sf3a2 D. rerio MUTL5F transgenic line single locus CAGE endogeneous sf3a2 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     MUTL5F_endogenous_R1.fastq MUTL5F_endogenous_R2.fastq fastq fastq 85325883.0 1236607.0 D. rerio MUTL5F transgenic line single locus CAGE endogeneous sf3a2 0:34 1:35 A:22831000;C:22316529;G:23804395;T:16340044;N:33915 34 35     22831000 22316529 23804395 16340044 33915 SRX363380 SRS490047 SRA104816 University of Bergen ZEPROME consortium 2 0.59785 0.01902 0.00632 0.00081 0.99941 0.99993 0.00056 0.11235 34 35 B T mate2 technical by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37191 37191 SRR1010328 SRX363379 SRS490046 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio MUTL2F transgenic line   strain:AB strain MUTL2F line|development stage:high 3.3 hpf                 D. rerio MUTL2F transgenic line single locus CAGE mutated sf3a2:mCherry transgene D. rerio MUTL2F transgenic line single locus CAGE mutated sf3a2:mCherry transgene 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     MUTL2F_transgene_R1.fastq MUTL2F_transgene_R2.fastq fastq fastq 68247900.0 989100.0 D. rerio MUTL2F transgenic line single locus CAGE mutated sf3a2:mCherry transgene 0:34 1:35 A:13037092;C:16853304;G:21557175;T:16772703;N:27626 34 35     13037092 16853304 21557175 16772703 27626 SRX363379 SRS490046 SRA104816 University of Bergen ZEPROME consortium 2 0.37746 0.14836 0.00135 0.00215 0.99912 0.99995 0.00128 0.0 34 35 B B mate2-mate1 similar by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37192 37192 SRR1010327 SRX363378 SRS490046 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio MUTL2F transgenic line   strain:AB strain MUTL2F line|development stage:high 3.3 hpf                 D. rerio MUTL2F transgenic line single locus CAGE endogeneous sf3a2 D. rerio MUTL2F transgenic line single locus CAGE endogeneous sf3a2 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     MUTL2F_endogenous_R1.fastq MUTL2F_endogenous_R2.fastq fastq fastq 85300215.0 1236235.0 D. rerio MUTL2F transgenic line single locus CAGE endogeneous sf3a2 0:34 1:35 A:22860161;C:22364533;G:24027064;T:16015109;N:33348 34 35     22860161 22364533 24027064 16015109 33348 SRX363378 SRS490046 SRA104816 University of Bergen ZEPROME consortium 2 0.57324 0.0117 0.01138 0.00049 0.99943 0.99993 0.00087 0.02941 34 35 B T mate2 technical by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37193 37193 SRR1010326 SRX363377 SRS490045 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with wild type sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio WTL3F transgenic line   strain:AB strain WTL3F line|development stage:high 3.3 hpf                 D. rerio WTL3F transgenic line single locus CAGE wild type sf3a2:mCherry transgene D. rerio WTL3F transgenic line single locus CAGE wild type sf3a2:mCherry transgene 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     WTL3F_transgene_R1.fastq WTL3F_transgene_R2.fastq fastq fastq 36051879.0 522491.0 D. rerio WTL3F transgenic line single locus CAGE wild type sf3a2:mCherry transgene 0:34 1:35 A:6990071;C:8680451;G:10883119;T:9484027;N:14211 34 35     6990071 8680451 10883119 9484027 14211 SRX363377 SRS490045 SRA104816 University of Bergen ZEPROME consortium 2 0.43354 0.14606 0.00247 9e-05 0.99896 0.99991 0.00217 0.00032 34 35 B B mate2-mate1 similar by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37194 37194 SRR1010325 SRX363376 SRS490045 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with wild type sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio WTL3F transgenic line   strain:AB strain WTL3F line|development stage:high 3.3 hpf                 D. rerio WTL3F transgenic line single locus CAGE endogenous sf3a2 D. rerio WTL3F transgenic line single locus CAGE endogenous sf3a2 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     WTL3F_endogenous_R1.fastq WTL3F_endogenous_R2.fastq fastq fastq 78469284.0 1137236.0 D. rerio WTL3F transgenic line single locus CAGE endogenous sf3a2 0:34 1:35 A:21059562;C:20597989;G:21976657;T:14804744;N:30332 34 35     21059562 20597989 21976657 14804744 30332 SRX363376 SRS490045 SRA104816 University of Bergen ZEPROME consortium 2 0.54772 0.02239 3e-05 0.0 0.99979 0.99993 0.00012 0.06756 34 35 B T mate2 technical by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37195 37195 SRR1010324 SRX363375 SRS490044 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with wild type sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio WTL2F transgenic line   strain:AB strain WTL2F line|development stage:high 3.3 hpf                 D. rerio WTL2F transgenic line single locus CAGE wild type sf3a2:mCherry transgene D. rerio WTL2F transgenic line single locus CAGE wild type sf3a2:mCherry transgene 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     WTL2F_transgene_R1.fastq WTL2F_transgene_R2.fastq fastq fastq 67052544.0 971776.0 D. rerio WTL2F transgenic line single locus CAGE wild type sf3a2:mCherry transgene 0:34 1:35 A:12413417;C:16491074;G:20506887;T:17614500;N:26666 34 35     12413417 16491074 20506887 17614500 26666 SRX363375 SRS490044 SRA104816 University of Bergen ZEPROME consortium 2 0.47234 0.16966 0.00033 0.00039 0.99918 0.99993 0.00051 0.0 34 35 B B mate2-mate1 similar by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37196 37196 SRR1010323 SRX363374 SRS490044 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with wild type sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio WTL2F transgenic line   strain:AB strain WTL2F line|development stage:high 3.3 hpf                 D. rerio WTL2F transgenic line single locus CAGE endogenous sf3a2 D. rerio WTL2F transgenic line single locus CAGE endogenous sf3a2 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     WTL2F_endogenous_R1.fastq WTL2F_endogenous_R2.fastq fastq fastq 71493591.0 1036139.0 D. rerio WTL2F transgenic line single locus CAGE endogenous sf3a2 0:34 1:35 A:19123161;C:18705556;G:20092193;T:13545180;N:27501 34 35     19123161 18705556 20092193 13545180 27501 SRX363374 SRS490044 SRA104816 University of Bergen ZEPROME consortium 2 0.56581 0.02161 0.00279 0.00056 0.99949 0.99991 0.00025 0.09333 34 35 B T mate2 technical by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37197 37197 SRR1010322 SRX363361 SRS490033 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with wild type sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio WTL1F transgenic line   strain:AB strain WTL1F line|dev stage:high 3.3 hpf                 D. rerio WTL1F transgenic line single locus CAGE wild type sf3a2:mCherry transgene D. rerio WTL1F transgenic line single locus CAGE wild type sf3a2:mCherry transgene 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     WTL1F_transgene_R1.fastq WTL1F_transgene_R2.fastq fastq fastq 95222070.0 1380030.0 D. rerio WTL1F transgenic line single locus CAGE wild type sf3a2:mCherry transgene 0:34 1:35 A:17371572;C:23537350;G:29495884;T:24779827;N:37437 34 35     17371572 23537350 29495884 24779827 37437 SRX363361 SRS490033 SRA104816 University of Bergen ZEPROME consortium 2 0.44573 0.30978 0.00036 0.00019 0.99943 0.99991 0.00023 0.00124 34 35 B B mate2-mate1 similar by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37198 37198 SRR1010321 SRX363360 SRS490033 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with wild type sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio WTL1F transgenic line   strain:AB strain WTL1F line|dev stage:high 3.3 hpf                 D. rerio WTL1F transgenic line single locus CAGE endogenous sf3a2 D. rerio WTL1F transgenic line single locus CAGE endogeneous sf3a2 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     WTL1F_endogenous_R1.fastq WTL1F_endogenous_R2.fastq fastq fastq 64955082.0 941378.0 D. rerio WTL1F transgenic line single locus CAGE endogeneous sf3a2 0:34 1:35 A:17404375;C:16997013;G:18318738;T:12210960;N:23996 34 35     17404375 16997013 18318738 12210960 23996 SRX363360 SRS490033 SRA104816 University of Bergen ZEPROME consortium 2 0.55528 0.02138 9e-05 0.00135 0.99963 0.99991 9e-05 0.10169 34 35 B T mate2 technical by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
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
55270 55270 SRR10215486 SRX6935169 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 Prim5 nAnTiCAGE Prim5 nAnTiCAGE nAnTiCAGE     RNA-Seq TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2500   SRP223930     S06_Prim5_nAnTiCAGE_1.fastq.gz S06_Prim5_nAnTiCAGE_2.fastq.gz fastq fastq 2672456099.0 13565767.0 S06 Prim5 nAnTiCAGE 1.fastq.gz 0:97 1:100 A:641958912;C:678208106;G:686299870;T:662301091;N:3688120 97 100     641958912 678208106 686299870 662301091 3688120 SRX6935169 SRS5465204 SRA971223 University of Birmingham|Cancer and Genomic Sciences University of Birmingham 2 0.94637 0.95975 0.15027 0.16177 0.74119 0.7441 0.50314 0.54386 97 100 B B biological fallback assumption illumina hiseq_era full_length cage unknown bulk unknown unknown   United Kingdom 2019-10-02 Pharyngula Embryo Whole Organism All anatomical structures
55271 55271 SRR10215487 SRX6935168 SRS5465203 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         S05 4 Somies   strain:AB|dev stage:4 5 somites|sex:N/A|tissue:whole embryo|BioSampleModel:Model organism or animal                 CAGE seq of Danio rerio whole embryo 4 5 somites stage 4Somites nAnTiCAGE 4Somites nAnTiCAGE nAnTiCAGE     RNA-Seq TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2500   SRP223930     S05_4Somites_nAnTiCAGE_1.fastq.gz S05_4Somites_nAnTiCAGE_2.fastq.gz fastq fastq 1532850499.0 7780967.0 S05 4Somites nAnTiCAGE 1.fastq.gz 0:97 1:100 A:368505591;C:387404999;G:393120996;T:381726796;N:2092117 97 100     368505591 387404999 393120996 381726796 2092117 SRX6935168 SRS5465203 SRA971223 University of Birmingham|Cancer and Genomic Sciences University of Birmingham 2 0.93818 0.96364 0.10425 0.1218 0.75116 0.74852 0.54456 0.54636 97 100 B B biological fallback assumption illumina hiseq_era full_length cage unknown bulk unknown unknown   United Kingdom 2019-10-02 Segmentation 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
55275 55275 SRR10215491 SRX6935164 SRS5465199 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         S01 1Cell   strain:AB|dev stage:1cell|sex:N/A|tissue:whole embryo|BioSampleModel:Model organism or animal                 CAGE seq of Danio rerio whole embryo 1 cell stage 1Cell nAnTiCAGE 1Cell nAnTiCAGE nAnTiCAGE     RNA-Seq TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2500   SRP223930     S01_1Cells_nAnTiCAGE_1.fastq.gz S01_1Cells_nAnTiCAGE_2.fastq.gz fastq fastq 1193891117.0 6060361.0 S01 1Cells nAnTiCAGE 1.fastq.gz 0:97 1:100 A:286037352;C:298140071;G:310668851;T:297430066;N:1614777 97 100     286037352 298140071 310668851 297430066 1614777 SRX6935164 SRS5465199 SRA971223 University of Birmingham|Cancer and Genomic Sciences University of Birmingham 2 0.93733 0.97059 0.08219 0.07881 0.76682 0.75834 0.53879 0.54537 97 100 B B biological fallback assumption illumina hiseq_era full_length cage unknown bulk unknown unknown   United Kingdom 2019-10-02 Zygote Embryo Whole Organism All anatomical structures
68254 68254 SRR18327318 SRX14464504 SRS11744581 SRP356302 PRJNA799647 Epigenomic analysis reveals prevalent contribution of transposable elements to cis regulatory elements tissue specific expression and alternative promoters in zebrafish PRJNA799647 Other Transposable elements TEs encode regulatory elements that impact gene expression in multiple species yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here we systematically investigate the epigenomic and transcriptomic landscape of TEs across eleven adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE derived transcriptional units expressed in a tissue specific manner. Finally we show that novel TE derived promoters can initiate tissue specific transcription of alternative isoforms. This work provides a 10 comprehensive profile of TE activity across normal zebrafish tissues shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.         zebrafish TU testis rep2   strain:Tuebingen|isolate:rep2|age:6 mpf|dev stage:adult|sex:male|tissue:testis|BioSampleModel:Model organism or animal                 nanoCAGE seq of Danio rerio Tubingen: adult male testis shallow nanoCAGE zebrafish TU testis rep2 nanoCAGE zebrafish TU testis rep2 nanoCAGE seq with polyA pulldown     RNA-Seq TRANSCRIPTOMIC CAGE PAIRED ILLUMINA NextSeq 500   SRP356302     nano_TUzfish_combined_deep_testis_BR2.R1.fastq.gz nano_TUzfish_combined_deep_testis_BR2.R2.fastq.gz fastq fastq 2408261400.0 15886644.0 nano TUzfish combined deep testis BR2.R1.fastq.gz 0:75.80 1:75.80 A:589293804;C:562741604;G:604867589;T:650872884;N:485519 75 75     589293804 562741604 604867589 650872884 485519 SRX14464504 SRS11744581 SRA1385043 Washington University in St. Louis|Department of Genetics Washington University in St. Louis 2 0.05991 0.93925 0.00631 0.04834 0.91364 0.67671 0.54402 0.49323 150 150 T B mate1 technical by mapping diff illumina nextseq unknown cage unknown bulk unknown unknown   United States 2022-03-17 Adult Adult Gonad Reproductive System
68255 68255 SRR18327319 SRX14464503 SRS11744582 SRP356302 PRJNA799647 Epigenomic analysis reveals prevalent contribution of transposable elements to cis regulatory elements tissue specific expression and alternative promoters in zebrafish PRJNA799647 Other Transposable elements TEs encode regulatory elements that impact gene expression in multiple species yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here we systematically investigate the epigenomic and transcriptomic landscape of TEs across eleven adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE derived transcriptional units expressed in a tissue specific manner. Finally we show that novel TE derived promoters can initiate tissue specific transcription of alternative isoforms. This work provides a 10 comprehensive profile of TE activity across normal zebrafish tissues shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.         zebrafish TU testis rep1   strain:Tuebingen|isolate:rep1|age:6 mpf|dev stage:adult|sex:male|tissue:testis|BioSampleModel:Model organism or animal                 nanoCAGE seq of Danio rerio Tubingen: adult male testis shallow nanoCAGE zebrafish TU testis rep1 nanoCAGE zebrafish TU testis rep1 nanoCAGE seq with polyA pulldown     RNA-Seq TRANSCRIPTOMIC CAGE PAIRED ILLUMINA NextSeq 500   SRP356302     nano_TUzfish_combined_deep_testis_BR1.R1.fastq.gz nano_TUzfish_combined_deep_testis_BR1.R2.fastq.gz fastq fastq 2655464100.0 17518322.0 nano TUzfish combined deep testis BR1.R1.fastq.gz 0:75.79 1:75.79 A:648423774;C:624425183;G:667510545;T:714557704;N:546894 75 75     648423774 624425183 667510545 714557704 546894 SRX14464503 SRS11744582 SRA1385043 Washington University in St. Louis|Department of Genetics Washington University in St. Louis 2 0.05205 0.9337 0.00433 0.0458 0.92086 0.68631 0.5426 0.50321 150 150 T B mate1 technical by mapping diff illumina nextseq unknown cage unknown bulk unknown unknown   United States 2022-03-17 Adult Adult Gonad Reproductive System
68256 68256 SRR18327320 SRX14464502 SRS11744580 SRP356302 PRJNA799647 Epigenomic analysis reveals prevalent contribution of transposable elements to cis regulatory elements tissue specific expression and alternative promoters in zebrafish PRJNA799647 Other Transposable elements TEs encode regulatory elements that impact gene expression in multiple species yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here we systematically investigate the epigenomic and transcriptomic landscape of TEs across eleven adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE derived transcriptional units expressed in a tissue specific manner. Finally we show that novel TE derived promoters can initiate tissue specific transcription of alternative isoforms. This work provides a 10 comprehensive profile of TE activity across normal zebrafish tissues shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.         zebrafish TU brain rep2   strain:Tuebingen|isolate:rep2|age:6 mpf|dev stage:adult|sex:female|tissue:brain|BioSampleModel:Model organism or animal                 nanoCAGE seq of Danio rerio Tubingen: adult male brain shallow nanoCAGE zebrafish TU brain rep2 nanoCAGE zebrafish TU brain rep2 nanoCAGE seq with polyA pulldown     RNA-Seq TRANSCRIPTOMIC CAGE PAIRED ILLUMINA NextSeq 500   SRP356302     nano_TUzfish_combined_deep_brain_BR2.R1.fastq.gz nano_TUzfish_combined_deep_brain_BR2.R2.fastq.gz fastq fastq 2120070300.0 13983927.0 nano TUzfish combined deep brain BR2.R1.fastq.gz 0:75.80 1:75.80 A:521597394;C:502052046;G:539140115;T:556851976;N:428769 75 75     521597394 502052046 539140115 556851976 428769 SRX14464502 SRS11744580 SRA1385043 Washington University in St. Louis|Department of Genetics Washington University in St. Louis 2 0.05946 0.93361 0.00648 0.07284 0.91739 0.70025 0.57506 0.48669 150 150 T B mate1 technical by mapping diff illumina nextseq unknown cage unknown bulk unknown unknown   United States 2022-03-17 Adult Adult Brain Nervous System
68257 68257 SRR18327321 SRX14464501 SRS11744579 SRP356302 PRJNA799647 Epigenomic analysis reveals prevalent contribution of transposable elements to cis regulatory elements tissue specific expression and alternative promoters in zebrafish PRJNA799647 Other Transposable elements TEs encode regulatory elements that impact gene expression in multiple species yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here we systematically investigate the epigenomic and transcriptomic landscape of TEs across eleven adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE derived transcriptional units expressed in a tissue specific manner. Finally we show that novel TE derived promoters can initiate tissue specific transcription of alternative isoforms. This work provides a 10 comprehensive profile of TE activity across normal zebrafish tissues shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.         zebrafish TU brain rep1   strain:Tuebingen|isolate:rep1|age:6 mpf|dev stage:adult|sex:female|tissue:brain|BioSampleModel:Model organism or animal                 nanoCAGE seq of Danio rerio Tubingen: adult male brain shallow nanoCAGE zebrafish TU brain rep1 nanoCAGE zebrafish TU brain rep1 nanoCAGE seq with polyA pulldown     RNA-Seq TRANSCRIPTOMIC CAGE PAIRED ILLUMINA NextSeq 500   SRP356302     nano_TUzfish_combined_deep_brain_BR1.R1.fastq.gz nano_TUzfish_combined_deep_brain_BR1.R2.fastq.gz fastq fastq 1958802000.0 12919047.0 nano TUzfish combined deep brain BR1.R1.fastq.gz 0:75.81 1:75.81 A:485271176;C:461368873;G:496521163;T:515247447;N:393341 75 75     485271176 461368873 496521163 515247447 393341 SRX14464501 SRS11744579 SRA1385043 Washington University in St. Louis|Department of Genetics Washington University in St. Louis 2 0.0666 0.93487 0.00689 0.0747 0.91175 0.70027 0.57062 0.49364 150 150 T B mate1 technical by mapping diff illumina nextseq unknown cage unknown bulk unknown unknown   United States 2022-03-17 Adult Adult Brain Nervous System
68258 68258 SRR17709722 SRX13872770 SRS11744581 SRP356302 PRJNA799647 Epigenomic analysis reveals prevalent contribution of transposable elements to cis regulatory elements tissue specific expression and alternative promoters in zebrafish PRJNA799647 Other Transposable elements TEs encode regulatory elements that impact gene expression in multiple species yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here we systematically investigate the epigenomic and transcriptomic landscape of TEs across eleven adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE derived transcriptional units expressed in a tissue specific manner. Finally we show that novel TE derived promoters can initiate tissue specific transcription of alternative isoforms. This work provides a 10 comprehensive profile of TE activity across normal zebrafish tissues shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.         zebrafish TU testis rep2   strain:Tuebingen|isolate:rep2|age:6 mpf|dev stage:adult|sex:male|tissue:testis|BioSampleModel:Model organism or animal                 nanoCAGE seq of Danio rerio Tubingen: adult male testis nanoCAGE zebrafish TU testis rep2 nanoCAGE zebrafish TU testis shallow rep2 nanoCAGE seq with polyA pulldown     RNA-Seq TRANSCRIPTOMIC CAGE PAIRED ILLUMINA NextSeq 500   SRP356302     nanoCAGE_zebrafish_TU_testis_rep2.R1.fastq.gz nanoCAGE_zebrafish_TU_testis_rep2.R2.fastq.gz fastq fastq 1257997200.0 8218216.0 nanoCAGE zebrafish TU testis rep2.R1.fastq.gz 0:76.54 1:76.54 A:307675653;C:294445668;G:315944501;T:339570175;N:361203 76 76     307675653 294445668 315944501 339570175 361203 SRX13872770 SRS11744581 SRA1360415 Washington University in St. Louis|Department of Genetics Washington University in St. Louis 2 0.06846 0.93772 0.00675 0.04699 0.90293 0.67986 0.52867 0.49221 150 150 T B mate1 technical by mapping diff illumina nextseq unknown cage unknown bulk unknown unknown   United States 2022-01-23 Adult Adult Gonad Reproductive System
68259 68259 SRR17709723 SRX13872769 SRS11744582 SRP356302 PRJNA799647 Epigenomic analysis reveals prevalent contribution of transposable elements to cis regulatory elements tissue specific expression and alternative promoters in zebrafish PRJNA799647 Other Transposable elements TEs encode regulatory elements that impact gene expression in multiple species yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here we systematically investigate the epigenomic and transcriptomic landscape of TEs across eleven adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE derived transcriptional units expressed in a tissue specific manner. Finally we show that novel TE derived promoters can initiate tissue specific transcription of alternative isoforms. This work provides a 10 comprehensive profile of TE activity across normal zebrafish tissues shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.         zebrafish TU testis rep1   strain:Tuebingen|isolate:rep1|age:6 mpf|dev stage:adult|sex:male|tissue:testis|BioSampleModel:Model organism or animal                 nanoCAGE seq of Danio rerio Tubingen: adult male testis nanoCAGE zebrafish TU testis rep1 nanoCAGE zebrafish TU testis shallow rep1 nanoCAGE seq with polyA pulldown     RNA-Seq TRANSCRIPTOMIC CAGE PAIRED ILLUMINA NextSeq 500   SRP356302     nanoCAGE_zebrafish_TU_testis_rep1.R1.fastq.gz nanoCAGE_zebrafish_TU_testis_rep1.R2.fastq.gz fastq fastq 1351312800.0 8823980.0 nanoCAGE zebrafish TU testis rep1.R1.fastq.gz 0:76.57 1:76.57 A:329750139;C:318355694;G:339653380;T:363149300;N:404287 76 76     329750139 318355694 339653380 363149300 404287 SRX13872769 SRS11744582 SRA1360415 Washington University in St. Louis|Department of Genetics Washington University in St. Louis 2 0.06051 0.93247 0.00473 0.0437 0.91088 0.68943 0.52768 0.49868 150 150 T B mate1 technical by mapping diff illumina nextseq unknown cage unknown bulk unknown unknown   United States 2022-01-23 Adult Adult Gonad Reproductive System
68260 68260 SRR17709724 SRX13872768 SRS11744580 SRP356302 PRJNA799647 Epigenomic analysis reveals prevalent contribution of transposable elements to cis regulatory elements tissue specific expression and alternative promoters in zebrafish PRJNA799647 Other Transposable elements TEs encode regulatory elements that impact gene expression in multiple species yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here we systematically investigate the epigenomic and transcriptomic landscape of TEs across eleven adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE derived transcriptional units expressed in a tissue specific manner. Finally we show that novel TE derived promoters can initiate tissue specific transcription of alternative isoforms. This work provides a 10 comprehensive profile of TE activity across normal zebrafish tissues shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.         zebrafish TU brain rep2   strain:Tuebingen|isolate:rep2|age:6 mpf|dev stage:adult|sex:female|tissue:brain|BioSampleModel:Model organism or animal                 nanoCAGE seq of Danio rerio Tubingen: adult female brain nanoCAGE zebrafish TU brain rep2 nanoCAGE zebrafish TU brain shallow rep2 nanoCAGE seq with polyA pulldown     RNA-Seq TRANSCRIPTOMIC CAGE PAIRED ILLUMINA NextSeq 500   SRP356302     nanoCAGE_zebrafish_TU_brain_rep2.R1.fastq.gz nanoCAGE_zebrafish_TU_brain_rep2.R2.fastq.gz fastq fastq 1114647450.0 7281108.0 nanoCAGE zebrafish TU brain rep2.R1.fastq.gz 0:76.54 1:76.54 A:273967636;C:264512491;G:283567362;T:292276557;N:323404 76 76     273967636 264512491 283567362 292276557 323404 SRX13872768 SRS11744580 SRA1360415 Washington University in St. Louis|Department of Genetics Washington University in St. Louis 2 0.06736 0.93327 0.00663 0.0712 0.90792 0.70283 0.55337 0.4859 150 150 T B mate1 technical by mapping diff illumina nextseq unknown cage unknown bulk unknown unknown   United States 2022-01-23 Adult Adult Brain Nervous System
68261 68261 SRR17709725 SRX13872767 SRS11744579 SRP356302 PRJNA799647 Epigenomic analysis reveals prevalent contribution of transposable elements to cis regulatory elements tissue specific expression and alternative promoters in zebrafish PRJNA799647 Other Transposable elements TEs encode regulatory elements that impact gene expression in multiple species yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here we systematically investigate the epigenomic and transcriptomic landscape of TEs across eleven adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE derived transcriptional units expressed in a tissue specific manner. Finally we show that novel TE derived promoters can initiate tissue specific transcription of alternative isoforms. This work provides a 10 comprehensive profile of TE activity across normal zebrafish tissues shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.         zebrafish TU brain rep1   strain:Tuebingen|isolate:rep1|age:6 mpf|dev stage:adult|sex:female|tissue:brain|BioSampleModel:Model organism or animal                 nanoCAGE seq of Danio rerio Tubingen: adult female brain nanoCAGE zebrafish TU brain rep1 nanoCAGE zebrafish TU brain shallow rep1 nanoCAGE seq with polyA pulldown     RNA-Seq TRANSCRIPTOMIC CAGE PAIRED ILLUMINA NextSeq 500   SRP356302     nanoCAGE_zebrafish_TU_brain_rep1.R1.fastq.gz nanoCAGE_zebrafish_TU_brain_rep1.R2.fastq.gz fastq fastq 1040194800.0 6794999.0 nanoCAGE zebrafish TU brain rep1.R1.fastq.gz 0:76.54 1:76.54 A:257427323;C:245563114;G:263853643;T:273054571;N:296149 76 76     257427323 245563114 263853643 273054571 296149 SRX13872767 SRS11744579 SRA1360415 Washington University in St. Louis|Department of Genetics Washington University in St. Louis 2 0.07308 0.93461 0.00714 0.07167 0.9051 0.70199 0.56162 0.48821 150 150 T B mate1 technical by mapping diff illumina nextseq unknown cage unknown bulk unknown unknown   United States 2022-01-23 Adult Adult Brain Nervous System
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");;