{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", experiment.library_selection = \"CAGE\" and tissue_curation = \"Whole Organism\"", "rows": [[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", null, "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. 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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", null, "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. 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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", null, "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", null, null, null, null, null, null, null, null, "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. 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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", null, "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", null, null, null, null, null, null, null, null, "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. 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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", null, "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. 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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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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, null, null, 179369537, 157573419, 260889303, 157277751, 70360, "ERX3918372", "ERS4309130", "ERA2381432", "UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive", "UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive", 1, 0.00451, null, 0.00099, null, 0.99314, null, 0.66248, null, 45, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cage", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-02-13", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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, null, null, 189173618, 170597494, 286250625, 173188944, 78174, "ERX3918371", "ERS4309129", "ERA2381432", "UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive", "UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive", 1, 0.00439, null, 0.001, null, 0.99377, null, 0.68367, null, 45, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cage", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-02-13", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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, null, null, 160028926, 147075253, 245773112, 145025474, 68610, "ERX3918370", "ERS4309128", "ERA2381432", "UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive", "UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive", 1, 0.00489, null, 0.00085, null, 0.99586, null, 0.80163, null, 45, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cage", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-02-13", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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, null, null, 193728088, 171605661, 287824557, 173352680, 84654, "ERX3918369", "ERS4309127", "ERA2381432", "UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive", "UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive", 1, 0.00505, null, 0.00101, null, 0.99287, null, 0.58198, null, 45, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cage", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-02-13", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, null, "sa37 16hpf 2", "GSM4144779", null, "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", null, "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. 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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.", null, null, null, "sa37 12hpf 2", "GSM4144778", null, "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", null, "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. 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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.", null, null, null, "WT 16hpf 2", "GSM4144777", null, "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", null, "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. 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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.", null, null, null, "WT 12hpf 2", "GSM4144776", null, "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", null, "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. 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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.", null, null, null, "sa37 16hpf", "GSM3141418", null, "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", null, "Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2\u03bcg 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\u2032 linker  which includes the three nucleotide barcodes  followed by 3\u2032 linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer  creating the final double stranded DNA product. 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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.", null, null, null, "sa37 12hpf", "GSM3141417", null, "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", null, "Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2\u03bcg 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\u2032 linker  which includes the three nucleotide barcodes  followed by 3\u2032 linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer  creating the final double stranded DNA product. 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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.", null, null, null, "WT 16hpf", "GSM3141416", null, "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", null, "Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2\u03bcg 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\u2032 linker  which includes the three nucleotide barcodes  followed by 3\u2032 linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer  creating the final double stranded DNA product. 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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.", null, null, null, "WT 12hpf", "GSM3141415", null, "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", null, "Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2\u03bcg 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\u2032 linker  which includes the three nucleotide barcodes  followed by 3\u2032 linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer  creating the final double stranded DNA product. 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