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,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,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,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,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,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,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,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,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,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
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,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
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,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,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,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,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,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,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,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
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
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
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,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
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,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,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