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
36409,SRR516560,SRX156356,SRS347213,SRP013950,PRJNA169500,Danio rerio embryonic promoterome,PRJNA169500,Transcriptome Analysis,Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.,,pubmed:24531765,Zebrafish wild type AB strain   embryo prim20 stage,D. rerio prim20 embryo,D. rerio prim20 embryo,,,,,,,,,,,CAGE   D. rerio prim20 embryo,CAGE   D. rerio prim20 embryo run2,D. rerio prim20 embryo,1,,,OTHER,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013950,,,CAGE_prim20_run1.fastq,fastq,76770666.0,2843358.0,CAGE   D. rerio prim20 embryo run1,0:27,A:19320047;C:17585086;G:22511175;T:17354358;N:0,27,,,,19320047,17585086,22511175,17354358,0,SRX156356,SRS347213,SRA055273,University of Bergen,ZEPROME consortium,1,0.56472,,0.10044,,0.77469,,0.74192,,27,,B,,usable mapping rate,illumina,early_illumina,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2012-06-28,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
36410,SRR516561,SRX156356,SRS347213,SRP013950,PRJNA169500,Danio rerio embryonic promoterome,PRJNA169500,Transcriptome Analysis,Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.,,pubmed:24531765,Zebrafish wild type AB strain   embryo prim20 stage,D. rerio prim20 embryo,D. rerio prim20 embryo,,,,,,,,,,,CAGE   D. rerio prim20 embryo,CAGE   D. rerio prim20 embryo run2,D. rerio prim20 embryo,1,,,OTHER,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013950,,,CAGE_prim20_run2.fastq,fastq,163254906.0,6046478.0,CAGE   D. rerio prim20 embryo run2,0:27,A:40211042;C:36959797;G:46866669;T:39217398;N:0,27,,,,40211042,36959797,46866669,39217398,0,SRX156356,SRS347213,SRA055273,University of Bergen,ZEPROME consortium,1,0.47475,,0.06947,,0.78409,,0.78014,,27,,B,,usable mapping rate,illumina,early_illumina,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2013-08-31,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
36411,SRR516559,SRX156355,SRS347212,SRP013950,PRJNA169500,Danio rerio embryonic promoterome,PRJNA169500,Transcriptome Analysis,Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.,,pubmed:24531765,Zebrafish wild type AB strain   embryo prim6 stage,D. rerio prim6 embryo,D. rerio prim6 embryo,,,,,,,,,,,CAGE   D. rerio prim6 embryo,CAGE   D. rerio prim6 embryo,D. rerio prim6 embryo,1,,,OTHER,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013950,,,CAGE_prim6.fastq,fastq,283414275.0,10496825.0,CAGE   D. rerio prim6 embryo,0:27,A:70974303;C:66202040;G:80064124;T:66173808;N:0,27,,,,70974303,66202040,80064124,66173808,0,SRX156355,SRS347212,SRA055273,University of Bergen,ZEPROME consortium,1,0.53395,,0.07806,,0.78255,,0.77575,,27,,B,,usable mapping rate,illumina,early_illumina,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2013-08-31,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
36412,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
36414,SRR516555,SRX156350,SRS347210,SRP013950,PRJNA169500,Danio rerio embryonic promoterome,PRJNA169500,Transcriptome Analysis,Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.,,pubmed:24531765,Zebrafish wild type AB strain   embryo shield stage,D. rerio shield embryo,D. rerio shield embryo,,,,,,,,,,,CAGE   D. rerio shield embryo,CAGE   D. rerio shield embryo run2,D. rerio shield embryo,1,,,OTHER,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013950,,,,,81086886.0,3003218.0,CAGE   D. rerio shield embryo run1,0:27,A:20800196;C:18582826;G:23491216;T:18212648;N:0,27,,,,20800196,18582826,23491216,18212648,0,SRX156350,SRS347210,SRA055273,University of Bergen,ZEPROME consortium,1,0.60434,,0.09948,,0.80432,,0.72631,,27,,B,,usable mapping rate,illumina,early_illumina,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2012-06-28,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
36415,SRR516556,SRX156350,SRS347210,SRP013950,PRJNA169500,Danio rerio embryonic promoterome,PRJNA169500,Transcriptome Analysis,Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.,,pubmed:24531765,Zebrafish wild type AB strain   embryo shield stage,D. rerio shield embryo,D. rerio shield embryo,,,,,,,,,,,CAGE   D. rerio shield embryo,CAGE   D. rerio shield embryo run2,D. rerio shield embryo,1,,,OTHER,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013950,,,CAGE_shield_run2.fastq,fastq,81675891.0,3025033.0,CAGE   D. rerio shield embryo run2,0:27,A:21590166;C:17662459;G:22692127;T:19731139;N:0,27,,,,21590166,17662459,22692127,19731139,0,SRX156350,SRS347210,SRA055273,University of Bergen,ZEPROME consortium,1,0.52624,,0.08062,,0.81793,,0.76291,,27,,B,,usable mapping rate,illumina,early_illumina,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2012-06-28,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
36416,SRR516554,SRX156349,SRS347209,SRP013950,PRJNA169500,Danio rerio embryonic promoterome,PRJNA169500,Transcriptome Analysis,Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.,,pubmed:24531765,Zebrafish wild type AB strain   embryo dome/zfs:0000015 stage,D. rerio dome/zfs:0000015 embryo,D. rerio dome/zfs:0000015 embryo,,,,,,,,,,,CAGE   D. rerio dome/zfs:0000015 embryo,CAGE   D. rerio dome/zfs:0000015 embryo,D. rerio dome/zfs:0000015 embryo,1,,,OTHER,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013950,,,CAGE_30p_dome.fastq,fastq,165690819.0,6136697.0,CAGE   D. rerio dome/zfs:0000015 embryo,0:27,A:42721293;C:36492232;G:46154926;T:40322368;N:0,27,,,,42721293,36492232,46154926,40322368,0,SRX156349,SRS347209,SRA055273,University of Bergen,ZEPROME consortium,1,0.50236,,0.0905,,0.81824,,0.8156,,27,,B,,usable mapping rate,illumina,early_illumina,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2012-06-28,Blastula,Embryo,Embryo Imprecise,All anatomical structures
36417,SRR516552,SRX156347,SRS347208,SRP013950,PRJNA169500,Danio rerio embryonic promoterome,PRJNA169500,Transcriptome Analysis,Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.,,pubmed:24531765,Zebrafish wild type AB strain   embryo sphere/dome stage,D. rerio sphere/dome embryo,D. rerio sphere/dome embryo,,,,,,,,,,,CAGE   D. rerio sphere/dome embryo,CAGE   D. rerio sphere/dome embryo run2,D. rerio sphere/dome embryo,1,,,OTHER,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013950,,,CAGE_sphere_dome_run1.fastq,fastq,78937740.0,2923620.0,CAGE   D. rerio sphere/dome embryo run1,0:27,A:20705496;C:17020957;G:22237043;T:18974244;N:0,27,,,,20705496,17020957,22237043,18974244,0,SRX156347,SRS347208,SRA055273,University of Bergen,ZEPROME consortium,1,0.50917,,0.09193,,0.81523,,0.8084,,27,,B,,usable mapping rate,illumina,early_illumina,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2012-06-28,Blastula,Embryo,Embryo Imprecise,All anatomical structures
36418,SRR516553,SRX156347,SRS347208,SRP013950,PRJNA169500,Danio rerio embryonic promoterome,PRJNA169500,Transcriptome Analysis,Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.,,pubmed:24531765,Zebrafish wild type AB strain   embryo sphere/dome stage,D. rerio sphere/dome embryo,D. rerio sphere/dome embryo,,,,,,,,,,,CAGE   D. rerio sphere/dome embryo,CAGE   D. rerio sphere/dome embryo run2,D. rerio sphere/dome embryo,1,,,OTHER,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013950,,,CAGE_sphere_dome_run2.fastq,fastq,82071009.0,3039667.0,CAGE   D. rerio sphere/dome embryo run2,0:27,A:20823133;C:17914934;G:22973465;T:20359477;N:0,27,,,,20823133,17914934,22973465,20359477,0,SRX156347,SRS347208,SRA055273,University of Bergen,ZEPROME consortium,1,0.47213,,0.07583,,0.82384,,0.8313,,27,,B,,usable mapping rate,illumina,early_illumina,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2012-06-28,Blastula,Embryo,Embryo Imprecise,All anatomical structures
36419,SRR516551,SRX156338,SRS347207,SRP013950,PRJNA169500,Danio rerio embryonic promoterome,PRJNA169500,Transcriptome Analysis,Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.,,pubmed:24531765,Zebrafish wild type AB strain   embryo oblong stage,D. rerio oblong embryo,D. rerio oblong embryo,,,,,,,,,,,CAGE   D. rerio oblong embryo,CAGE   D. rerio oblong embryo,D. rerio oblong embryo,1,,,OTHER,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013950,,,,,135892080.0,5033040.0,CAGE   D. rerio oblong embryo,0:27,A:34565898;C:30442218;G:38967845;T:31916119;N:0,27,,,,34565898,30442218,38967845,31916119,0,SRX156338,SRS347207,SRA055273,University of Bergen,ZEPROME consortium,1,0.56265,,0.09335,,0.80068,,0.70759,,27,,B,,usable mapping rate,illumina,early_illumina,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2012-06-28,Blastula,Embryo,Embryo Imprecise,All anatomical structures
36420,SRR516550,SRX156337,SRS347206,SRP013950,PRJNA169500,Danio rerio embryonic promoterome,PRJNA169500,Transcriptome Analysis,Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.,,pubmed:24531765,Zebrafish wild type AB strain   embryo high stage,D. rerio high embryo,D. rerio high embryo,,,,,,,,,,,CAGE   D. rerio high embryo,CAGE   D. rerio high embryo,D. rerio high embryo,1,,,OTHER,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013950,,,CAGE_high.fastq,fastq,128592846.0,4762698.0,CAGE   D. rerio high embryo,0:27,A:33693838;C:27629256;G:36692263;T:30577489;N:0,27,,,,33693838,27629256,36692263,30577489,0,SRX156337,SRS347206,SRA055273,University of Bergen,ZEPROME consortium,1,0.53282,,0.08323,,0.80854,,0.77395,,27,,B,,usable mapping rate,illumina,early_illumina,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2013-08-31,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
36421,SRR516549,SRX156336,SRS347204,SRP013950,PRJNA169500,Danio rerio embryonic promoterome,PRJNA169500,Transcriptome Analysis,Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.,,pubmed:24531765,Zebrafish wild type AB strain   embryo 512 cells stage,D. rerio 512 cells embryo,D. rerio 512 cells embyo,,,,,,,,,,,CAGE   D. rerio 512 cells embryo,CAGE   D. rerio 512 cells embryo,D. rerio 512 cells embryo,1,,,OTHER,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013950,,,CAGE_512cells.fastq,fastq,150228810.0,5564030.0,CAGE   D. rerio 512 cells embryo,0:27,A:37826960;C:33838922;G:43403014;T:35159914;N:0,27,,,,37826960,33838922,43403014,35159914,0,SRX156336,SRS347204,SRA055273,University of Bergen,ZEPROME consortium,1,0.57925,,0.08753,,0.79933,,0.72579,,27,,B,,usable mapping rate,illumina,early_illumina,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2012-06-28,Blastula,Embryo,Embryo Imprecise,All anatomical structures
36422,SRR516548,SRX156334,SRS347202,SRP013950,PRJNA169500,Danio rerio embryonic promoterome,PRJNA169500,Transcriptome Analysis,Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.,,pubmed:24531765,Zebrafish wild type AB strain   embryo 64 cells stage,D. rerio 64 cells embryo,D. rerio 64 cells embryo,,,,,,,,,,,CAGE   D. rerio 64 cells embryo,CAGE   D. rerio 64 cells embryo,D. rerio 64 cells embryo,1,,,OTHER,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013950,,,CAGE_64cells.fastq,fastq,162784188.0,6029044.0,CAGE   D. rerio 64 cells embryo,0:27,A:41192860;C:36547869;G:46848833;T:38194626;N:0,27,,,,41192860,36547869,46848833,38194626,0,SRX156334,SRS347202,SRA055273,University of Bergen,ZEPROME consortium,,,,,,,,,,,,B,,usable mapping rate,illumina,early_illumina,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2013-08-31,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
36423,SRR516547,SRX156325,SRS347201,SRP013950,PRJNA169500,Danio rerio embryonic promoterome,PRJNA169500,Transcriptome Analysis,Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.,,pubmed:24531765,Zebrafish wild type AB strain   fertilized egg,D. rerio fertilized egg,D. rerio fertilized egg,,,,,,,,,,,CAGE   D. rerio fertilized egg,CAGE   D. rerio fertilized egg,D. rerio fertilized egg,1,,,OTHER,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013950,,,CAGE_fertilized_egg.fastq,fastq,160948350.0,5961050.0,CAGE   D. rerio fertilized egg,0:27,A:42030009;C:34700589;G:45399755;T:38817997;N:0,27,,,,42030009,34700589,45399755,38817997,0,SRX156325,SRS347201,SRA055273,University of Bergen,ZEPROME consortium,1,0.49394,,0.07554,,0.81684,,0.79759,,27,,B,,usable mapping rate,illumina,early_illumina,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2012-06-28,Undetermined,Embryo,Undetermined,Embryo Imprecise
36424,SRR516545,SRX156307,SRS347187,SRP013950,PRJNA169500,Danio rerio embryonic promoterome,PRJNA169500,Transcriptome Analysis,Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.,,pubmed:24531765,Zebrafish wild type AB strain   unfertilized egg,D. rerio unfertilized egg,D. rerio unfertilized egg,,,,,,,,,,,CAGE   D. rerio unfertilized egg,CAGE   D. rerio unfertilized egg run2,D. rerio unfertilized egg,1,,,OTHER,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013950,,,,,115273233.0,4269379.0,CAGE   D. rerio unfertilized egg run1,0:27,A:29909511;C:24823784;G:32519899;T:28020039;N:0,27,,,,29909511,24823784,32519899,28020039,0,SRX156307,SRS347187,SRA055273,University of Bergen,ZEPROME consortium,1,0.49872,,0.07655,,0.81673,,0.80445,,27,,B,,usable mapping rate,illumina,early_illumina,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2012-06-28,Zygote,Embryo,Oocyte,Reproductive System
36425,SRR516546,SRX156307,SRS347187,SRP013950,PRJNA169500,Danio rerio embryonic promoterome,PRJNA169500,Transcriptome Analysis,Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.,,pubmed:24531765,Zebrafish wild type AB strain   unfertilized egg,D. rerio unfertilized egg,D. rerio unfertilized egg,,,,,,,,,,,CAGE   D. rerio unfertilized egg,CAGE   D. rerio unfertilized egg run2,D. rerio unfertilized egg,1,,,OTHER,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013950,,,,,112673943.0,4173109.0,CAGE   D. rerio unfertilized egg run2,0:27,A:28315221;C:24199098;G:32599482;T:27560142;N:0,27,,,,28315221,24199098,32599482,27560142,0,SRX156307,SRS347187,SRA055273,University of Bergen,ZEPROME consortium,1,0.46201,,0.06422,,0.82118,,0.82184,,27,,B,,usable mapping rate,illumina,early_illumina,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2012-06-28,Zygote,Embryo,Oocyte,Reproductive System
37185,SRR1010334,SRX363385,SRS490049,SRP030770,PRJNA222234,Danio rerio Targeted Locus Loci,PRJNA222234,Transcriptome Analysis,Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter  which guide transcription start site selection for that promoter in the zebrafish oocyte.,,pubmed:24531765,stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry,Generic sample from Danio rerio,D. rerio MUTL7F transgenic line,,strain:AB strain MUTL7F line|development stage:high 3.3 hpf,,,,,,,,,D. rerio MUTL7F transgenic line   single locus CAGE mutated sf3a2:mCherry transgene,D. rerio MUTL7F transgenic line   single locus CAGE mutated sf3a2:mCherry transgene,1,1,,,OTHER,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP030770,,,MUTL7F_transgene_R1.fastq MUTL7F_transgene_R2.fastq,fastq fastq,30678849.0,444621.0,D. rerio MUTL7F transgenic line   single locus CAGE mutated sf3a2:mCherry transgene,0:34 1:35,A:5994534;C:7452275;G:9596502;T:7623459;N:12079,34,35,,,5994534,7452275,9596502,7623459,12079,SRX363385,SRS490049,SRA104816,University of Bergen,ZEPROME consortium,2,0.38487,0.37445,0.0013,9e-05,0.99841,0.99991,0.00309,0.00012,34,35,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2014-02-10,Blastula,Embryo,Undetermined,Embryo Imprecise
37186,SRR1010333,SRX363384,SRS490049,SRP030770,PRJNA222234,Danio rerio Targeted Locus Loci,PRJNA222234,Transcriptome Analysis,Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter  which guide transcription start site selection for that promoter in the zebrafish oocyte.,,pubmed:24531765,stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry,Generic sample from Danio rerio,D. rerio MUTL7F transgenic line,,strain:AB strain MUTL7F line|development stage:high 3.3 hpf,,,,,,,,,D. rerio MUTL7F transgenic line   single locus CAGE endogeneous sf3a2,D. rerio MUTL7F transgenic line   single locus CAGE endogeneous sf3a2,1,1,,,OTHER,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP030770,,,MUTL7F_endogenous_R2.fastq MUTL7F_endogenous_R1.fastq,fastq fastq,78367233.0,1135757.0,D. rerio MUTL7F transgenic line   single locus CAGE endogeneous sf3a2,0:34 1:35,A:21010895;C:20506800;G:21883789;T:14935556;N:30193,34,35,,,21010895,20506800,21883789,14935556,30193,SRX363384,SRS490049,SRA104816,University of Bergen,ZEPROME consortium,2,0.56643,0.02972,6e-05,0.00056,0.99965,0.99995,0.00017,0.05769,34,35,B,T,mate2 technical by mapping diff,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2014-02-10,Blastula,Embryo,Undetermined,Embryo Imprecise
37187,SRR1010332,SRX363383,SRS490048,SRP030770,PRJNA222234,Danio rerio Targeted Locus Loci,PRJNA222234,Transcriptome Analysis,Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter  which guide transcription start site selection for that promoter in the zebrafish oocyte.,,pubmed:24531765,stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry,Generic sample from Danio rerio,D. rerio MUTL6F transgenic line,,strain:AB strain MUTL6F line|development stage:high 3.3 hpf,,,,,,,,,D. rerio MUTL6F transgenic line   single locus CAGE mutated sf3a2:mCherry transgene,D. rerio MUTL6F transgenic line   single locus CAGE mutated sf3a2:mCherry transgene,1,1,,,OTHER,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP030770,,,MUTL6F_transgene_R2.fastq MUTL6F_transgene_R1.fastq,fastq fastq,36838272.0,533888.0,D. rerio MUTL6F transgenic line   single locus CAGE mutated sf3a2:mCherry transgene,0:34 1:35,A:7267891;C:8939911;G:11513757;T:9101861;N:14852,34,35,,,7267891,8939911,11513757,9101861,14852,SRX363383,SRS490048,SRA104816,University of Bergen,ZEPROME consortium,2,0.35237,0.20738,0.00196,4e-05,0.9991,0.99987,0.00131,0.00022,34,35,B,B,mate2-mate1 similar by mapping diff,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2014-02-10,Blastula,Embryo,Undetermined,Embryo Imprecise
37188,SRR1010331,SRX363382,SRS490048,SRP030770,PRJNA222234,Danio rerio Targeted Locus Loci,PRJNA222234,Transcriptome Analysis,Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter  which guide transcription start site selection for that promoter in the zebrafish oocyte.,,pubmed:24531765,stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry,Generic sample from Danio rerio,D. rerio MUTL6F transgenic line,,strain:AB strain MUTL6F line|development stage:high 3.3 hpf,,,,,,,,,D. rerio MUTL6F transgenic line   single locus CAGE endogeneous sf3a2,D. rerio MUTL6F transgenic line   single locus CAGE endogeneous sf3a2,1,1,,,OTHER,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP030770,,,MUTL6F_endogenous_R1.fastq MUTL6F_endogenous_R2.fastq,fastq fastq,67887582.0,983878.0,D. rerio MUTL6F transgenic line   single locus CAGE endogeneous sf3a2,0:34 1:35,A:18224546;C:17687428;G:19119778;T:12829091;N:26739,34,35,,,18224546,17687428,19119778,12829091,26739,SRX363382,SRS490048,SRA104816,University of Bergen,ZEPROME consortium,2,0.57761,0.02201,0.0001,0.00048,0.99975,0.99991,0.00011,0.02247,34,35,B,T,mate2 technical by mapping diff,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2014-02-10,Blastula,Embryo,Undetermined,Embryo Imprecise
37189,SRR1010330,SRX363381,SRS490047,SRP030770,PRJNA222234,Danio rerio Targeted Locus Loci,PRJNA222234,Transcriptome Analysis,Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter  which guide transcription start site selection for that promoter in the zebrafish oocyte.,,pubmed:24531765,stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry,Generic sample from Danio rerio,D. rerio MUTL5F transgenic line,,strain:AB strain MUTL5F line|development stage:high 3.3 hpf,,,,,,,,,D. rerio MUTL5F transgenic line   single locus CAGE mutated sf3a2:mCherry transgene,D. rerio MUTL5F transgenic line   single locus CAGE mutated sf3a2:mCherry transgene,1,1,,,OTHER,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP030770,,,MUTL5F_transgene_R1.fastq MUTL5F_transgene_R2.fastq,fastq fastq,48750708.0,706532.0,D. rerio MUTL5F transgenic line   single locus CAGE mutated sf3a2:mCherry transgene,0:34 1:35,A:9468865;C:11866504;G:15193605;T:12203213;N:18521,34,35,,,9468865,11866504,15193605,12203213,18521,SRX363381,SRS490047,SRA104816,University of Bergen,ZEPROME consortium,2,0.37677,0.39423,0.0018,0.00013,0.99801,0.99989,0.00295,0.00011,34,35,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2014-02-10,Blastula,Embryo,Undetermined,Embryo Imprecise
37190,SRR1010329,SRX363380,SRS490047,SRP030770,PRJNA222234,Danio rerio Targeted Locus Loci,PRJNA222234,Transcriptome Analysis,Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter  which guide transcription start site selection for that promoter in the zebrafish oocyte.,,pubmed:24531765,stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry,Generic sample from Danio rerio,D. rerio MUTL5F transgenic line,,strain:AB strain MUTL5F line|development stage:high 3.3 hpf,,,,,,,,,D. rerio MUTL5F transgenic line   single locus CAGE endogeneous sf3a2,D. rerio MUTL5F transgenic line   single locus CAGE endogeneous sf3a2,1,1,,,OTHER,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP030770,,,MUTL5F_endogenous_R1.fastq MUTL5F_endogenous_R2.fastq,fastq fastq,85325883.0,1236607.0,D. rerio MUTL5F transgenic line   single locus CAGE endogeneous sf3a2,0:34 1:35,A:22831000;C:22316529;G:23804395;T:16340044;N:33915,34,35,,,22831000,22316529,23804395,16340044,33915,SRX363380,SRS490047,SRA104816,University of Bergen,ZEPROME consortium,2,0.59785,0.01902,0.00632,0.00081,0.99941,0.99993,0.00056,0.11235,34,35,B,T,mate2 technical by mapping diff,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2014-02-10,Blastula,Embryo,Undetermined,Embryo Imprecise
37191,SRR1010328,SRX363379,SRS490046,SRP030770,PRJNA222234,Danio rerio Targeted Locus Loci,PRJNA222234,Transcriptome Analysis,Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter  which guide transcription start site selection for that promoter in the zebrafish oocyte.,,pubmed:24531765,stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry,Generic sample from Danio rerio,D. rerio MUTL2F transgenic line,,strain:AB strain MUTL2F line|development stage:high 3.3 hpf,,,,,,,,,D. rerio MUTL2F transgenic line   single locus CAGE mutated sf3a2:mCherry transgene,D. rerio MUTL2F transgenic line   single locus CAGE mutated sf3a2:mCherry transgene,1,1,,,OTHER,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP030770,,,MUTL2F_transgene_R1.fastq MUTL2F_transgene_R2.fastq,fastq fastq,68247900.0,989100.0,D. rerio MUTL2F transgenic line   single locus CAGE mutated sf3a2:mCherry transgene,0:34 1:35,A:13037092;C:16853304;G:21557175;T:16772703;N:27626,34,35,,,13037092,16853304,21557175,16772703,27626,SRX363379,SRS490046,SRA104816,University of Bergen,ZEPROME consortium,2,0.37746,0.14836,0.00135,0.00215,0.99912,0.99995,0.00128,0.0,34,35,B,B,mate2-mate1 similar by mapping diff,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2014-02-10,Blastula,Embryo,Undetermined,Embryo Imprecise
37192,SRR1010327,SRX363378,SRS490046,SRP030770,PRJNA222234,Danio rerio Targeted Locus Loci,PRJNA222234,Transcriptome Analysis,Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter  which guide transcription start site selection for that promoter in the zebrafish oocyte.,,pubmed:24531765,stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry,Generic sample from Danio rerio,D. rerio MUTL2F transgenic line,,strain:AB strain MUTL2F line|development stage:high 3.3 hpf,,,,,,,,,D. rerio MUTL2F transgenic line   single locus CAGE endogeneous sf3a2,D. rerio MUTL2F transgenic line   single locus CAGE endogeneous sf3a2,1,1,,,OTHER,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP030770,,,MUTL2F_endogenous_R1.fastq MUTL2F_endogenous_R2.fastq,fastq fastq,85300215.0,1236235.0,D. rerio MUTL2F transgenic line   single locus CAGE endogeneous sf3a2,0:34 1:35,A:22860161;C:22364533;G:24027064;T:16015109;N:33348,34,35,,,22860161,22364533,24027064,16015109,33348,SRX363378,SRS490046,SRA104816,University of Bergen,ZEPROME consortium,2,0.57324,0.0117,0.01138,0.00049,0.99943,0.99993,0.00087,0.02941,34,35,B,T,mate2 technical by mapping diff,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2014-02-10,Blastula,Embryo,Undetermined,Embryo Imprecise
37193,SRR1010326,SRX363377,SRS490045,SRP030770,PRJNA222234,Danio rerio Targeted Locus Loci,PRJNA222234,Transcriptome Analysis,Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter  which guide transcription start site selection for that promoter in the zebrafish oocyte.,,pubmed:24531765,stable transgenic line with wild type sf3a2 promoter construct driving expression of mCherry,Generic sample from Danio rerio,D. rerio WTL3F transgenic line,,strain:AB strain WTL3F line|development stage:high 3.3 hpf,,,,,,,,,D. rerio WTL3F transgenic line   single locus CAGE wild type sf3a2:mCherry transgene,D. rerio WTL3F transgenic line   single locus CAGE wild type sf3a2:mCherry transgene,1,1,,,OTHER,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP030770,,,WTL3F_transgene_R1.fastq WTL3F_transgene_R2.fastq,fastq fastq,36051879.0,522491.0,D. rerio WTL3F transgenic line   single locus CAGE wild type sf3a2:mCherry transgene,0:34 1:35,A:6990071;C:8680451;G:10883119;T:9484027;N:14211,34,35,,,6990071,8680451,10883119,9484027,14211,SRX363377,SRS490045,SRA104816,University of Bergen,ZEPROME consortium,2,0.43354,0.14606,0.00247,9e-05,0.99896,0.99991,0.00217,0.00032,34,35,B,B,mate2-mate1 similar by mapping diff,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2014-02-10,Blastula,Embryo,Undetermined,Embryo Imprecise
37194,SRR1010325,SRX363376,SRS490045,SRP030770,PRJNA222234,Danio rerio Targeted Locus Loci,PRJNA222234,Transcriptome Analysis,Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter  which guide transcription start site selection for that promoter in the zebrafish oocyte.,,pubmed:24531765,stable transgenic line with wild type sf3a2 promoter construct driving expression of mCherry,Generic sample from Danio rerio,D. rerio WTL3F transgenic line,,strain:AB strain WTL3F line|development stage:high 3.3 hpf,,,,,,,,,D. rerio WTL3F transgenic line   single locus CAGE endogenous sf3a2,D. rerio WTL3F transgenic line   single locus CAGE endogenous sf3a2,1,1,,,OTHER,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP030770,,,WTL3F_endogenous_R1.fastq WTL3F_endogenous_R2.fastq,fastq fastq,78469284.0,1137236.0,D. rerio WTL3F transgenic line   single locus CAGE endogenous sf3a2,0:34 1:35,A:21059562;C:20597989;G:21976657;T:14804744;N:30332,34,35,,,21059562,20597989,21976657,14804744,30332,SRX363376,SRS490045,SRA104816,University of Bergen,ZEPROME consortium,2,0.54772,0.02239,3e-05,0.0,0.99979,0.99993,0.00012,0.06756,34,35,B,T,mate2 technical by mapping diff,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2014-02-10,Blastula,Embryo,Undetermined,Embryo Imprecise
37195,SRR1010324,SRX363375,SRS490044,SRP030770,PRJNA222234,Danio rerio Targeted Locus Loci,PRJNA222234,Transcriptome Analysis,Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter  which guide transcription start site selection for that promoter in the zebrafish oocyte.,,pubmed:24531765,stable transgenic line with wild type sf3a2 promoter construct driving expression of mCherry,Generic sample from Danio rerio,D. rerio WTL2F transgenic line,,strain:AB strain WTL2F line|development stage:high 3.3 hpf,,,,,,,,,D. rerio WTL2F transgenic line   single locus CAGE wild type sf3a2:mCherry transgene,D. rerio WTL2F transgenic line   single locus CAGE wild type sf3a2:mCherry transgene,1,1,,,OTHER,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP030770,,,WTL2F_transgene_R1.fastq WTL2F_transgene_R2.fastq,fastq fastq,67052544.0,971776.0,D. rerio WTL2F transgenic line   single locus CAGE wild type sf3a2:mCherry transgene,0:34 1:35,A:12413417;C:16491074;G:20506887;T:17614500;N:26666,34,35,,,12413417,16491074,20506887,17614500,26666,SRX363375,SRS490044,SRA104816,University of Bergen,ZEPROME consortium,2,0.47234,0.16966,0.00033,0.00039,0.99918,0.99993,0.00051,0.0,34,35,B,B,mate2-mate1 similar by mapping diff,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2014-02-10,Blastula,Embryo,Undetermined,Embryo Imprecise
37196,SRR1010323,SRX363374,SRS490044,SRP030770,PRJNA222234,Danio rerio Targeted Locus Loci,PRJNA222234,Transcriptome Analysis,Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter  which guide transcription start site selection for that promoter in the zebrafish oocyte.,,pubmed:24531765,stable transgenic line with wild type sf3a2 promoter construct driving expression of mCherry,Generic sample from Danio rerio,D. rerio WTL2F transgenic line,,strain:AB strain WTL2F line|development stage:high 3.3 hpf,,,,,,,,,D. rerio WTL2F transgenic line   single locus CAGE endogenous sf3a2,D. rerio WTL2F transgenic line   single locus CAGE endogenous sf3a2,1,1,,,OTHER,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP030770,,,WTL2F_endogenous_R1.fastq WTL2F_endogenous_R2.fastq,fastq fastq,71493591.0,1036139.0,D. rerio WTL2F transgenic line   single locus CAGE endogenous sf3a2,0:34 1:35,A:19123161;C:18705556;G:20092193;T:13545180;N:27501,34,35,,,19123161,18705556,20092193,13545180,27501,SRX363374,SRS490044,SRA104816,University of Bergen,ZEPROME consortium,2,0.56581,0.02161,0.00279,0.00056,0.99949,0.99991,0.00025,0.09333,34,35,B,T,mate2 technical by mapping diff,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2014-02-10,Blastula,Embryo,Undetermined,Embryo Imprecise
37197,SRR1010322,SRX363361,SRS490033,SRP030770,PRJNA222234,Danio rerio Targeted Locus Loci,PRJNA222234,Transcriptome Analysis,Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter  which guide transcription start site selection for that promoter in the zebrafish oocyte.,,pubmed:24531765,stable transgenic line with wild type sf3a2 promoter construct driving expression of mCherry,Generic sample from Danio rerio,D. rerio WTL1F transgenic line,,strain:AB strain WTL1F line|dev stage:high 3.3 hpf,,,,,,,,,D. rerio WTL1F transgenic line   single locus CAGE wild type sf3a2:mCherry transgene,D. rerio WTL1F transgenic line   single locus CAGE wild type sf3a2:mCherry transgene,1,1,,,OTHER,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP030770,,,WTL1F_transgene_R1.fastq WTL1F_transgene_R2.fastq,fastq fastq,95222070.0,1380030.0,D. rerio WTL1F transgenic line   single locus CAGE wild type sf3a2:mCherry transgene,0:34 1:35,A:17371572;C:23537350;G:29495884;T:24779827;N:37437,34,35,,,17371572,23537350,29495884,24779827,37437,SRX363361,SRS490033,SRA104816,University of Bergen,ZEPROME consortium,2,0.44573,0.30978,0.00036,0.00019,0.99943,0.99991,0.00023,0.00124,34,35,B,B,mate2-mate1 similar by mapping diff,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2014-02-10,Blastula,Embryo,Undetermined,Embryo Imprecise
37198,SRR1010321,SRX363360,SRS490033,SRP030770,PRJNA222234,Danio rerio Targeted Locus Loci,PRJNA222234,Transcriptome Analysis,Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter  which guide transcription start site selection for that promoter in the zebrafish oocyte.,,pubmed:24531765,stable transgenic line with wild type sf3a2 promoter construct driving expression of mCherry,Generic sample from Danio rerio,D. rerio WTL1F transgenic line,,strain:AB strain WTL1F line|dev stage:high 3.3 hpf,,,,,,,,,D. rerio WTL1F transgenic line   single locus CAGE endogenous sf3a2,D. rerio WTL1F transgenic line   single locus CAGE endogeneous sf3a2,1,1,,,OTHER,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP030770,,,WTL1F_endogenous_R1.fastq WTL1F_endogenous_R2.fastq,fastq fastq,64955082.0,941378.0,D. rerio WTL1F transgenic line   single locus CAGE endogeneous sf3a2,0:34 1:35,A:17404375;C:16997013;G:18318738;T:12210960;N:23996,34,35,,,17404375,16997013,18318738,12210960,23996,SRX363360,SRS490033,SRA104816,University of Bergen,ZEPROME consortium,2,0.55528,0.02138,9e-05,0.00135,0.99963,0.99991,9e-05,0.10169,34,35,B,T,mate2 technical by mapping diff,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2014-02-10,Blastula,Embryo,Undetermined,Embryo Imprecise
48305,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
55266,SRR10418684,SRX7116713,SRS5465204,SRP223930,PRJNA575342,CAGE /CappedRNA sequencig,PRJNA575342,Other,CAGE and full length capped RNA sequencing for identification of transcription start TSS utilisation during Zebrafish Danio rerio embryonic development,,,,,S06 Prim5,,strain:AB|dev stage:Prim 5|sex:N/A|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq of Danio rerio  whole embryo  Prim 5  stage  Cycloheximide treated for 2 hours,Prim5 tagCAGE CHX,Prim5 tagCAGE CHX,Tagging CAGE,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP223930,,,S06_Prim5_tagCAGE-CHX.fastq.gz,fastq,272077515.0,10076945.0,S06 Prim5 tagCAGE CHX.fastq.gz,0:27,A:67002738;C:62164745;G:73707100;T:69202932;N:0,27,,,,67002738,62164745,73707100,69202932,0,SRX7116713,SRS5465204,SRA993027,University of Birmingham|Cancer and Genomic Sciences,University of Birmingham,1,0.44237,,0.05018,,0.80296,,0.84125,,27,,B,,usable mapping rate,illumina,early_illumina,full_length,cage,unknown,bulk,unknown,unknown,,United Kingdom,2019-11-08,Pharyngula,Embryo,Whole Organism,All anatomical structures
55267,SRR10418685,SRX7116712,SRS5465204,SRP223930,PRJNA575342,CAGE /CappedRNA sequencig,PRJNA575342,Other,CAGE and full length capped RNA sequencing for identification of transcription start TSS utilisation during Zebrafish Danio rerio embryonic development,,,,,S06 Prim5,,strain:AB|dev stage:Prim 5|sex:N/A|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq of Danio rerio  whole embryo  Prim 5  stage  DMSO control,Prim5 tagCAGE DMSO,Prim5 tagCAGE DMSO,Tagging CAGE,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP223930,,,S06_Prim5_tagCAGE-DMSO.fastq.gz,fastq,339322419.0,12567497.0,S06 Prim5 tagCAGE DMSO.fastq.gz,0:27,A:81884992;C:78138597;G:89012923;T:90285907;N:0,27,,,,81884992,78138597,89012923,90285907,0,SRX7116712,SRS5465204,SRA993027,University of Birmingham|Cancer and Genomic Sciences,University of Birmingham,1,0.43876,,0.05032,,0.82404,,0.85765,,27,,B,,usable mapping rate,illumina,early_illumina,full_length,cage,unknown,bulk,unknown,unknown,,United Kingdom,2019-11-08,Pharyngula,Embryo,Whole Organism,All anatomical structures
55269,SRR10215485,SRX6935170,SRS5465205,SRP223930,PRJNA575342,CAGE /CappedRNA sequencig,PRJNA575342,Other,CAGE and full length capped RNA sequencing for identification of transcription start TSS utilisation during Zebrafish Danio rerio embryonic development,,,,,S07 LongPec,,strain:AB|dev stage:Long pec|sex:N/A|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq of Danio rerio  whole embryo   Long pec stage,LongPec nAnTiCAGE,LongPec nAnTiCAGE,nAnTiCAGE,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,NextSeq 500,,SRP223930,,,S07_LongPec_nAnTiCAGE.fastq.gz,fastq,1326115656.0,18418273.0,S07 LongPec nAnTiCAGE.fastq.gz,0:72 1:0,A:355337919;C:317217156;G:362577018;T:290983563;N:0,72,0,,,355337919,317217156,362577018,290983563,0,SRX6935170,SRS5465205,SRA971223,University of Birmingham|Cancer and Genomic Sciences,University of Birmingham,1,0.94675,,0.13499,,0.77512,,0.56663,,72,,B,,usable mapping rate,illumina,nextseq,full_length,cage,unknown,bulk,unknown,unknown,,United Kingdom,2019-10-02,Hatching,Embryo,Whole Organism,All anatomical structures
55270,SRR10215486,SRX6935169,SRS5465204,SRP223930,PRJNA575342,CAGE /CappedRNA sequencig,PRJNA575342,Other,CAGE and full length capped RNA sequencing for identification of transcription start TSS utilisation during Zebrafish Danio rerio embryonic development,,,,,S06 Prim5,,strain:AB|dev stage:Prim 5|sex:N/A|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq of Danio rerio  whole embryo  Prim 5  stage,Prim5 nAnTiCAGE,Prim5 nAnTiCAGE,nAnTiCAGE,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP223930,,,S06_Prim5_nAnTiCAGE_1.fastq.gz S06_Prim5_nAnTiCAGE_2.fastq.gz,fastq fastq,2672456099.0,13565767.0,S06 Prim5 nAnTiCAGE 1.fastq.gz,0:97 1:100,A:641958912;C:678208106;G:686299870;T:662301091;N:3688120,97,100,,,641958912,678208106,686299870,662301091,3688120,SRX6935169,SRS5465204,SRA971223,University of Birmingham|Cancer and Genomic Sciences,University of Birmingham,2,0.94637,0.95975,0.15027,0.16177,0.74119,0.7441,0.50314,0.54386,97,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cage,unknown,bulk,unknown,unknown,,United Kingdom,2019-10-02,Pharyngula,Embryo,Whole Organism,All anatomical structures
55271,SRR10215487,SRX6935168,SRS5465203,SRP223930,PRJNA575342,CAGE /CappedRNA sequencig,PRJNA575342,Other,CAGE and full length capped RNA sequencing for identification of transcription start TSS utilisation during Zebrafish Danio rerio embryonic development,,,,,S05 4 Somies,,strain:AB|dev stage:4 5 somites|sex:N/A|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq of Danio rerio  whole embryo  4 5 somites stage,4Somites nAnTiCAGE,4Somites nAnTiCAGE,nAnTiCAGE,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP223930,,,S05_4Somites_nAnTiCAGE_1.fastq.gz S05_4Somites_nAnTiCAGE_2.fastq.gz,fastq fastq,1532850499.0,7780967.0,S05 4Somites nAnTiCAGE 1.fastq.gz,0:97 1:100,A:368505591;C:387404999;G:393120996;T:381726796;N:2092117,97,100,,,368505591,387404999,393120996,381726796,2092117,SRX6935168,SRS5465203,SRA971223,University of Birmingham|Cancer and Genomic Sciences,University of Birmingham,2,0.93818,0.96364,0.10425,0.1218,0.75116,0.74852,0.54456,0.54636,97,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cage,unknown,bulk,unknown,unknown,,United Kingdom,2019-10-02,Segmentation,Embryo,Whole Organism,All anatomical structures
55272,SRR10215488,SRX6935167,SRS5465202,SRP223930,PRJNA575342,CAGE /CappedRNA sequencig,PRJNA575342,Other,CAGE and full length capped RNA sequencing for identification of transcription start TSS utilisation during Zebrafish Danio rerio embryonic development,,,,,S04 30Epi,,strain:AB|dev stage:zfs:0000015|sex:N/A|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq of Danio rerio  whole embryo  zfs:0000015 stage,zfs:0000015 nAnTiCAGE,zfs:0000015 nAnTiCAGE,nAnTiCAGE,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP223930,,,S04_30pEpib_nAnTiCAGE.fastq.gz,fastq,629440272.0,13113339.0,S04 30pEpib nAnTiCAGE.fastq.gz,0:48 1:0,A:170201862;C:150343558;G:166046900;T:141987430;N:860522,48,0,,,170201862,150343558,166046900,141987430,860522,SRX6935167,SRS5465202,SRA971223,University of Birmingham|Cancer and Genomic Sciences,University of Birmingham,1,0.83843,,0.15935,,0.81499,,0.71304,,48,,B,,usable mapping rate,illumina,hiseq_era,full_length,cage,unknown,bulk,unknown,unknown,,United Kingdom,2019-10-02,Blastula,Embryo,Whole Organism,All anatomical structures
55273,SRR10215489,SRX6935166,SRS5465201,SRP223930,PRJNA575342,CAGE /CappedRNA sequencig,PRJNA575342,Other,CAGE and full length capped RNA sequencing for identification of transcription start TSS utilisation during Zebrafish Danio rerio embryonic development,,,,,S03 512Cells,,strain:AB|dev stage:512 cell|sex:N/A|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq of Danio rerio  whole embryo  512 cell stage,512Cells nAnTiCAGE,512Cells nAnTiCAGE,nAnTiCAGE,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP223930,,,S03_512Cells_nAnTiCAGE.fastq.gz,fastq,725783040.0,15120480.0,S03 512Cells nAnTiCAGE.fastq.gz,0:48 1:0,A:196224130;C:171017037;G:189882541;T:167660445;N:998887,48,0,,,196224130,171017037,189882541,167660445,998887,SRX6935166,SRS5465201,SRA971223,University of Birmingham|Cancer and Genomic Sciences,University of Birmingham,1,0.85441,,0.14832,,0.79659,,0.68016,,48,,B,,usable mapping rate,illumina,hiseq_era,full_length,cage,unknown,bulk,unknown,unknown,,United Kingdom,2019-10-02,Blastula,Embryo,Whole Organism,All anatomical structures
55274,SRR10215490,SRX6935165,SRS5465200,SRP223930,PRJNA575342,CAGE /CappedRNA sequencig,PRJNA575342,Other,CAGE and full length capped RNA sequencing for identification of transcription start TSS utilisation during Zebrafish Danio rerio embryonic development,,,,,S02 128Cells,,strain:AB|dev stage:128 cell|sex:N/A|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq of Danio rerio  whole embryo  128 cell stage,128Cells nAnTiCAGE,128Cells nAnTiCAGE,nAnTiCAGE,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP223930,,,S02_128Cells_nAnTiCAGE.fastq.gz,fastq,510549408.0,10636446.0,S02 128Cells nAnTiCAGE.fastq.gz,0:48 1:0,A:135389960;C:121538362;G:140642547;T:112273195;N:705344,48,0,,,135389960,121538362,140642547,112273195,705344,SRX6935165,SRS5465200,SRA971223,University of Birmingham|Cancer and Genomic Sciences,University of Birmingham,1,0.84843,,0.14523,,0.79845,,0.68592,,48,,B,,usable mapping rate,illumina,hiseq_era,full_length,cage,unknown,bulk,unknown,unknown,,United Kingdom,2019-10-02,Blastula,Embryo,Whole Organism,All anatomical structures
55275,SRR10215491,SRX6935164,SRS5465199,SRP223930,PRJNA575342,CAGE /CappedRNA sequencig,PRJNA575342,Other,CAGE and full length capped RNA sequencing for identification of transcription start TSS utilisation during Zebrafish Danio rerio embryonic development,,,,,S01 1Cell,,strain:AB|dev stage:1cell|sex:N/A|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq of Danio rerio  whole embryo  1 cell stage,1Cell nAnTiCAGE,1Cell nAnTiCAGE,nAnTiCAGE,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP223930,,,S01_1Cells_nAnTiCAGE_1.fastq.gz S01_1Cells_nAnTiCAGE_2.fastq.gz,fastq fastq,1193891117.0,6060361.0,S01 1Cells nAnTiCAGE 1.fastq.gz,0:97 1:100,A:286037352;C:298140071;G:310668851;T:297430066;N:1614777,97,100,,,286037352,298140071,310668851,297430066,1614777,SRX6935164,SRS5465199,SRA971223,University of Birmingham|Cancer and Genomic Sciences,University of Birmingham,2,0.93733,0.97059,0.08219,0.07881,0.76682,0.75834,0.53879,0.54537,97,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cage,unknown,bulk,unknown,unknown,,United Kingdom,2019-10-02,Zygote,Embryo,Whole Organism,All anatomical structures
68254,SRR18327318,SRX14464504,SRS11744581,SRP356302,PRJNA799647,Epigenomic analysis reveals prevalent contribution of transposable elements to cis regulatory elements  tissue specific expression  and alternative promoters in zebrafish,PRJNA799647,Other,Transposable elements TEs encode regulatory elements that impact gene expression in multiple species  yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here  we systematically investigate the epigenomic and transcriptomic landscape of TEs across eleven adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE derived transcriptional units expressed in a tissue specific manner. Finally  we show that novel TE derived promoters can initiate tissue specific transcription of alternative isoforms. This work provides a 10 comprehensive profile of TE activity across normal zebrafish tissues  shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.,,,,,zebrafish TU testis rep2,,strain:Tuebingen|isolate:rep2|age:6 mpf|dev stage:adult|sex:male|tissue:testis|BioSampleModel:Model organism or animal,,,,,,,,,nanoCAGE seq of Danio rerio Tubingen: adult male testis shallow,nanoCAGE zebrafish TU testis rep2,nanoCAGE zebrafish TU testis rep2,nanoCAGE seq with polyA pulldown,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,NextSeq 500,,SRP356302,,,nano_TUzfish_combined_deep_testis_BR2.R1.fastq.gz nano_TUzfish_combined_deep_testis_BR2.R2.fastq.gz,fastq fastq,2408261400.0,15886644.0,nano TUzfish combined deep testis BR2.R1.fastq.gz,0:75.80 1:75.80,A:589293804;C:562741604;G:604867589;T:650872884;N:485519,75,75,,,589293804,562741604,604867589,650872884,485519,SRX14464504,SRS11744581,SRA1385043,Washington University in St. Louis|Department of Genetics,Washington University in St. Louis,2,0.05991,0.93925,0.00631,0.04834,0.91364,0.67671,0.54402,0.49323,150,150,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cage,unknown,bulk,unknown,unknown,,United States,2022-03-17,Adult,Adult,Gonad,Reproductive System
68255,SRR18327319,SRX14464503,SRS11744582,SRP356302,PRJNA799647,Epigenomic analysis reveals prevalent contribution of transposable elements to cis regulatory elements  tissue specific expression  and alternative promoters in zebrafish,PRJNA799647,Other,Transposable elements TEs encode regulatory elements that impact gene expression in multiple species  yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here  we systematically investigate the epigenomic and transcriptomic landscape of TEs across eleven adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE derived transcriptional units expressed in a tissue specific manner. Finally  we show that novel TE derived promoters can initiate tissue specific transcription of alternative isoforms. This work provides a 10 comprehensive profile of TE activity across normal zebrafish tissues  shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.,,,,,zebrafish TU testis rep1,,strain:Tuebingen|isolate:rep1|age:6 mpf|dev stage:adult|sex:male|tissue:testis|BioSampleModel:Model organism or animal,,,,,,,,,nanoCAGE seq of Danio rerio Tubingen: adult male testis shallow,nanoCAGE zebrafish TU testis rep1,nanoCAGE zebrafish TU testis rep1,nanoCAGE seq with polyA pulldown,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,NextSeq 500,,SRP356302,,,nano_TUzfish_combined_deep_testis_BR1.R1.fastq.gz nano_TUzfish_combined_deep_testis_BR1.R2.fastq.gz,fastq fastq,2655464100.0,17518322.0,nano TUzfish combined deep testis BR1.R1.fastq.gz,0:75.79 1:75.79,A:648423774;C:624425183;G:667510545;T:714557704;N:546894,75,75,,,648423774,624425183,667510545,714557704,546894,SRX14464503,SRS11744582,SRA1385043,Washington University in St. Louis|Department of Genetics,Washington University in St. Louis,2,0.05205,0.9337,0.00433,0.0458,0.92086,0.68631,0.5426,0.50321,150,150,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cage,unknown,bulk,unknown,unknown,,United States,2022-03-17,Adult,Adult,Gonad,Reproductive System
68256,SRR18327320,SRX14464502,SRS11744580,SRP356302,PRJNA799647,Epigenomic analysis reveals prevalent contribution of transposable elements to cis regulatory elements  tissue specific expression  and alternative promoters in zebrafish,PRJNA799647,Other,Transposable elements TEs encode regulatory elements that impact gene expression in multiple species  yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here  we systematically investigate the epigenomic and transcriptomic landscape of TEs across eleven adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE derived transcriptional units expressed in a tissue specific manner. Finally  we show that novel TE derived promoters can initiate tissue specific transcription of alternative isoforms. This work provides a 10 comprehensive profile of TE activity across normal zebrafish tissues  shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.,,,,,zebrafish TU brain rep2,,strain:Tuebingen|isolate:rep2|age:6 mpf|dev stage:adult|sex:female|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,nanoCAGE seq of Danio rerio Tubingen: adult male brain shallow,nanoCAGE zebrafish TU brain rep2,nanoCAGE zebrafish TU brain rep2,nanoCAGE seq with polyA pulldown,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,NextSeq 500,,SRP356302,,,nano_TUzfish_combined_deep_brain_BR2.R1.fastq.gz nano_TUzfish_combined_deep_brain_BR2.R2.fastq.gz,fastq fastq,2120070300.0,13983927.0,nano TUzfish combined deep brain BR2.R1.fastq.gz,0:75.80 1:75.80,A:521597394;C:502052046;G:539140115;T:556851976;N:428769,75,75,,,521597394,502052046,539140115,556851976,428769,SRX14464502,SRS11744580,SRA1385043,Washington University in St. Louis|Department of Genetics,Washington University in St. Louis,2,0.05946,0.93361,0.00648,0.07284,0.91739,0.70025,0.57506,0.48669,150,150,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cage,unknown,bulk,unknown,unknown,,United States,2022-03-17,Adult,Adult,Brain,Nervous System
68257,SRR18327321,SRX14464501,SRS11744579,SRP356302,PRJNA799647,Epigenomic analysis reveals prevalent contribution of transposable elements to cis regulatory elements  tissue specific expression  and alternative promoters in zebrafish,PRJNA799647,Other,Transposable elements TEs encode regulatory elements that impact gene expression in multiple species  yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here  we systematically investigate the epigenomic and transcriptomic landscape of TEs across eleven adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE derived transcriptional units expressed in a tissue specific manner. Finally  we show that novel TE derived promoters can initiate tissue specific transcription of alternative isoforms. This work provides a 10 comprehensive profile of TE activity across normal zebrafish tissues  shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.,,,,,zebrafish TU brain rep1,,strain:Tuebingen|isolate:rep1|age:6 mpf|dev stage:adult|sex:female|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,nanoCAGE seq of Danio rerio Tubingen: adult male brain shallow,nanoCAGE zebrafish TU brain rep1,nanoCAGE zebrafish TU brain rep1,nanoCAGE seq with polyA pulldown,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,NextSeq 500,,SRP356302,,,nano_TUzfish_combined_deep_brain_BR1.R1.fastq.gz nano_TUzfish_combined_deep_brain_BR1.R2.fastq.gz,fastq fastq,1958802000.0,12919047.0,nano TUzfish combined deep brain BR1.R1.fastq.gz,0:75.81 1:75.81,A:485271176;C:461368873;G:496521163;T:515247447;N:393341,75,75,,,485271176,461368873,496521163,515247447,393341,SRX14464501,SRS11744579,SRA1385043,Washington University in St. Louis|Department of Genetics,Washington University in St. Louis,2,0.0666,0.93487,0.00689,0.0747,0.91175,0.70027,0.57062,0.49364,150,150,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cage,unknown,bulk,unknown,unknown,,United States,2022-03-17,Adult,Adult,Brain,Nervous System
68258,SRR17709722,SRX13872770,SRS11744581,SRP356302,PRJNA799647,Epigenomic analysis reveals prevalent contribution of transposable elements to cis regulatory elements  tissue specific expression  and alternative promoters in zebrafish,PRJNA799647,Other,Transposable elements TEs encode regulatory elements that impact gene expression in multiple species  yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here  we systematically investigate the epigenomic and transcriptomic landscape of TEs across eleven adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE derived transcriptional units expressed in a tissue specific manner. Finally  we show that novel TE derived promoters can initiate tissue specific transcription of alternative isoforms. This work provides a 10 comprehensive profile of TE activity across normal zebrafish tissues  shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.,,,,,zebrafish TU testis rep2,,strain:Tuebingen|isolate:rep2|age:6 mpf|dev stage:adult|sex:male|tissue:testis|BioSampleModel:Model organism or animal,,,,,,,,,nanoCAGE seq of Danio rerio Tubingen: adult male testis,nanoCAGE zebrafish TU testis rep2,nanoCAGE zebrafish TU testis shallow rep2,nanoCAGE seq with polyA pulldown,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,NextSeq 500,,SRP356302,,,nanoCAGE_zebrafish_TU_testis_rep2.R1.fastq.gz nanoCAGE_zebrafish_TU_testis_rep2.R2.fastq.gz,fastq fastq,1257997200.0,8218216.0,nanoCAGE zebrafish TU testis rep2.R1.fastq.gz,0:76.54 1:76.54,A:307675653;C:294445668;G:315944501;T:339570175;N:361203,76,76,,,307675653,294445668,315944501,339570175,361203,SRX13872770,SRS11744581,SRA1360415,Washington University in St. Louis|Department of Genetics,Washington University in St. Louis,2,0.06846,0.93772,0.00675,0.04699,0.90293,0.67986,0.52867,0.49221,150,150,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cage,unknown,bulk,unknown,unknown,,United States,2022-01-23,Adult,Adult,Gonad,Reproductive System
68259,SRR17709723,SRX13872769,SRS11744582,SRP356302,PRJNA799647,Epigenomic analysis reveals prevalent contribution of transposable elements to cis regulatory elements  tissue specific expression  and alternative promoters in zebrafish,PRJNA799647,Other,Transposable elements TEs encode regulatory elements that impact gene expression in multiple species  yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here  we systematically investigate the epigenomic and transcriptomic landscape of TEs across eleven adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE derived transcriptional units expressed in a tissue specific manner. Finally  we show that novel TE derived promoters can initiate tissue specific transcription of alternative isoforms. This work provides a 10 comprehensive profile of TE activity across normal zebrafish tissues  shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.,,,,,zebrafish TU testis rep1,,strain:Tuebingen|isolate:rep1|age:6 mpf|dev stage:adult|sex:male|tissue:testis|BioSampleModel:Model organism or animal,,,,,,,,,nanoCAGE seq of Danio rerio Tubingen: adult male testis,nanoCAGE zebrafish TU testis rep1,nanoCAGE zebrafish TU testis shallow rep1,nanoCAGE seq with polyA pulldown,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,NextSeq 500,,SRP356302,,,nanoCAGE_zebrafish_TU_testis_rep1.R1.fastq.gz nanoCAGE_zebrafish_TU_testis_rep1.R2.fastq.gz,fastq fastq,1351312800.0,8823980.0,nanoCAGE zebrafish TU testis rep1.R1.fastq.gz,0:76.57 1:76.57,A:329750139;C:318355694;G:339653380;T:363149300;N:404287,76,76,,,329750139,318355694,339653380,363149300,404287,SRX13872769,SRS11744582,SRA1360415,Washington University in St. Louis|Department of Genetics,Washington University in St. Louis,2,0.06051,0.93247,0.00473,0.0437,0.91088,0.68943,0.52768,0.49868,150,150,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cage,unknown,bulk,unknown,unknown,,United States,2022-01-23,Adult,Adult,Gonad,Reproductive System
68260,SRR17709724,SRX13872768,SRS11744580,SRP356302,PRJNA799647,Epigenomic analysis reveals prevalent contribution of transposable elements to cis regulatory elements  tissue specific expression  and alternative promoters in zebrafish,PRJNA799647,Other,Transposable elements TEs encode regulatory elements that impact gene expression in multiple species  yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here  we systematically investigate the epigenomic and transcriptomic landscape of TEs across eleven adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE derived transcriptional units expressed in a tissue specific manner. Finally  we show that novel TE derived promoters can initiate tissue specific transcription of alternative isoforms. This work provides a 10 comprehensive profile of TE activity across normal zebrafish tissues  shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.,,,,,zebrafish TU brain rep2,,strain:Tuebingen|isolate:rep2|age:6 mpf|dev stage:adult|sex:female|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,nanoCAGE seq of Danio rerio Tubingen: adult female brain,nanoCAGE zebrafish TU brain rep2,nanoCAGE zebrafish TU brain shallow rep2,nanoCAGE seq with polyA pulldown,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,NextSeq 500,,SRP356302,,,nanoCAGE_zebrafish_TU_brain_rep2.R1.fastq.gz nanoCAGE_zebrafish_TU_brain_rep2.R2.fastq.gz,fastq fastq,1114647450.0,7281108.0,nanoCAGE zebrafish TU brain rep2.R1.fastq.gz,0:76.54 1:76.54,A:273967636;C:264512491;G:283567362;T:292276557;N:323404,76,76,,,273967636,264512491,283567362,292276557,323404,SRX13872768,SRS11744580,SRA1360415,Washington University in St. Louis|Department of Genetics,Washington University in St. Louis,2,0.06736,0.93327,0.00663,0.0712,0.90792,0.70283,0.55337,0.4859,150,150,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cage,unknown,bulk,unknown,unknown,,United States,2022-01-23,Adult,Adult,Brain,Nervous System
68261,SRR17709725,SRX13872767,SRS11744579,SRP356302,PRJNA799647,Epigenomic analysis reveals prevalent contribution of transposable elements to cis regulatory elements  tissue specific expression  and alternative promoters in zebrafish,PRJNA799647,Other,Transposable elements TEs encode regulatory elements that impact gene expression in multiple species  yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here  we systematically investigate the epigenomic and transcriptomic landscape of TEs across eleven adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE derived transcriptional units expressed in a tissue specific manner. Finally  we show that novel TE derived promoters can initiate tissue specific transcription of alternative isoforms. This work provides a 10 comprehensive profile of TE activity across normal zebrafish tissues  shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.,,,,,zebrafish TU brain rep1,,strain:Tuebingen|isolate:rep1|age:6 mpf|dev stage:adult|sex:female|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,nanoCAGE seq of Danio rerio Tubingen: adult female brain,nanoCAGE zebrafish TU brain rep1,nanoCAGE zebrafish TU brain shallow rep1,nanoCAGE seq with polyA pulldown,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,NextSeq 500,,SRP356302,,,nanoCAGE_zebrafish_TU_brain_rep1.R1.fastq.gz nanoCAGE_zebrafish_TU_brain_rep1.R2.fastq.gz,fastq fastq,1040194800.0,6794999.0,nanoCAGE zebrafish TU brain rep1.R1.fastq.gz,0:76.54 1:76.54,A:257427323;C:245563114;G:263853643;T:273054571;N:296149,76,76,,,257427323,245563114,263853643,273054571,296149,SRX13872767,SRS11744579,SRA1360415,Washington University in St. Louis|Department of Genetics,Washington University in St. Louis,2,0.07308,0.93461,0.00714,0.07167,0.9051,0.70199,0.56162,0.48821,150,150,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cage,unknown,bulk,unknown,unknown,,United States,2022-01-23,Adult,Adult,Brain,Nervous System
69378,SRR18516702,SRX14647801,SRS12413210,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007475BS,,strain:WT|age:4.7hpf|dev stage:zfs:0000015|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq zfs:0000015 Whole cell CAGE,DCD003740SQ,DCD003740SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0013AS.DCD003740SQ.USERdanio-user.R1.fastq.gz,fastq,57981552.0,1207949.0,CAGE seq Mueller lab 0013AS.DCD003740SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:13228227;C:15492921;G:15505739;T:13750626;N:4039,48,0,,,13228227,15492921,15505739,13750626,4039,SRX14647801,SRS12413210,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.18388,,0.02619,,0.85811,,0.52264,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Blastula,Embryo,Embryo Imprecise,All anatomical structures
69379,SRR18516703,SRX14647800,SRS12413216,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007476BS,,strain:WT|age:24hpf|dev stage:Prim 5|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq Prim Nuclear CAGE,DCD003719SQ,DCD003719SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0014AS.DCD003719SQ.USERdanio-user.R1.fastq.gz,fastq,585510192.0,12198129.0,CAGE seq Mueller lab 0014AS.DCD003719SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:129885703;C:153766182;G:160138903;T:141666883;N:52521,48,0,,,129885703,153766182,160138903,141666883,52521,SRX14647800,SRS12413216,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.20391,,0.04196,,0.83453,,0.4979,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
69380,SRR18516704,SRX14647799,SRS12413216,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007476BS,,strain:WT|age:24hpf|dev stage:Prim 5|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq Prim Nuclear CAGE,DCD003718SQ,DCD003718SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0014AS.DCD003718SQ.USERdanio-user.R1.fastq.gz,fastq,593136528.0,12357011.0,CAGE seq Mueller lab 0014AS.DCD003718SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:130366174;C:156810351;G:159219365;T:146691922;N:48716,48,0,,,130366174,156810351,159219365,146691922,48716,SRX14647799,SRS12413216,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.14873,,0.03239,,0.86557,,0.49634,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
69381,SRR18516705,SRX14647798,SRS12413216,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007476BS,,strain:WT|age:24hpf|dev stage:Prim 5|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq Prim Nuclear CAGE,DCD003723SQ,DCD003723SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0014AS.DCD003723SQ.USERdanio-user.R1.fastq.gz,fastq,422696256.0,8806172.0,CAGE seq Mueller lab 0014AS.DCD003723SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:92712632;C:111696999;G:115145846;T:103105611;N:35168,48,0,,,92712632,111696999,115145846,103105611,35168,SRX14647798,SRS12413216,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.1594,,0.02997,,0.85591,,0.48496,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
69382,SRR18516706,SRX14647797,SRS12413215,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007477BS,,strain:WT|age:42hpf|dev stage:High pec|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq High pec Nuclear CAGE,DCD003737SQ,DCD003737SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0014AS.DCD003737SQ.USERdanio-user.R1.fastq.gz,fastq,1041108672.0,21689764.0,CAGE seq Mueller lab 0014AS.DCD003737SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:233996885;C:276232291;G:275987771;T:254800016;N:91709,48,0,,,233996885,276232291,275987771,254800016,91709,SRX14647797,SRS12413215,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.19665,,0.0423,,0.84271,,0.49525,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
69383,SRR18516707,SRX14647796,SRS12413215,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007477BS,,strain:WT|age:42hpf|dev stage:High pec|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq High pec Nuclear CAGE,DCD003729SQ,DCD003729SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0014AS.DCD003729SQ.USERdanio-user.R1.fastq.gz,fastq,383268528.0,7984761.0,CAGE seq Mueller lab 0014AS.DCD003729SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:83789437;C:103371728;G:102876480;T:93198236;N:32647,48,0,,,83789437,103371728,102876480,93198236,32647,SRX14647796,SRS12413215,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.15605,,0.03059,,0.86951,,0.50369,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
69384,SRR18516708,SRX14647795,SRS12413215,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007477BS,,strain:WT|age:42hpf|dev stage:High pec|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq High pec Nuclear CAGE,DCD003734SQ,DCD003734SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0014AS.DCD003734SQ.USERdanio-user.R1.fastq.gz,fastq,560665392.0,11680529.0,CAGE seq Mueller lab 0014AS.DCD003734SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:123278501;C:149059346;G:152514412;T:135763704;N:49429,48,0,,,123278501,149059346,152514412,135763704,49429,SRX14647795,SRS12413215,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.16518,,0.02906,,0.85283,,0.47924,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
69385,SRR18516709,SRX14647794,SRS12413214,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007471BS,,strain:WT|age:42hpf|dev stage:High pec|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq High pec Whole cell CAGE,DCD003731SQ,DCD003731SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0013AS.DCD003731SQ.USERdanio-user.R1.fastq.gz,fastq,534745104.0,11140523.0,CAGE seq Mueller lab 0013AS.DCD003731SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:122900964;C:145291239;G:142314928;T:124199394;N:38579,48,0,,,122900964,145291239,142314928,124199394,38579,SRX14647794,SRS12413214,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.21193,,0.03662,,0.8576,,0.51061,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
69386,SRR18516710,SRX14647793,SRS12413214,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007471BS,,strain:WT|age:42hpf|dev stage:High pec|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq High pec Whole cell CAGE,DCD003733SQ,DCD003733SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0013AS.DCD003733SQ.USERdanio-user.R1.fastq.gz,fastq,1106623152.0,23054649.0,CAGE seq Mueller lab 0013AS.DCD003733SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:244437769;C:302018709;G:293780395;T:266329857;N:56422,48,0,,,244437769,302018709,293780395,266329857,56422,SRX14647793,SRS12413214,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.25973,,0.02959,,0.84778,,0.50948,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
69387,SRR18516711,SRX14647792,SRS12413214,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007471BS,,strain:WT|age:42hpf|dev stage:High pec|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq High pec Whole cell CAGE,DCD003735SQ,DCD003735SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0013AS.DCD003735SQ.USERdanio-user.R1.fastq.gz,fastq,829987920.0,17291415.0,CAGE seq Mueller lab 0013AS.DCD003735SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:189638839;C:226118233;G:218991435;T:195178858;N:60555,48,0,,,189638839,226118233,218991435,195178858,60555,SRX14647792,SRS12413214,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.20953,,0.03562,,0.85285,,0.52927,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
69388,SRR18516712,SRX14647791,SRS12413213,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007472BS,,strain:WT|age:14hpf|dev stage:5 9 somites|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq 5 9 somites Whole cell CAGE,DCD003730SQ,DCD003730SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0013AS.DCD003730SQ.USERdanio-user.R1.fastq.gz,fastq,358730736.0,7473557.0,CAGE seq Mueller lab 0013AS.DCD003730SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:82114871;C:96481695;G:97889447;T:82217691;N:27032,48,0,,,82114871,96481695,97889447,82217691,27032,SRX14647791,SRS12413213,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.22955,,0.03488,,0.84719,,0.51204,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
69389,SRR18516713,SRX14647790,SRS12413209,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007478BS,,strain:WT|age:4.7hpf|dev stage:zfs:0000015|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq zfs:0000015 Nuclear CAGE,DCD003732SQ,DCD003732SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0014AS.DCD003732SQ.USERdanio-user.R1.fastq.gz,fastq,833831760.0,17371495.0,CAGE seq Mueller lab 0014AS.DCD003732SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:184529953;C:221676233;G:220734592;T:206820467;N:70515,48,0,,,184529953,221676233,220734592,206820467,70515,SRX14647790,SRS12413209,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.16336,,0.03655,,0.88633,,0.47894,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Blastula,Embryo,Embryo Imprecise,All anatomical structures
69390,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
69392,SRR18516716,SRX14647787,SRS12413212,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007473BS,,strain:WT|age:24hpf|dev stage:Prim 5|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq Prim Whole cell CAGE,DCD003727SQ,DCD003727SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0013AS.DCD003727SQ.USERdanio-user.R1.fastq.gz,fastq,924879888.0,19268331.0,CAGE seq Mueller lab 0013AS.DCD003727SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:214005056;C:251321459;G:244648845;T:214835794;N:68734,48,0,,,214005056,251321459,244648845,214835794,68734,SRX14647787,SRS12413212,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.2165,,0.03701,,0.84768,,0.54102,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
69393,SRR18516717,SRX14647786,SRS12413212,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007473BS,,strain:WT|age:24hpf|dev stage:Prim 5|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq Prim Whole cell CAGE,DCD003717SQ,DCD003717SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0013AS.DCD003717SQ.USERdanio-user.R1.fastq.gz,fastq,1485845376.0,30955112.0,CAGE seq Mueller lab 0013AS.DCD003717SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:329122121;C:402514173;G:390388645;T:363745867;N:74570,48,0,,,329122121,402514173,390388645,363745867,74570,SRX14647786,SRS12413212,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.23893,,0.0248,,0.86125,,0.50849,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
69394,SRR18516718,SRX14647785,SRS12413212,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007473BS,,strain:WT|age:24hpf|dev stage:Prim 5|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq Prim Whole cell CAGE,DCD003739SQ,DCD003739SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0013AS.DCD003739SQ.USERdanio-user.R1.fastq.gz,fastq,1372622736.0,28596307.0,CAGE seq Mueller lab 0013AS.DCD003739SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:306709302;C:373224967;G:360990874;T:331626639;N:70954,48,0,,,306709302,373224967,360990874,331626639,70954,SRX14647785,SRS12413212,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.26574,,0.02914,,0.85113,,0.52147,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
69395,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
69398,SRR18516722,SRX14647781,SRS12413210,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007475BS,,strain:WT|age:4.7hpf|dev stage:zfs:0000015|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq zfs:0000015 Whole cell CAGE,DCD003720SQ,DCD003720SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0013AS.DCD003720SQ.USERdanio-user.R1.fastq.gz,fastq,536292432.0,11172759.0,CAGE seq Mueller lab 0013AS.DCD003720SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:122756671;C:142850582;G:140364671;T:130293257;N:27251,48,0,,,122756671,142850582,140364671,130293257,27251,SRX14647781,SRS12413210,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.23072,,0.04674,,0.89572,,0.59187,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Blastula,Embryo,Embryo Imprecise,All anatomical structures
69399,SRR18516723,SRX14647780,SRS12413210,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007475BS,,strain:WT|age:4.7hpf|dev stage:zfs:0000015|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq zfs:0000015 Whole cell CAGE,DCD003725SQ,DCD003725SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0013AS.DCD003725SQ.USERdanio-user.R1.fastq.gz,fastq,1839979776.0,38332912.0,CAGE seq Mueller lab 0013AS.DCD003725SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:422772310;C:484519947;G:479159876;T:453437875;N:89768,48,0,,,422772310,484519947,479159876,453437875,89768,SRX14647780,SRS12413210,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.22646,,0.03978,,0.88574,,0.556,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Blastula,Embryo,Embryo Imprecise,All anatomical structures
69400,SRR18516724,SRX14647779,SRS12413209,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007478BS,,strain:WT|age:4.7hpf|dev stage:zfs:0000015|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq zfs:0000015 Nuclear CAGE,DCD003728SQ,DCD003728SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0014AS.DCD003728SQ.USERdanio-user.R1.fastq.gz,fastq,778510272.0,16218964.0,CAGE seq Mueller lab 0014AS.DCD003728SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:170505572;C:207531743;G:206655879;T:193751108;N:65970,48,0,,,170505572,207531743,206655879,193751108,65970,SRX14647779,SRS12413209,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.1419,,0.02783,,0.8954,,0.49693,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Blastula,Embryo,Embryo Imprecise,All anatomical structures
69401,SRR18516725,SRX14647778,SRS12413209,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007478BS,,strain:WT|age:4.7hpf|dev stage:zfs:0000015|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq zfs:0000015 Nuclear CAGE,DCD003724SQ,DCD003724SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0014AS.DCD003724SQ.USERdanio-user.R1.fastq.gz,fastq,641108496.0,13356427.0,CAGE seq Mueller lab 0014AS.DCD003724SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:143927298;C:167543966;G:171107575;T:158473503;N:56154,48,0,,,143927298,167543966,171107575,158473503,56154,SRX14647778,SRS12413209,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.20203,,0.0454,,0.87091,,0.51364,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Blastula,Embryo,Embryo Imprecise,All anatomical structures