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
77,DRR032747,DRX029553,DRS049952,DRP003810,PRJDB3785,EXPANDE project,DRP003810,Other,EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief  taking advantages of Illumina sequencing  RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.,,,mRNA extracted from pooled embryos of 50 individuals,Dr 6somite 2,SAMD00028144,,sample name:Dr 6somite 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:6somite|genotype:wild type|phenotype:wild type|sex:male  female  and mixed,,,,,,,,,Illumina HiSeq 2000 sequencing of SAMD00028144,DRX029553,Dr 6somite 2,1,Total RNA QIAGEN RNeasy followed by TruSeq,,RNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>,DRP003810,Illumina HiSeq 2000 sequencing of SAMD00028144,,,,3704431000.0,37044310.0,DRR032747,0:100 1:0,A:1001844161;C:856702913;G:850695568;T:995148798;N:39560,100,0,,,1001844161,856702913,850695568,995148798,39560,DRX029553,DRS049952,DRA003460,"UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo","UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo",1,0.92633,,0.09211,,0.72107,,0.47195,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,Japan,2017-09-20,Segmentation,Embryo,Whole Organism,All anatomical structures
78,DRR032746,DRX029552,DRS049951,DRP003810,PRJDB3785,EXPANDE project,DRP003810,Other,EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief  taking advantages of Illumina sequencing  RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.,,,mRNA extracted from pooled embryos of 50 individuals,Dr 6somite 1,SAMD00028143,,sample name:Dr 6somite 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:6somite|genotype:wild type|phenotype:wild type|sex:male  female  and mixed,,,,,,,,,Illumina HiSeq 2000 sequencing of SAMD00028143,DRX029552,Dr 6somite 1,1,Total RNA QIAGEN RNeasy followed by TruSeq,,RNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>,DRP003810,Illumina HiSeq 2000 sequencing of SAMD00028143,,,,3529311900.0,35293119.0,DRR032746,0:100 1:0,A:953957996;C:816824469;G:811403696;T:947089530;N:36209,100,0,,,953957996,816824469,811403696,947089530,36209,DRX029552,DRS049951,DRA003460,"UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo","UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo",1,0.92437,,0.09257,,0.72113,,0.47004,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,Japan,2017-09-20,Segmentation,Embryo,Whole Organism,All anatomical structures
92,DRR032732,DRX029538,DRS049937,DRP003810,PRJDB3785,EXPANDE project,DRP003810,Other,EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief  taking advantages of Illumina sequencing  RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.,,,mRNA extracted from pooled embryos of 80 individuals,Dr 14somite 3,SAMD00028129,,sample name:Dr 14somite 3|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:14somite|genotype:wild type|phenotype:wild type|sex:male  female  and mixed,,,,,,,,,Illumina HiSeq 2000 sequencing of SAMD00028129,DRX029538,Dr 14somite 3,1,Total RNA QIAGEN RNeasy followed by TruSeq,,RNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>,DRP003810,Illumina HiSeq 2000 sequencing of SAMD00028129,,,,3734610500.0,37346105.0,DRR032732,0:100 1:0,A:1009418541;C:863710067;G:858061383;T:1003378800;N:41709,100,0,,,1009418541,863710067,858061383,1003378800,41709,DRX029538,DRS049937,DRA003460,"UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo","UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo",1,0.92401,,0.08815,,0.70816,,0.46602,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,Japan,2017-09-20,Segmentation,Embryo,Whole Organism,All anatomical structures
93,DRR032731,DRX029537,DRS049936,DRP003810,PRJDB3785,EXPANDE project,DRP003810,Other,EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief  taking advantages of Illumina sequencing  RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.,,,mRNA extracted from pooled embryos of 80 individuals,Dr 14somite 2,SAMD00028128,,sample name:Dr 14somite 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:14somite|genotype:wild type|phenotype:wild type|sex:male  female  and mixed,,,,,,,,,Illumina HiSeq 2000 sequencing of SAMD00028128,DRX029537,Dr 14somite 2,1,Total RNA QIAGEN RNeasy followed by TruSeq,,RNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>,DRP003810,Illumina HiSeq 2000 sequencing of SAMD00028128,,,,3715174200.0,37151742.0,DRR032731,0:100 1:0,A:1000703508;C:862290629;G:858173468;T:993968396;N:38199,100,0,,,1000703508,862290629,858173468,993968396,38199,DRX029537,DRS049936,DRA003460,"UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo","UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo",1,0.92491,,0.0819,,0.71068,,0.46957,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,Japan,2017-09-20,Segmentation,Embryo,Whole Organism,All anatomical structures
94,DRR032730,DRX029536,DRS049935,DRP003810,PRJDB3785,EXPANDE project,DRP003810,Other,EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief  taking advantages of Illumina sequencing  RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.,,,mRNA extracted from pooled embryos of 80 individuals,Dr 14somite 1,SAMD00028127,,sample name:Dr 14somite 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:14somite|genotype:wild type|phenotype:wild type|sex:male  female  and mixed,,,,,,,,,Illumina HiSeq 2000 sequencing of SAMD00028127,DRX029536,Dr 14somite 1,1,Total RNA QIAGEN RNeasy followed by TruSeq,,RNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>,DRP003810,Illumina HiSeq 2000 sequencing of SAMD00028127,,,,3744386000.0,37443860.0,DRR032730,0:100 1:0,A:1014537326;C:864070910;G:859190201;T:1006549502;N:38061,100,0,,,1014537326,864070910,859190201,1006549502,38061,DRX029536,DRS049935,DRA003460,"UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo","UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo",1,0.92378,,0.08957,,0.7068,,0.47493,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,Japan,2017-09-20,Segmentation,Embryo,Whole Organism,All anatomical structures
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
25170,SRR25661605,SRX21387413,SRS18627977,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,hand2 FLD+/? 20 hpf CMs rep3,GSM7714404,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 mutants|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,hand2 FLD+/? 20 hpf CMs rep3,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 mutants|treatment:sorted cells by FACS,GSM7714404,GSM7714404: hand2 FLD+/? 20 hpf CMs rep3; Danio rerio; RNA Seq,GSM7714404 r1,GSM7714404,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_WT_het_3_R1.fastq.gz,fastq,2441736984.0,34141777.0,GSM7714404 r1,0:71.52,A:706186414;C:496261994;G:526176364;T:713112212;N:0,71,,,,706186414,496261994,526176364,713112212,0,SRX21387413,SRS18627977,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.9026,,0.15816,,0.76278,,0.44042,,72,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
25171,SRR25661606,SRX21387412,SRS18627976,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,hand2 FLD+/? 20 hpf CMs rep2,GSM7714403,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 mutants|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,hand2 FLD+/? 20 hpf CMs rep2,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 mutants|treatment:sorted cells by FACS,GSM7714403,GSM7714403: hand2 FLD+/? 20 hpf CMs rep2; Danio rerio; RNA Seq,GSM7714403 r1,GSM7714403,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_WT_het_2_R1.fastq.gz,fastq,2185611269.0,30558084.0,GSM7714403 r1,0:71.52,A:612617675;C:458632518;G:474458738;T:639902338;N:0,71,,,,612617675,458632518,474458738,639902338,0,SRX21387412,SRS18627976,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.90042,,0.14005,,0.75424,,0.44277,,72,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
25172,SRR25661607,SRX21387411,SRS18627975,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,hand2 FLD+/? 20 hpf CMs rep1,GSM7714402,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 mutants|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,hand2 FLD+/? 20 hpf CMs rep1,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 mutants|treatment:sorted cells by FACS,GSM7714402,GSM7714402: hand2 FLD+/? 20 hpf CMs rep1; Danio rerio; RNA Seq,GSM7714402 r1,GSM7714402,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_WT_het_1_R1.fastq.gz,fastq,2291884894.0,32043147.0,GSM7714402 r1,0:71.52,A:635094975;C:489594953;G:499909828;T:667285138;N:0,71,,,,635094975,489594953,499909828,667285138,0,SRX21387411,SRS18627975,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.90883,,0.14288,,0.75331,,0.44459,,71,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
25173,SRR25661608,SRX21387410,SRS18627974,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,WT 20 hpf CMs rep3,GSM7714401,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,WT 20 hpf CMs rep3,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS,GSM7714401,GSM7714401: WT 20 hpf CMs rep3; Danio rerio; RNA Seq,GSM7714401 r1,GSM7714401,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_WT_CMs_3_R1.fastq.gz,fastq,2268251602.0,31717610.0,GSM7714401 r1,0:71.51,A:637196241;C:477782543;G:497683941;T:655588877;N:0,71,,,,637196241,477782543,497683941,655588877,0,SRX21387410,SRS18627974,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.90026,,0.13291,,0.78707,,0.40811,,71,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
25174,SRR25661609,SRX21387409,SRS18627973,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,WT 20 hpf CMs rep2,GSM7714400,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,WT 20 hpf CMs rep2,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS,GSM7714400,GSM7714400: WT 20 hpf CMs rep2; Danio rerio; RNA Seq,GSM7714400 r1,GSM7714400,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_WT_CMs_2_R1.fastq.gz,fastq,2195524610.0,30700033.0,GSM7714400 r1,0:71.52,A:615401741;C:462686936;G:481135567;T:636300366;N:0,71,,,,615401741,462686936,481135567,636300366,0,SRX21387409,SRS18627973,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.90323,,0.1476,,0.78744,,0.41728,,72,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
25175,SRR25661610,SRX21387408,SRS18627972,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,WT 20 hpf CMs rep1,GSM7714399,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,WT 20 hpf CMs rep1,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS,GSM7714399,GSM7714399: WT 20 hpf CMs rep1; Danio rerio; RNA Seq,GSM7714399 r1,GSM7714399,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_WT_CMs_1_R1.fastq.gz,fastq,2258160684.0,31576661.0,GSM7714399 r1,0:71.51,A:641254288;C:471580136;G:491501482;T:653824778;N:0,71,,,,641254288,471580136,491501482,653824778,0,SRX21387408,SRS18627972,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.9,,0.13993,,0.78445,,0.40575,,72,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
25176,SRR25661611,SRX21387407,SRS18627971,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,hand2 OE 20 hpf CMs rep3,GSM7714398,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,hand2 OE 20 hpf CMs rep3,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS,GSM7714398,GSM7714398: hand2 OE 20 hpf CMs rep3; Danio rerio; RNA Seq,GSM7714398 r1,GSM7714398,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_OE_CMs_3_R1.fastq.gz,fastq,1886569909.0,26380170.0,GSM7714398 r1,0:71.51,A:534874421;C:392168718;G:411533838;T:547992932;N:0,71,,,,534874421,392168718,411533838,547992932,0,SRX21387407,SRS18627971,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.89968,,0.14763,,0.77881,,0.42601,,72,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
25177,SRR25661612,SRX21387406,SRS18627970,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,hand2 OE 20 hpf CMs rep2,GSM7714397,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,hand2 OE 20 hpf CMs rep2,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS,GSM7714397,GSM7714397: hand2 OE 20 hpf CMs rep2; Danio rerio; RNA Seq,GSM7714397 r1,GSM7714397,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_OE_CMs_2_R1.fastq.gz,fastq,2197151812.0,30722639.0,GSM7714397 r1,0:71.52,A:617116635;C:461951919;G:481371246;T:636712012;N:0,71,,,,617116635,461951919,481371246,636712012,0,SRX21387406,SRS18627970,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.90877,,0.14744,,0.77191,,0.42845,,72,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
25178,SRR25661613,SRX21387405,SRS18627969,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,hand2 OE 20 hpf CMs rep1,GSM7714396,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,hand2 OE 20 hpf CMs rep1,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS,GSM7714396,GSM7714396: hand2 OE 20 hpf CMs rep1; Danio rerio; RNA Seq,GSM7714396 r1,GSM7714396,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_OE_CMs_1_R1.fastq.gz,fastq,1773398936.0,24797998.0,GSM7714396 r1,0:71.51,A:495618212;C:375438077;G:390377060;T:511965587;N:0,71,,,,495618212,375438077,390377060,511965587,0,SRX21387405,SRS18627969,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.90769,,0.1387,,0.7768,,0.42096,,72,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
25179,SRR25661614,SRX21387404,SRS18627968,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,hand2 FLD /  20 hpf CMs rep3,GSM7714395,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,hand2 FLD /  20 hpf CMs rep3,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS,GSM7714395,GSM7714395: hand2 FLD /  20 hpf CMs rep3; Danio rerio; RNA Seq,GSM7714395 r1,GSM7714395,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_Mut_3_R1.fastq.gz,fastq,2179400259.0,30471965.0,GSM7714395 r1,0:71.52,A:600555691;C:468535203;G:483122661;T:627186704;N:0,71,,,,600555691,468535203,483122661,627186704,0,SRX21387404,SRS18627968,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.91581,,0.12256,,0.75209,,0.43413,,71,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
25180,SRR25661615,SRX21387403,SRS18627967,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,hand2 FLD /  20 hpf CMs rep2,GSM7714394,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,hand2 FLD /  20 hpf CMs rep2,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS,GSM7714394,GSM7714394: hand2 FLD /  20 hpf CMs rep2; Danio rerio; RNA Seq,GSM7714394 r1,GSM7714394,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_Mut_2_R1.fastq.gz,fastq,2340991168.0,32733068.0,GSM7714394 r1,0:71.52,A:647423337;C:500120073;G:514803152;T:678644606;N:0,71,,,,647423337,500120073,514803152,678644606,0,SRX21387403,SRS18627967,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.91231,,0.12561,,0.75118,,0.44445,,71,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
25181,SRR25661616,SRX21387402,SRS18627966,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,hand2 FLD /  20 hpf CMs rep1,GSM7714393,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,hand2 FLD /  20 hpf CMs rep1,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS,GSM7714393,GSM7714393: hand2 FLD /  20 hpf CMs rep1; Danio rerio; RNA Seq,GSM7714393 r1,GSM7714393,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_Mut_1_R1.fastq.gz,fastq,2727863036.0,38140997.0,GSM7714393 r1,0:71.52,A:760867462;C:577539041;G:596986102;T:792470431;N:0,71,,,,760867462,577539041,596986102,792470431,0,SRX21387402,SRS18627966,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.91175,,0.1342,,0.75282,,0.44063,,72,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
26499,SRR26031755,SRX21749012,SRS18856550,SRP459729,PRJNA1015262,Rtf1 dependent transcriptional pausing regulates cardiogenesis,PRJNA1015262,Other,During heart development  an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II  as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis  we found that Rtf1 is essential for cardiogenesis and that without xxx activity  cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain  which confers interaction with the pausing/elongation factor Spt5  was required for Rtf1's ability to support cardiac progenitor formation  while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced  suggesting a reduction in transcriptional pausing. Intriguingly  pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.,,,,,RNAseq hand2FACS rtf1MO 3,,strain:TgBAChand2:EGFPpd24|dev stage:10 12 somite stage|collection date:2020 07 14|geo loc name:USA:California Los Angeles|sex:n/a|tissue:hand2:GFP positive cells|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of hand2:GFP positive cells from 10 12 somite stage zebrafish embryos,M3,MO3,NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina from 5 10 ng input RNA,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP459729,,,RNAseq_hand2FACS_rtf1MO_3.fastq,fastq,793876754.0,15197870.0,RNAseq hand2FACS rtf1MO 3.fastq,0:52.24,A:208793415;C:174763420;G:174630814;T:235479388;N:209717,52,,,,208793415,174763420,174630814,235479388,209717,SRX21749012,SRS18856550,SRA1709841,"University of California, Los Angeles|Molecular, Cell, and Developmental Biology","University of California, Los Angeles",1,0.88868,,0.1097,,0.77644,,0.51136,,53,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-09-11,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
26500,SRR26031756,SRX21749011,SRS18856545,SRP459729,PRJNA1015262,Rtf1 dependent transcriptional pausing regulates cardiogenesis,PRJNA1015262,Other,During heart development  an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II  as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis  we found that Rtf1 is essential for cardiogenesis and that without xxx activity  cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain  which confers interaction with the pausing/elongation factor Spt5  was required for Rtf1's ability to support cardiac progenitor formation  while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced  suggesting a reduction in transcriptional pausing. Intriguingly  pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.,,,,,RNAseq hand2FACS rtf1MO 2,,strain:TgBAChand2:EGFPpd24|dev stage:10 12 somite stage|collection date:2020 07 07|geo loc name:USA:California Los Angeles|sex:n/a|tissue:hand2:GFP positive cells|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of hand2:GFP positive cells from 10 12 somite stage zebrafish embryos,M2,MO2,NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina from 5 10 ng input RNA,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP459729,,,RNAseq_hand2FACS_rtf1MO_2.fastq,fastq,864787205.0,16568310.0,RNAseq hand2FACS rtf1MO 2.fastq,0:52.20,A:227648729;C:189720880;G:190025417;T:257026454;N:365725,52,,,,227648729,189720880,190025417,257026454,365725,SRX21749011,SRS18856545,SRA1709841,"University of California, Los Angeles|Molecular, Cell, and Developmental Biology","University of California, Los Angeles",1,0.87433,,0.10781,,0.77366,,0.50792,,53,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-09-11,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
26501,SRR26031757,SRX21749010,SRS18856549,SRP459729,PRJNA1015262,Rtf1 dependent transcriptional pausing regulates cardiogenesis,PRJNA1015262,Other,During heart development  an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II  as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis  we found that Rtf1 is essential for cardiogenesis and that without xxx activity  cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain  which confers interaction with the pausing/elongation factor Spt5  was required for Rtf1's ability to support cardiac progenitor formation  while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced  suggesting a reduction in transcriptional pausing. Intriguingly  pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.,,,,,RNAseq hand2FACS rtf1MO 1,,strain:TgBAChand2:EGFPpd24|dev stage:10 12 somite stage|collection date:2020 03 04|geo loc name:USA:California Los Angeles|sex:n/a|tissue:hand2:GFP positive cells|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of hand2:GFP positive cells from 10 12 somite stage zebrafish embryos,M1,MO1,NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina from 5 10 ng input RNA,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP459729,,,RNAseq_hand2FACS_rtf1MO_1.fastq,fastq,821983134.0,15737564.0,RNAseq hand2FACS rtf1MO 1.fastq,0:52.23,A:216610704;C:179969953;G:180145537;T:245093230;N:163710,52,,,,216610704,179969953,180145537,245093230,163710,SRX21749010,SRS18856549,SRA1709841,"University of California, Los Angeles|Molecular, Cell, and Developmental Biology","University of California, Los Angeles",1,0.88099,,0.09837,,0.78007,,0.50262,,53,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-09-11,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
26502,SRR26031758,SRX21749009,SRS18856546,SRP459729,PRJNA1015262,Rtf1 dependent transcriptional pausing regulates cardiogenesis,PRJNA1015262,Other,During heart development  an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II  as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis  we found that Rtf1 is essential for cardiogenesis and that without xxx activity  cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain  which confers interaction with the pausing/elongation factor Spt5  was required for Rtf1's ability to support cardiac progenitor formation  while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced  suggesting a reduction in transcriptional pausing. Intriguingly  pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.,,,,,RNAseq hand2FACS control 3,,strain:TgBAChand2:EGFPpd24|dev stage:10 12 somite stage|collection date:2020 02 26|geo loc name:USA:California Los Angeles|sex:n/a|tissue:hand2:GFP positive cells|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of hand2:GFP positive cells from 10 12 somite stage zebrafish embryos,C3,CTL3,NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina from 5 10 ng input RNA,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP459729,,,RNAseq_hand2FACS_control_3.fastq,fastq,880285441.0,16931477.0,RNAseq hand2FACS control 3.fastq,0:51.99,A:233959122;C:192477087;G:190893530;T:262700285;N:255417,51,,,,233959122,192477087,190893530,262700285,255417,SRX21749009,SRS18856546,SRA1709841,"University of California, Los Angeles|Molecular, Cell, and Developmental Biology","University of California, Los Angeles",1,0.90285,,0.10232,,0.76982,,0.50837,,53,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-09-11,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
26503,SRR26031759,SRX21749008,SRS18856548,SRP459729,PRJNA1015262,Rtf1 dependent transcriptional pausing regulates cardiogenesis,PRJNA1015262,Other,During heart development  an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II  as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis  we found that Rtf1 is essential for cardiogenesis and that without xxx activity  cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain  which confers interaction with the pausing/elongation factor Spt5  was required for Rtf1's ability to support cardiac progenitor formation  while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced  suggesting a reduction in transcriptional pausing. Intriguingly  pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.,,,,,RNAseq hand2FACS control 2,,strain:TgBAChand2:EGFPpd24|dev stage:10 12 somite stage|collection date:2019 12 19|geo loc name:USA:California Los Angeles|sex:n/a|tissue:hand2:GFP positive cells|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of hand2:GFP positive cells from 10 12 somite stage zebrafish embryos,C2,CTL2,NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina from 5 10 ng input RNA,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP459729,,,RNAseq_hand2FACS_control_2.fastq,fastq,317458963.0,6417814.0,RNAseq hand2FACS control 2.fastq,0:49.47,A:83925064;C:70621123;G:68872886;T:93923129;N:116761,49,,,,83925064,70621123,68872886,93923129,116761,SRX21749008,SRS18856548,SRA1709841,"University of California, Los Angeles|Molecular, Cell, and Developmental Biology","University of California, Los Angeles",1,0.85587,,0.08493,,0.75558,,0.51678,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-09-11,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
26504,SRR26031760,SRX21749007,SRS18856543,SRP459729,PRJNA1015262,Rtf1 dependent transcriptional pausing regulates cardiogenesis,PRJNA1015262,Other,During heart development  an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II  as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis  we found that Rtf1 is essential for cardiogenesis and that without xxx activity  cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain  which confers interaction with the pausing/elongation factor Spt5  was required for Rtf1's ability to support cardiac progenitor formation  while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced  suggesting a reduction in transcriptional pausing. Intriguingly  pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.,,,,,RNAseq hand2FACS control 1,,strain:TgBAChand2:EGFPpd24|dev stage:10 12 somite stage|collection date:2019 11 29|geo loc name:USA:California Los Angeles|sex:n/a|tissue:hand2:GFP positive cells|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of hand2:GFP positive cells from 10 12 somite stage zebrafish embryos,C1,CTL1,NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina from 5 10 ng input RNA,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP459729,,,RNAseq_hand2FACS_control_1.fastq,fastq,448273888.0,9055865.0,RNAseq hand2FACS control 1.fastq,0:49.50,A:119317727;C:99863109;G:96352533;T:132659621;N:80898,49,,,,119317727,99863109,96352533,132659621,80898,SRX21749007,SRS18856543,SRA1709841,"University of California, Los Angeles|Molecular, Cell, and Developmental Biology","University of California, Los Angeles",1,0.88622,,0.09573,,0.76086,,0.42689,,49,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-09-11,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
34551,SRR32104356,SRX27449954,SRS23876475,SRP559533,PRJNA1214751,Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq],GSE287815,Transcriptome Analysis,During vertebrate development  the heart primarily arises from mesoderm  with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives.  Here  by integrating bulk and single cell RNAseq with ATAC seq  we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1  sox9a  tfap2a and ets1. Notably  we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore  expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together  our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination  with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry   were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.,,,,17hpf Positive CNC 3,GSM8751787,,source name:cardiac neural crest from midbrain hindbrain boundary to somite 6|tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6|cell type:migratory cardiac neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry +|geo loc name:missing|collection date:missing,17hpf Positive CNC 3,Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples,cardiac neural crest from midbrain hindbrain boundary to somite 6,,mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.,,tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6|cell type:migratory cardiac neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry +,GSM8751787,GSM8751787: 17hpf Positive CNC 3; Danio rerio; RNA Seq,GSM8751787 r1,GSM8751787,1,mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP559533,,,Sox10_pos_17hpf_CNC_3_22028_combined_filtered.fastq.gz,fastq,5836253400.0,58362534.0,GSM8751787 r1,0:100,A:1666874971;C:1250406201;G:1263794016;T:1655113176;N:65036,100,,,,1666874971,1250406201,1263794016,1655113176,65036,SRX27449954,SRS23876475,SRA2058978,"Martik Lab, Molecular and Cell Biology, University of California Berkeley","Martik Lab, Molecular and Cell Biology, University of California Berkeley",,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2025-01-23,Segmentation,Embryo,Multi-tissue,Multi-system
34552,SRR32104357,SRX27449953,SRS23876474,SRP559533,PRJNA1214751,Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq],GSE287815,Transcriptome Analysis,During vertebrate development  the heart primarily arises from mesoderm  with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives.  Here  by integrating bulk and single cell RNAseq with ATAC seq  we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1  sox9a  tfap2a and ets1. Notably  we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore  expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together  our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination  with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry   were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.,,,,17hpf Positive CNC 2,GSM8751786,,source name:cardiac neural crest from midbrain hindbrain boundary to somite 6|tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6|cell type:migratory cardiac neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry +|geo loc name:missing|collection date:missing,17hpf Positive CNC 2,Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples,cardiac neural crest from midbrain hindbrain boundary to somite 6,,mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.,,tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6|cell type:migratory cardiac neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry +,GSM8751786,GSM8751786: 17hpf Positive CNC 2; Danio rerio; RNA Seq,GSM8751786 r1,GSM8751786,1,mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP559533,,,Sox10_pos_17hpf_CNC_2_21338_combined_filtered.fastq.gz,fastq,2444486550.0,48889731.0,GSM8751786 r1,0:50,A:706384494;C:515182895;G:525593789;T:697319091;N:6281,50,,,,706384494,515182895,525593789,697319091,6281,SRX27449953,SRS23876474,SRA2058978,"Martik Lab, Molecular and Cell Biology, University of California Berkeley","Martik Lab, Molecular and Cell Biology, University of California Berkeley",,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2025-01-23,Segmentation,Embryo,Multi-tissue,Multi-system
34553,SRR32104358,SRX27449952,SRS23876472,SRP559533,PRJNA1214751,Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq],GSE287815,Transcriptome Analysis,During vertebrate development  the heart primarily arises from mesoderm  with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives.  Here  by integrating bulk and single cell RNAseq with ATAC seq  we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1  sox9a  tfap2a and ets1. Notably  we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore  expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together  our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination  with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry   were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.,,,,17hpf Positive CNC 1,GSM8751785,,source name:cardiac neural crest from midbrain hindbrain boundary to somite 6|tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6|cell type:migratory cardiac neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry +|geo loc name:missing|collection date:missing,17hpf Positive CNC 1,Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples,cardiac neural crest from midbrain hindbrain boundary to somite 6,,mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.,,tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6|cell type:migratory cardiac neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry +,GSM8751785,GSM8751785: 17hpf Positive CNC 1; Danio rerio; RNA Seq,GSM8751785 r1,GSM8751785,1,mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP559533,,,Sox10_pos_17hpf_CNC_1_21309_combined_filtered.fastq.gz,fastq,3136080950.0,62721619.0,GSM8751785 r1,0:50,A:867446661;C:707750289;G:716376649;T:844460193;N:47158,50,,,,867446661,707750289,716376649,844460193,47158,SRX27449952,SRS23876472,SRA2058978,"Martik Lab, Molecular and Cell Biology, University of California Berkeley","Martik Lab, Molecular and Cell Biology, University of California Berkeley",,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2025-01-23,Segmentation,Embryo,Multi-tissue,Multi-system
34554,SRR32104359,SRX27449951,SRS23876473,SRP559533,PRJNA1214751,Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq],GSE287815,Transcriptome Analysis,During vertebrate development  the heart primarily arises from mesoderm  with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives.  Here  by integrating bulk and single cell RNAseq with ATAC seq  we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1  sox9a  tfap2a and ets1. Notably  we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore  expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together  our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination  with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry   were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.,,,,17hpf Negative CNC 3,GSM8751784,,source name:non neural crest from midbrain hindbrain boundary to somite 6|tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry  |geo loc name:missing|collection date:missing,17hpf Negative CNC 3,Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples,non neural crest from midbrain hindbrain boundary to somite 6,,mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.,,tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry  ,GSM8751784,GSM8751784: 17hpf Negative CNC 3; Danio rerio; RNA Seq,GSM8751784 r1,GSM8751784,1,mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP559533,,,Sox10_neg_17hpf_CNC_3_22029_combined_filtered.fastq.gz,fastq,6549316700.0,65493167.0,GSM8751784 r1,0:100,A:1904137226;C:1372226751;G:1395882591;T:1876995541;N:74591,100,,,,1904137226,1372226751,1395882591,1876995541,74591,SRX27449951,SRS23876473,SRA2058978,"Martik Lab, Molecular and Cell Biology, University of California Berkeley","Martik Lab, Molecular and Cell Biology, University of California Berkeley",,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2025-01-23,Segmentation,Embryo,Brain,Nervous System
34555,SRR32104360,SRX27449950,SRS23876471,SRP559533,PRJNA1214751,Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq],GSE287815,Transcriptome Analysis,During vertebrate development  the heart primarily arises from mesoderm  with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives.  Here  by integrating bulk and single cell RNAseq with ATAC seq  we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1  sox9a  tfap2a and ets1. Notably  we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore  expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together  our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination  with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry   were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.,,,,17hpf Negative CNC 2,GSM8751783,,source name:non neural crest from midbrain hindbrain boundary to somite 6|tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry  |geo loc name:missing|collection date:missing,17hpf Negative CNC 2,Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples,non neural crest from midbrain hindbrain boundary to somite 6,,mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.,,tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry  ,GSM8751783,GSM8751783: 17hpf Negative CNC 2; Danio rerio; RNA Seq,GSM8751783 r1,GSM8751783,1,mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP559533,,,Sox10_neg_17hpf_CNC_2_21339_combined_filtered.fastq.gz,fastq,2595442300.0,51908846.0,GSM8751783 r1,0:50,A:735396784;C:561568693;G:572114011;T:726356371;N:6441,50,,,,735396784,561568693,572114011,726356371,6441,SRX27449950,SRS23876471,SRA2058978,"Martik Lab, Molecular and Cell Biology, University of California Berkeley","Martik Lab, Molecular and Cell Biology, University of California Berkeley",,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2025-01-23,Segmentation,Embryo,Brain,Nervous System
34556,SRR32104361,SRX27449949,SRS23876470,SRP559533,PRJNA1214751,Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq],GSE287815,Transcriptome Analysis,During vertebrate development  the heart primarily arises from mesoderm  with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives.  Here  by integrating bulk and single cell RNAseq with ATAC seq  we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1  sox9a  tfap2a and ets1. Notably  we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore  expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together  our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination  with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry   were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.,,,,17hpf Negative CNC 1,GSM8751782,,source name:non neural crest from midbrain hindbrain boundary to somite 6|tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry  |geo loc name:missing|collection date:missing,17hpf Negative CNC 1,Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples,non neural crest from midbrain hindbrain boundary to somite 6,,mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.,,tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry  ,GSM8751782,GSM8751782: 17hpf Negative CNC 1; Danio rerio; RNA Seq,GSM8751782 r1,GSM8751782,1,mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP559533,,,Sox10_neg_17hpf_CNC_1_21310_combined_filtered.fastq.gz,fastq,2554400850.0,51088017.0,GSM8751782 r1,0:50,A:739730182;C:537827580;G:551508245;T:725296198;N:38645,50,,,,739730182,537827580,551508245,725296198,38645,SRX27449949,SRS23876470,SRA2058978,"Martik Lab, Molecular and Cell Biology, University of California Berkeley","Martik Lab, Molecular and Cell Biology, University of California Berkeley",,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2025-01-23,Segmentation,Embryo,Brain,Nervous System
34977,SRR32588734,SRX27895217,SRS24266222,SRP568323,PRJNA1232602,Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains,PRJNA1232602,Other,In this study  Iso Seq was performed on different zebrafish body organs  enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues  including the brain  testis  liver  eye  muscle  ovary  inner ear and kidney  to identify novel isoforms  tissue specific transcripts  and alternative splicing events. We also made available the Iso Seq data from embryos from different time points  hpf  0  6  12  and 24. This dataset enhances gene annotation  improves reference genome annotations  and provides insights into zebrafish organ specific gene expression.,,,,Iso Seq RNA from embryo zero hpf,C2 F2 12,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:time 12 hours|dev stage:Embyoys|collection date:2024 06|geo loc name:USA|sex:male|tissue:muscle|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from embyo 12 hpf,C2 F2 12,C2 F2 12,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m54313U_231111_191642.hifi_reads.flnc.fastq.gz,fastq,7627931284.0,3897936.0,m54313U 231111 191642.hifi reads.flnc.fastq.gz,0:1956.92,A:2146633241;C:1706673950;G:1799625470;T:1974998623;N:0,1956,,,,2146633241,1706673950,1799625470,1974998623,0,SRX27895217,SRS24266222,SRA2089085,National Human Genome Research Institute|Translational and Functional Genomics Branch,National Human Genome Research Institute National Human Genome Research Institute,,,,,,,,,,,,T,,long read,pacbio,pacbio_modern,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2025-03-06,Segmentation,Embryo,Muscle,Muscular System
35578,SRR32928209,SRX28203108,SRS24552814,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.,,expt1.12.bead.P1.H3.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:bead|replicate:22|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  bead dissociation  replicate 22,22,22,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.bead.P1.H3.fq.gz,fastq,1098724956.0,13080059.0,expt1.12.bead.P1.H3.fq.gz,0:84,A:504518768;C:161484922;G:183535740;T:248983693;N:201833,84,,,,504518768,161484922,183535740,248983693,201833,SRX28203108,SRS24552814,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35589,SRR32928220,SRX28203097,SRS24552805,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.,,expt1.12.bead.P1.G5.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:bead|replicate:21|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  bead dissociation  replicate 21,21,21,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.bead.P1.G5.fq.gz,fastq,561441468.0,6683827.0,expt1.12.bead.P1.G5.fq.gz,0:84,A:234940814;C:88191402;G:96728695;T:141478801;N:101756,84,,,,234940814,88191402,96728695,141478801,101756,SRX28203097,SRS24552805,SRA2104467,University of Washington|Genome Sciences,University of Washington,1,0.50019,,0.4034,,0.85959,,0.49922,,84,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35590,SRR32928221,SRX28203096,SRS24552802,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.,,expt1.12.bead.P1.A5.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:bead|replicate:3|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  bead dissociation  replicate 3,3,3,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.bead.P1.A5.fq.gz,fastq,490718256.0,5841884.0,expt1.12.bead.P1.A5.fq.gz,0:84,A:207644706;C:75241234;G:85463387;T:122279492;N:89437,84,,,,207644706,75241234,85463387,122279492,89437,SRX28203096,SRS24552802,SRA2104467,University of Washington|Genome Sciences,University of Washington,1,0.50293,,0.39872,,0.85916,,0.50964,,84,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35601,SRR32928232,SRX28203085,SRS24552792,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.,,expt1.12.bead.P1.G4.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:bead|replicate:20|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  bead dissociation  replicate 20,20,20,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.bead.P1.G4.fq.gz,fastq,515444412.0,6136243.0,expt1.12.bead.P1.G4.fq.gz,0:84,A:215225166;C:80082472;G:88915670;T:131127655;N:93449,84,,,,215225166,80082472,88915670,131127655,93449,SRX28203085,SRS24552792,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35604,SRR32928235,SRX28203082,SRS24552787,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.,,expt1.12.bead.P1.D3.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:bead|replicate:10|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  bead dissociation  replicate 10,10,10,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.bead.P1.D3.fq.gz,fastq,629856780.0,7498295.0,expt1.12.bead.P1.D3.fq.gz,0:84,A:273859568;C:96165073;G:108875157;T:150842309;N:114673,84,,,,273859568,96165073,108875157,150842309,114673,SRX28203082,SRS24552787,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35615,SRR32928246,SRX28203071,SRS24552777,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.,,expt1.12.bead.P1.C5.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:bead|replicate:9|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  bead dissociation  replicate 9,9,9,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.bead.P1.C5.fq.gz,fastq,461470968.0,5493702.0,expt1.12.bead.P1.C5.fq.gz,0:84,A:188895160;C:72428601;G:79983141;T:120080226;N:83840,84,,,,188895160,72428601,79983141,120080226,83840,SRX28203071,SRS24552777,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35626,SRR32928257,SRX28203060,SRS24552766,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.,,expt1.12.bead.P1.C4.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:bead|replicate:8|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  bead dissociation  replicate 8,8,8,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.bead.P1.C4.fq.gz,fastq,451683456.0,5377184.0,expt1.12.bead.P1.C4.fq.gz,0:84,A:188077465;C:71524093;G:79688471;T:112311489;N:81938,84,,,,188077465,71524093,79688471,112311489,81938,SRX28203060,SRS24552766,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35636,SRR32928267,SRX28203050,SRS24552757,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.,,expt1.12.bead.P1.G3.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:bead|replicate:19|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  bead dissociation  replicate 19,19,19,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.bead.P1.G3.fq.gz,fastq,615903456.0,7332184.0,expt1.12.bead.P1.G3.fq.gz,0:84,A:262286368;C:93846834;G:105834930;T:153823652;N:111672,84,,,,262286368,93846834,105834930,153823652,111672,SRX28203050,SRS24552757,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35647,SRR32928278,SRX28203039,SRS24552745,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.,,expt1.12.bead.P1.F5.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:bead|replicate:18|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  bead dissociation  replicate 18,18,18,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.bead.P1.F5.fq.gz,fastq,470902236.0,5605979.0,expt1.12.bead.P1.F5.fq.gz,0:84,A:195943515;C:74075531;G:81085740;T:119712297;N:85153,84,,,,195943515,74075531,81085740,119712297,85153,SRX28203039,SRS24552745,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35651,SRR32928360,SRX28203035,SRS24552741,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.,,expt1.12.enzymatic.P18.F9.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:enzymatic|replicate:23|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 05|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  enzymatic dissociation  replicate 23,47,47,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.enzymatic.P18.F9.fq.gz,fastq,65463048.0,779322.0,expt1.12.enzymatic.P18.F9.fq.gz,0:84,A:26680121;C:10235479;G:11460930;T:17074778;N:11740,84,,,,26680121,10235479,11460930,17074778,11740,SRX28203035,SRS24552741,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35652,SRR32928282,SRX28203034,SRS24552740,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.,,expt1.12.enzymatic.P18.F12.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:enzymatic|replicate:22|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 05|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  enzymatic dissociation  replicate 22,46,46,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.enzymatic.P18.F12.fq.gz,fastq,78852564.0,938721.0,expt1.12.enzymatic.P18.F12.fq.gz,0:84,A:31835768;C:12617722;G:13918857;T:20465816;N:14401,84,,,,31835768,12617722,13918857,20465816,14401,SRX28203034,SRS24552740,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35653,SRR32928283,SRX28203033,SRS24552739,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.,,expt1.12.enzymatic.P18.F11.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:enzymatic|replicate:21|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 05|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  enzymatic dissociation  replicate 21,45,45,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.enzymatic.P18.F11.fq.gz,fastq,48518148.0,577597.0,expt1.12.enzymatic.P18.F11.fq.gz,0:84,A:19703045;C:7650268;G:8411266;T:12744788;N:8781,84,,,,19703045,7650268,8411266,12744788,8781,SRX28203033,SRS24552739,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35654,SRR32928284,SRX28203032,SRS24552738,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.,,expt1.12.enzymatic.P18.F10.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:enzymatic|replicate:20|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 05|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  enzymatic dissociation  replicate 20,44,44,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.enzymatic.P18.F10.fq.gz,fastq,69879012.0,831893.0,expt1.12.enzymatic.P18.F10.fq.gz,0:84,A:28102461;C:11066956;G:12285446;T:18411491;N:12658,84,,,,28102461,11066956,12285446,18411491,12658,SRX28203032,SRS24552738,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35655,SRR32928285,SRX28203031,SRS24552737,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.,,expt1.12.enzymatic.P18.E9.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:enzymatic|replicate:19|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 05|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  enzymatic dissociation  replicate 19,43,43,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.enzymatic.P18.E9.fq.gz,fastq,73466652.0,874603.0,expt1.12.enzymatic.P18.E9.fq.gz,0:84,A:30049012;C:11512079;G:12932629;T:18959717;N:13215,84,,,,30049012,11512079,12932629,18959717,13215,SRX28203031,SRS24552737,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35656,SRR32928286,SRX28203030,SRS24552736,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.,,expt1.12.enzymatic.P18.E12.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:enzymatic|replicate:18|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 05|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  enzymatic dissociation  replicate 18,42,42,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.enzymatic.P18.E12.fq.gz,fastq,46559856.0,554284.0,expt1.12.enzymatic.P18.E12.fq.gz,0:84,A:18707105;C:7369117;G:8285427;T:12189718;N:8489,84,,,,18707105,7369117,8285427,12189718,8489,SRX28203030,SRS24552736,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35657,SRR32928287,SRX28203029,SRS24552735,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.,,expt1.12.enzymatic.P18.E11.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:enzymatic|replicate:17|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 05|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  enzymatic dissociation  replicate 17,41,41,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.enzymatic.P18.E11.fq.gz,fastq,50957256.0,606634.0,expt1.12.enzymatic.P18.E11.fq.gz,0:84,A:20649122;C:8019708;G:8855871;T:13423308;N:9247,84,,,,20649122,8019708,8855871,13423308,9247,SRX28203029,SRS24552735,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35658,SRR32928288,SRX28203028,SRS24552733,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.,,expt1.12.bead.P1.B4.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:bead|replicate:5|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  bead dissociation  replicate 5,5,5,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.bead.P1.B4.fq.gz,fastq,615855072.0,7331608.0,expt1.12.bead.P1.B4.fq.gz,0:84,A:259160966;C:97496208;G:105354232;T:153731811;N:111855,84,,,,259160966,97496208,105354232,153731811,111855,SRX28203028,SRS24552733,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35659,SRR32928289,SRX28203027,SRS24552734,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.,,expt1.12.enzymatic.P18.E10.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:enzymatic|replicate:16|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 05|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  enzymatic dissociation  replicate 16,40,40,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.enzymatic.P18.E10.fq.gz,fastq,69996948.0,833297.0,expt1.12.enzymatic.P18.E10.fq.gz,0:84,A:28524785;C:10983741;G:12267049;T:18208598;N:12775,84,,,,28524785,10983741,12267049,18208598,12775,SRX28203027,SRS24552734,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35660,SRR32928290,SRX28203026,SRS24552732,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.,,expt1.12.enzymatic.P18.D9.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:enzymatic|replicate:15|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 05|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  enzymatic dissociation  replicate 15,39,39,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.enzymatic.P18.D9.fq.gz,fastq,80656128.0,960192.0,expt1.12.enzymatic.P18.D9.fq.gz,0:84,A:33056742;C:12587584;G:14103652;T:20893622;N:14528,84,,,,33056742,12587584,14103652,20893622,14528,SRX28203026,SRS24552732,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35661,SRR32928291,SRX28203025,SRS24552731,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.,,expt1.12.enzymatic.P18.D12.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:enzymatic|replicate:14|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 05|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  enzymatic dissociation  replicate 14,38,38,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.enzymatic.P18.D12.fq.gz,fastq,51854880.0,617320.0,expt1.12.enzymatic.P18.D12.fq.gz,0:84,A:21118580;C:8107436;G:9141499;T:13477955;N:9410,84,,,,21118580,8107436,9141499,13477955,9410,SRX28203025,SRS24552731,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35662,SRR32928292,SRX28203024,SRS24552730,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.,,expt1.12.enzymatic.P18.D11.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:enzymatic|replicate:13|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 05|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  enzymatic dissociation  replicate 13,37,37,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.enzymatic.P18.D11.fq.gz,fastq,69585180.0,828395.0,expt1.12.enzymatic.P18.D11.fq.gz,0:84,A:27942625;C:11138327;G:12428227;T:18063636;N:12365,84,,,,27942625,11138327,12428227,18063636,12365,SRX28203024,SRS24552730,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35663,SRR32928293,SRX28203023,SRS24552728,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.,,expt1.12.enzymatic.P18.D10.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:enzymatic|replicate:12|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 05|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  enzymatic dissociation  replicate 12,36,36,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.enzymatic.P18.D10.fq.gz,fastq,83209140.0,990585.0,expt1.12.enzymatic.P18.D10.fq.gz,0:84,A:33904149;C:13026403;G:14694719;T:21568684;N:15185,84,,,,33904149,13026403,14694719,21568684,15185,SRX28203023,SRS24552728,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35664,SRR32928294,SRX28203022,SRS24552729,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.,,expt1.12.enzymatic.P18.C9.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:enzymatic|replicate:11|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 05|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  enzymatic dissociation  replicate 11,35,35,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.enzymatic.P18.C9.fq.gz,fastq,66058944.0,786416.0,expt1.12.enzymatic.P18.C9.fq.gz,0:84,A:26767185;C:10402625;G:11677135;T:17200217;N:11782,84,,,,26767185,10402625,11677135,17200217,11782,SRX28203022,SRS24552729,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35665,SRR32928295,SRX28203021,SRS24552727,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.,,expt1.12.enzymatic.P18.C12.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:enzymatic|replicate:10|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 05|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  enzymatic dissociation  replicate 10,34,34,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.enzymatic.P18.C12.fq.gz,fastq,67107012.0,798893.0,expt1.12.enzymatic.P18.C12.fq.gz,0:84,A:27361705;C:10550674;G:11662564;T:17520032;N:12037,84,,,,27361705,10550674,11662564,17520032,12037,SRX28203021,SRS24552727,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35666,SRR32928296,SRX28203020,SRS24552726,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.,,expt1.12.enzymatic.P18.C11.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:enzymatic|replicate:9|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 05|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  enzymatic dissociation  replicate 9,33,33,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.enzymatic.P18.C11.fq.gz,fastq,67110288.0,798932.0,expt1.12.enzymatic.P18.C11.fq.gz,0:84,A:27218998;C:10636824;G:11732458;T:17509684;N:12324,84,,,,27218998,10636824,11732458,17509684,12324,SRX28203020,SRS24552726,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35667,SRR32928297,SRX28203019,SRS24552725,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.,,expt1.12.enzymatic.P18.C10.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:enzymatic|replicate:8|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 05|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  enzymatic dissociation  replicate 8,32,32,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.enzymatic.P18.C10.fq.gz,fastq,102611712.0,1221568.0,expt1.12.enzymatic.P18.C10.fq.gz,0:84,A:41845743;C:16171961;G:18152793;T:26422597;N:18618,84,,,,41845743,16171961,18152793,26422597,18618,SRX28203019,SRS24552725,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35668,SRR32928298,SRX28203018,SRS24552723,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.,,expt1.12.enzymatic.P18.B9.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:enzymatic|replicate:7|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 05|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  enzymatic dissociation  replicate 7,31,31,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.enzymatic.P18.B9.fq.gz,fastq,54630408.0,650362.0,expt1.12.enzymatic.P18.B9.fq.gz,0:84,A:22296512;C:8610694;G:9541949;T:14171511;N:9742,84,,,,22296512,8610694,9541949,14171511,9742,SRX28203018,SRS24552723,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35669,SRR32928299,SRX28203017,SRS24552724,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.,,expt1.12.bead.P1.B3.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:bead|replicate:4|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  bead dissociation  replicate 4,4,4,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.bead.P1.B3.fq.gz,fastq,568189524.0,6764161.0,expt1.12.bead.P1.B3.fq.gz,0:84,A:241467351;C:85886692;G:102112476;T:138620034;N:102971,84,,,,241467351,85886692,102112476,138620034,102971,SRX28203017,SRS24552724,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35670,SRR32928300,SRX28203016,SRS24552722,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.,,expt1.12.enzymatic.P18.B12.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:enzymatic|replicate:6|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 05|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  enzymatic dissociation  replicate 6,30,30,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.enzymatic.P18.B12.fq.gz,fastq,67131372.0,799183.0,expt1.12.enzymatic.P18.B12.fq.gz,0:84,A:27300612;C:10648108;G:11936585;T:17233877;N:12190,84,,,,27300612,10648108,11936585,17233877,12190,SRX28203016,SRS24552722,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35671,SRR32928301,SRX28203015,SRS24552721,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.,,expt1.12.enzymatic.P18.B10.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:enzymatic|replicate:5|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 05|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  enzymatic dissociation  replicate 5,29,29,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.enzymatic.P18.B10.fq.gz,fastq,97941312.0,1165968.0,expt1.12.enzymatic.P18.B10.fq.gz,0:84,A:39872197;C:15359831;G:17187351;T:25504090;N:17843,84,,,,39872197,15359831,17187351,25504090,17843,SRX28203015,SRS24552721,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35672,SRR32928302,SRX28203014,SRS24552720,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.,,expt1.12.enzymatic.P18.A9.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:enzymatic|replicate:4|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 05|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  enzymatic dissociation  replicate 4,28,28,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.enzymatic.P18.A9.fq.gz,fastq,42532980.0,506345.0,expt1.12.enzymatic.P18.A9.fq.gz,0:84,A:17083834;C:6733985;G:7597780;T:11109522;N:7859,84,,,,17083834,6733985,7597780,11109522,7859,SRX28203014,SRS24552720,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35673,SRR32928303,SRX28203013,SRS24552719,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.,,expt1.12.enzymatic.P18.A12.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:enzymatic|replicate:3|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 05|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  enzymatic dissociation  replicate 3,27,27,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.enzymatic.P18.A12.fq.gz,fastq,58298436.0,694029.0,expt1.12.enzymatic.P18.A12.fq.gz,0:84,A:23520631;C:9225789;G:10260115;T:15281461;N:10440,84,,,,23520631,9225789,10260115,15281461,10440,SRX28203013,SRS24552719,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35674,SRR32928304,SRX28203012,SRS24552718,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.,,expt1.12.enzymatic.P18.A11.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:enzymatic|replicate:2|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 05|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  enzymatic dissociation  replicate 2,26,26,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.enzymatic.P18.A11.fq.gz,fastq,66007872.0,785808.0,expt1.12.enzymatic.P18.A11.fq.gz,0:84,A:26815123;C:10385722;G:11918948;T:16876066;N:12013,84,,,,26815123,10385722,11918948,16876066,12013,SRX28203012,SRS24552718,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35675,SRR32928305,SRX28203011,SRS24552716,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.,,expt1.12.enzymatic.P18.A10.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:enzymatic|replicate:1|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 05|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  enzymatic dissociation  replicate 1,25,25,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.enzymatic.P18.A10.fq.gz,fastq,73050432.0,869648.0,expt1.12.enzymatic.P18.A10.fq.gz,0:84,A:29513583;C:11740544;G:13034199;T:18749104;N:13002,84,,,,29513583,11740544,13034199,18749104,13002,SRX28203011,SRS24552716,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35676,SRR32928306,SRX28203010,SRS24552717,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.,,expt1.12.bead.P1.H5.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:bead|replicate:24|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  bead dissociation  replicate 24,24,24,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.bead.P1.H5.fq.gz,fastq,489818196.0,5831169.0,expt1.12.bead.P1.H5.fq.gz,0:84,A:203321748;C:75868277;G:86614922;T:123923946;N:89303,84,,,,203321748,75868277,86614922,123923946,89303,SRX28203010,SRS24552717,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35677,SRR32928307,SRX28203009,SRS24552715,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.,,expt1.12.bead.P1.H4.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:bead|replicate:23|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  bead dissociation  replicate 23,23,23,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.bead.P1.H4.fq.gz,fastq,669600540.0,7971435.0,expt1.12.bead.P1.H4.fq.gz,0:84,A:291253156;C:104575362;G:115118701;T:158531876;N:121445,84,,,,291253156,104575362,115118701,158531876,121445,SRX28203009,SRS24552715,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35684,SRR32928315,SRX28203002,SRS24552708,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.,,expt1.12.bead.P1.E5.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:bead|replicate:15|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  bead dissociation  replicate 15,15,15,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.bead.P1.E5.fq.gz,fastq,492289224.0,5860586.0,expt1.12.bead.P1.E5.fq.gz,0:84,A:205317888;C:78252282;G:84568048;T:124062066;N:88940,84,,,,205317888,78252282,84568048,124062066,88940,SRX28203002,SRS24552708,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35695,SRR32928326,SRX28202991,SRS24552697,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.,,expt1.12.bead.P1.E4.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:bead|replicate:14|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  bead dissociation  replicate 14,14,14,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.bead.P1.E4.fq.gz,fastq,524015940.0,6238285.0,expt1.12.bead.P1.E4.fq.gz,0:84,A:220133002;C:81423922;G:90135665;T:132227583;N:95768,84,,,,220133002,81423922,90135665,132227583,95768,SRX28202991,SRS24552697,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35713,SRR32928344,SRX28202973,SRS24552679,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.,,expt1.12.bead.P1.C3.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:bead|replicate:7|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  bead dissociation  replicate 7,7,7,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.bead.P1.C3.fq.gz,fastq,567597240.0,6757110.0,expt1.12.bead.P1.C3.fq.gz,0:84,A:239025884;C:87568932;G:98640895;T:142258194;N:103335,84,,,,239025884,87568932,98640895,142258194,103335,SRX28202973,SRS24552679,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35719,SRR32928350,SRX28202967,SRS24552673,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.,,expt1.12.enzymatic.P18.H9.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:enzymatic|replicate:31|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 05|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  enzymatic dissociation  replicate 31,55,55,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.enzymatic.P18.H9.fq.gz,fastq,84094920.0,1001130.0,expt1.12.enzymatic.P18.H9.fq.gz,0:84,A:34491105;C:13066515;G:14851182;T:21670722;N:15396,84,,,,34491105,13066515,14851182,21670722,15396,SRX28202967,SRS24552673,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35720,SRR32928351,SRX28202966,SRS24552671,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.,,expt1.12.enzymatic.P18.H12.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:enzymatic|replicate:30|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 05|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  enzymatic dissociation  replicate 30,54,54,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.enzymatic.P18.H12.fq.gz,fastq,52063620.0,619805.0,expt1.12.enzymatic.P18.H12.fq.gz,0:84,A:20955888;C:8318238;G:9231541;T:13548585;N:9368,84,,,,20955888,8318238,9231541,13548585,9368,SRX28202966,SRS24552671,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35721,SRR32928352,SRX28202965,SRS24552672,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.,,expt1.12.enzymatic.P18.H11.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:enzymatic|replicate:29|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 05|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  enzymatic dissociation  replicate 29,53,53,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.enzymatic.P18.H11.fq.gz,fastq,63054180.0,750645.0,expt1.12.enzymatic.P18.H11.fq.gz,0:84,A:25403586;C:9968979;G:11152412;T:16517630;N:11573,84,,,,25403586,9968979,11152412,16517630,11573,SRX28202965,SRS24552672,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35722,SRR32928353,SRX28202964,SRS24552670,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.,,expt1.12.enzymatic.P18.H10.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:enzymatic|replicate:28|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 05|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  enzymatic dissociation  replicate 28,52,52,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.enzymatic.P18.H10.fq.gz,fastq,73066896.0,869844.0,expt1.12.enzymatic.P18.H10.fq.gz,0:84,A:29577478;C:11430044;G:13081456;T:18964379;N:13539,84,,,,29577478,11430044,13081456,18964379,13539,SRX28202964,SRS24552670,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35723,SRR32928354,SRX28202963,SRS24552668,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.,,expt1.12.enzymatic.P18.G9.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:enzymatic|replicate:27|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 05|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  enzymatic dissociation  replicate 27,51,51,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.enzymatic.P18.G9.fq.gz,fastq,67784388.0,806957.0,expt1.12.enzymatic.P18.G9.fq.gz,0:84,A:27721038;C:10573613;G:11825298;T:17652184;N:12255,84,,,,27721038,10573613,11825298,17652184,12255,SRX28202963,SRS24552668,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35724,SRR32928355,SRX28202962,SRS24552669,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.,,expt1.12.bead.P1.B5.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:bead|replicate:6|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  bead dissociation  replicate 6,6,6,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.bead.P1.B5.fq.gz,fastq,487285512.0,5801018.0,expt1.12.bead.P1.B5.fq.gz,0:84,A:204027986;C:77669721;G:82587888;T:122911394;N:88523,84,,,,204027986,77669721,82587888,122911394,88523,SRX28202962,SRS24552669,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35725,SRR32928356,SRX28202961,SRS24552667,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.,,expt1.12.enzymatic.P18.G12.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:enzymatic|replicate:26|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 05|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  enzymatic dissociation  replicate 26,50,50,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.enzymatic.P18.G12.fq.gz,fastq,74616108.0,888287.0,expt1.12.enzymatic.P18.G12.fq.gz,0:84,A:30090964;C:11788901;G:13262334;T:19460525;N:13384,84,,,,30090964,11788901,13262334,19460525,13384,SRX28202961,SRS24552667,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35726,SRR32928357,SRX28202960,SRS24552666,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.,,expt1.12.enzymatic.P18.G11.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:enzymatic|replicate:25|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 05|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  enzymatic dissociation  replicate 25,49,49,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.enzymatic.P18.G11.fq.gz,fastq,79765140.0,949585.0,expt1.12.enzymatic.P18.G11.fq.gz,0:84,A:32420271;C:12603757;G:14008715;T:20718011;N:14386,84,,,,32420271,12603757,14008715,20718011,14386,SRX28202960,SRS24552666,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35727,SRR32928358,SRX28202959,SRS24552665,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.,,expt1.12.enzymatic.P18.G10.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:enzymatic|replicate:24|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 05|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  enzymatic dissociation  replicate 24,48,48,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.enzymatic.P18.G10.fq.gz,fastq,72218832.0,859748.0,expt1.12.enzymatic.P18.G10.fq.gz,0:84,A:29427915;C:11518942;G:12589461;T:18669344;N:13170,84,,,,29427915,11518942,12589461,18669344,13170,SRX28202959,SRS24552665,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35735,SRR32928367,SRX28202951,SRS24552657,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.,,expt1.12.bead.P1.F4.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:bead|replicate:17|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  bead dissociation  replicate 17,17,17,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.bead.P1.F4.fq.gz,fastq,821460864.0,9779296.0,expt1.12.bead.P1.F4.fq.gz,0:84,A:362411401;C:125923936;G:142209875;T:190765628;N:150024,84,,,,362411401,125923936,142209875,190765628,150024,SRX28202951,SRS24552657,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35746,SRR32928378,SRX28202940,SRS24552646,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.,,expt1.12.bead.P1.F3.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:bead|replicate:16|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  bead dissociation  replicate 16,16,16,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.bead.P1.F3.fq.gz,fastq,828699564.0,9865471.0,expt1.12.bead.P1.F3.fq.gz,0:84,A:364128694;C:128434439;G:144427038;T:191557981;N:151412,84,,,,364128694,128434439,144427038,191557981,151412,SRX28202940,SRS24552646,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35755,SRR32928387,SRX28202931,SRS24552637,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.,,expt1.12.bead.P1.E3.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:bead|replicate:13|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  bead dissociation  replicate 13,13,13,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.bead.P1.E3.fq.gz,fastq,598579044.0,7125941.0,expt1.12.bead.P1.E3.fq.gz,0:84,A:255119096;C:91437932;G:103052971;T:148859942;N:109103,84,,,,255119096,91437932,103052971,148859942,109103,SRX28202931,SRS24552637,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35766,SRR32928398,SRX28202920,SRS24552626,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.,,expt1.12.bead.P1.D5.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:bead|replicate:12|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  bead dissociation  replicate 12,12,12,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.bead.P1.D5.fq.gz,fastq,42649488.0,507732.0,expt1.12.bead.P1.D5.fq.gz,0:84,A:17108076;C:6770511;G:7261827;T:11501214;N:7860,84,,,,17108076,6770511,7261827,11501214,7860,SRX28202920,SRS24552626,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35777,SRR32928409,SRX28202909,SRS24552615,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.,,expt1.12.bead.P1.D4.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:bead|replicate:11|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  bead dissociation  replicate 11,11,11,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.bead.P1.D4.fq.gz,fastq,597160536.0,7109054.0,expt1.12.bead.P1.D4.fq.gz,0:84,A:254555427;C:92314635;G:104385607;T:145796377;N:108490,84,,,,254555427,92314635,104385607,145796377,108490,SRX28202909,SRS24552615,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35778,SRR32928410,SRX28202908,SRS24552614,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.,,expt1.12.bead.P1.A4.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:bead|replicate:2|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  bead dissociation  replicate 2,2,2,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.bead.P1.A4.fq.gz,fastq,514022040.0,6119310.0,expt1.12.bead.P1.A4.fq.gz,0:84,A:218932919;C:78767825;G:88631513;T:127596178;N:93605,84,,,,218932919,78767825,88631513,127596178,93605,SRX28202908,SRS24552614,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
35779,SRR32928411,SRX28202907,SRS24552613,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.,,expt1.12.bead.P1.A3.fq.gz,,seq depth:NA|Experiment id:1|dissociation method:bead|replicate:1|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  bead dissociation  replicate 1,1,1,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt1.12.bead.P1.A3.fq.gz,fastq,622618164.0,7412121.0,expt1.12.bead.P1.A3.fq.gz,0:84,A:265710998;C:96028378;G:108331719;T:152432800;N:114269,84,,,,265710998,96028378,108331719,152432800,114269,SRX28202907,SRS24552613,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Segmentation,Embryo,Whole Organism,All anatomical structures
36412,SRR516557,SRX156352,SRS347211,SRP013950,PRJNA169500,Danio rerio embryonic promoterome,PRJNA169500,Transcriptome Analysis,Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.,,pubmed:24531765,Zebrafish wild type AB strain   embryo 14 somites stage,D. rerio 14 somites embryo,D. rerio 14 somites embryo,,,,,,,,,,,CAGE   D. rerio 14 somites embryo,CAGE   D. rerio 14 somites embryo run2,D. rerio 14 somites embryo,1,,,OTHER,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013950,,,,,73689048.0,2729224.0,CAGE   D. rerio 14 somites embryo run1,0:27,A:19506796;C:16238588;G:21636330;T:16307334;N:0,27,,,,19506796,16238588,21636330,16307334,0,SRX156352,SRS347211,SRA055273,University of Bergen,ZEPROME consortium,1,0.63348,,0.09461,,0.76199,,0.68697,,27,,B,,usable mapping rate,illumina,early_illumina,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2012-06-28,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
36413,SRR516558,SRX156352,SRS347211,SRP013950,PRJNA169500,Danio rerio embryonic promoterome,PRJNA169500,Transcriptome Analysis,Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.,,pubmed:24531765,Zebrafish wild type AB strain   embryo 14 somites stage,D. rerio 14 somites embryo,D. rerio 14 somites embryo,,,,,,,,,,,CAGE   D. rerio 14 somites embryo,CAGE   D. rerio 14 somites embryo run2,D. rerio 14 somites embryo,1,,,OTHER,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013950,,,CAGE_14somites_run2.fastq,fastq,212381811.0,7865993.0,CAGE   D. rerio 14 somites embryo run2,0:27,A:53780820;C:47467464;G:59893810;T:51239717;N:0,27,,,,53780820,47467464,59893810,51239717,0,SRX156352,SRS347211,SRA055273,University of Bergen,ZEPROME consortium,1,0.5278,,0.0806,,0.77589,,0.72881,,27,,B,,usable mapping rate,illumina,early_illumina,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2012-06-28,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
36621,SRR658548,SRX222292,SRS389582,SRP018379,PRJNA188349,Tmem88a Mediates GATA dependent Specification of Cardiomyocyte Progenitors by Restricting Canonical WNT Signaling,GSE44026,Transcriptome Analysis,We sequenced mRNA from zebrafish wild type embryos  gata5 morphants  gata6 morphants  and gata5/6 morphants at bud and 6 somite developmental stages to identify genes co operatively regulated by gata5 and gata6 during cardiomyocyte progenitor specification. Overall design: Samples were collected in duplicate  with 40 embryos per sample. Single 36 base pair reads were sequenced on the Illumina Genome Analyzer IIx,,pubmed:23903195,,Gata5/6 morphant  6 somites  rep 2,GSM1076997,,source name:Whole embryo|development stage:6 somites|genotype/variation:Gata5/6 morphant|tissue:whole embryo,Gata5/6 morphant  6 somites  rep 2,All data processing steps were performed in GobyWeb Dorff  K. C. et al 2013 GobyWeb: simplified management and analysis of gene expression and DNA methylation sequencing data. Quantitative Methods q bio.QM; Genomics q bio.GN. in press arXiv:1211.6666. Alignments performed against Zv9.61 assembly. Genome build: Zv9 Supplementary files format and content: tab separated files include RPKM values for each Sample,Whole embryo,,40 embryos were collected per sample in Trizol Invitrogen  and polyA mRNA was prepared for sequencing using the Illumina mRNA seq Sample Preparation Kit. RNA libraries were prepared for sequencing using standard Illumina protocols,,developmental stage:6 somites|genotype/variation:Gata5/6 morphant|tissue:whole embryo,GSM1076997,GSM1076997: Gata5/6 morphant  6 somites  rep 2; Danio rerio; RNA Seq,GSM1076997 1,,1,,GEO Accession:GSM1076997,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP018379,,,,,1311595308.0,36433203.0,GSM1076997 r1,0:36,A:347481848;C:310758543;G:308678545;T:344219610;N:456762,36,,,,347481848,310758543,308678545,344219610,456762,SRX222292,SRS389582,SRA066053,GEO,Weill Medical College of Cornell University,1,0.92607,,0.10685,,0.71841,,0.4725,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2013-02-02,Segmentation,Embryo,Whole Organism,All anatomical structures
36622,SRR658547,SRX222291,SRS389581,SRP018379,PRJNA188349,Tmem88a Mediates GATA dependent Specification of Cardiomyocyte Progenitors by Restricting Canonical WNT Signaling,GSE44026,Transcriptome Analysis,We sequenced mRNA from zebrafish wild type embryos  gata5 morphants  gata6 morphants  and gata5/6 morphants at bud and 6 somite developmental stages to identify genes co operatively regulated by gata5 and gata6 during cardiomyocyte progenitor specification. Overall design: Samples were collected in duplicate  with 40 embryos per sample. Single 36 base pair reads were sequenced on the Illumina Genome Analyzer IIx,,pubmed:23903195,,Gata5/6 morphant  6 somites  rep 1,GSM1076996,,source name:Whole embryo|development stage:6 somites|genotype/variation:Gata5/6 morphant|tissue:whole embryo,Gata5/6 morphant  6 somites  rep 1,All data processing steps were performed in GobyWeb Dorff  K. C. et al 2013 GobyWeb: simplified management and analysis of gene expression and DNA methylation sequencing data. Quantitative Methods q bio.QM; Genomics q bio.GN. in press arXiv:1211.6666. Alignments performed against Zv9.61 assembly. Genome build: Zv9 Supplementary files format and content: tab separated files include RPKM values for each Sample,Whole embryo,,40 embryos were collected per sample in Trizol Invitrogen  and polyA mRNA was prepared for sequencing using the Illumina mRNA seq Sample Preparation Kit. RNA libraries were prepared for sequencing using standard Illumina protocols,,developmental stage:6 somites|genotype/variation:Gata5/6 morphant|tissue:whole embryo,GSM1076996,GSM1076996: Gata5/6 morphant  6 somites  rep 1; Danio rerio; RNA Seq,GSM1076996 1,,1,,GEO Accession:GSM1076996,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP018379,,,,,1409898888.0,39163858.0,GSM1076996 r1,0:36,A:366177620;C:336963203;G:340777461;T:365470814;N:509790,36,,,,366177620,336963203,340777461,365470814,509790,SRX222291,SRS389581,SRA066053,GEO,Weill Medical College of Cornell University,1,0.8957,,0.08616,,0.72776,,0.4702,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2013-02-02,Segmentation,Embryo,Whole Organism,All anatomical structures
36623,SRR658546,SRX222290,SRS389580,SRP018379,PRJNA188349,Tmem88a Mediates GATA dependent Specification of Cardiomyocyte Progenitors by Restricting Canonical WNT Signaling,GSE44026,Transcriptome Analysis,We sequenced mRNA from zebrafish wild type embryos  gata5 morphants  gata6 morphants  and gata5/6 morphants at bud and 6 somite developmental stages to identify genes co operatively regulated by gata5 and gata6 during cardiomyocyte progenitor specification. Overall design: Samples were collected in duplicate  with 40 embryos per sample. Single 36 base pair reads were sequenced on the Illumina Genome Analyzer IIx,,pubmed:23903195,,Gata6 morphant  6 somites  rep 2,GSM1076995,,source name:Whole embryo|development stage:6 somites|genotype/variation:Gata6 morphant|tissue:whole embryo,Gata6 morphant  6 somites  rep 2,All data processing steps were performed in GobyWeb Dorff  K. C. et al 2013 GobyWeb: simplified management and analysis of gene expression and DNA methylation sequencing data. Quantitative Methods q bio.QM; Genomics q bio.GN. in press arXiv:1211.6666. Alignments performed against Zv9.61 assembly. Genome build: Zv9 Supplementary files format and content: tab separated files include RPKM values for each Sample,Whole embryo,,40 embryos were collected per sample in Trizol Invitrogen  and polyA mRNA was prepared for sequencing using the Illumina mRNA seq Sample Preparation Kit. RNA libraries were prepared for sequencing using standard Illumina protocols,,developmental stage:6 somites|genotype/variation:Gata6 morphant|tissue:whole embryo,GSM1076995,GSM1076995: Gata6 morphant  6 somites  rep 2; Danio rerio; RNA Seq,GSM1076995 1,,1,,GEO Accession:GSM1076995,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP018379,,,12hpf_G6_2.txt.gz,fastq,1413551196.0,39265311.0,GSM1076995 r1,0:36,A:370616418;C:336932812;G:336785671;T:368764574;N:451721,36,,,,370616418,336932812,336785671,368764574,451721,SRX222290,SRS389580,SRA066053,GEO,Weill Medical College of Cornell University,1,0.92187,,0.11635,,0.72139,,0.48206,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2013-02-02,Segmentation,Embryo,Whole Organism,All anatomical structures
36624,SRR658545,SRX222289,SRS389579,SRP018379,PRJNA188349,Tmem88a Mediates GATA dependent Specification of Cardiomyocyte Progenitors by Restricting Canonical WNT Signaling,GSE44026,Transcriptome Analysis,We sequenced mRNA from zebrafish wild type embryos  gata5 morphants  gata6 morphants  and gata5/6 morphants at bud and 6 somite developmental stages to identify genes co operatively regulated by gata5 and gata6 during cardiomyocyte progenitor specification. Overall design: Samples were collected in duplicate  with 40 embryos per sample. Single 36 base pair reads were sequenced on the Illumina Genome Analyzer IIx,,pubmed:23903195,,Gata6 morphant  6 somites  rep 1,GSM1076994,,source name:Whole embryo|development stage:6 somites|genotype/variation:Gata6 morphant|tissue:whole embryo,Gata6 morphant  6 somites  rep 1,All data processing steps were performed in GobyWeb Dorff  K. C. et al 2013 GobyWeb: simplified management and analysis of gene expression and DNA methylation sequencing data. Quantitative Methods q bio.QM; Genomics q bio.GN. in press arXiv:1211.6666. Alignments performed against Zv9.61 assembly. Genome build: Zv9 Supplementary files format and content: tab separated files include RPKM values for each Sample,Whole embryo,,40 embryos were collected per sample in Trizol Invitrogen  and polyA mRNA was prepared for sequencing using the Illumina mRNA seq Sample Preparation Kit. RNA libraries were prepared for sequencing using standard Illumina protocols,,developmental stage:6 somites|genotype/variation:Gata6 morphant|tissue:whole embryo,GSM1076994,GSM1076994: Gata6 morphant  6 somites  rep 1; Danio rerio; RNA Seq,GSM1076994 1,,1,,GEO Accession:GSM1076994,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP018379,,,,,1420457688.0,39457158.0,GSM1076994 r1,0:36,A:372624153;C:335685093;G:342635312;T:368961287;N:551843,36,,,,372624153,335685093,342635312,368961287,551843,SRX222289,SRS389579,SRA066053,GEO,Weill Medical College of Cornell University,1,0.91516,,0.10146,,0.72255,,0.47116,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2013-02-02,Segmentation,Embryo,Whole Organism,All anatomical structures