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445 rows where experiment.library_layout = "SINGLE", experiment.library_strategy = "OTHER" and tissue_curation = "Whole Organism"

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devstage_curation 8

experiment.library_selection 4

technology 3

experiment.platform 2

experiment.library_source 2

devstage_curation_coarse 2

tissue_curation_coarse 1

tissue_curation 1

  • Whole Organism · 445 ✖

experiment.library_strategy 1

  • OTHER · 445 ✖

experiment.library_layout 1

  • SINGLE · 445 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
9803 9803 ERR3909553 ERX3918377 ERS4309135 ERP120006 PRJEB36776 CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E-MTAB-8795 Transcriptome Analysis The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics. ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 13   Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Total3 SAMEA6544760 UNIVERSITY OF BIRMINGHAM ENA FIRST PUBLIC:2020 06 19T17:05:18Z|ENA LAST UPDATE:2020 02 13T15:36:56Z|External Id:SAMEA6544760|INSDC center name:UNIVERSITY OF BIRMINGHAM|INSDC first public:2020 06 19T17:05:18Z|INSDC last update:2020 02 13T15:36:56Z|INSDC status:public|Submitter Id:E MTAB 8795:Total3|age:14|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|fraction:unsorted whole organism|organism part:whole organism|sample name:E MTAB 8795:Total3|scientific name:Danio rerio|sex:not available|strain:Dual FUCCI                 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E MTAB 8795:Total3 s Total3 s CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Experimental Factor: fraction:unsorted whole organism OTHER TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   ERP120006 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 25 14SomiteTotal3_TCGACG_L003_R1_001.fastq.gz fastq 652379310.0 14497318.0 E MTAB 8795:Total3 0:45 1:0 A:150840591;C:135992123;G:240098326;T:125390188;N:58082 45 0     150840591 135992123 240098326 125390188 58082 ERX3918377 ERS4309135 ERA2381432 UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive 1 0.00539   0.00111   0.99582   0.74079   45   T   under 1.2% mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   United Kingdom 2020-02-13 Segmentation Embryo Whole Organism All anatomical structures
9804 9804 ERR3909552 ERX3918376 ERS4309134 ERP120006 PRJEB36776 CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E-MTAB-8795 Transcriptome Analysis The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics. ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 13   Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Total2 SAMEA6544759 UNIVERSITY OF BIRMINGHAM ENA FIRST PUBLIC:2020 06 19T17:05:18Z|ENA LAST UPDATE:2020 02 13T15:36:56Z|External Id:SAMEA6544759|INSDC center name:UNIVERSITY OF BIRMINGHAM|INSDC first public:2020 06 19T17:05:18Z|INSDC last update:2020 02 13T15:36:56Z|INSDC status:public|Submitter Id:E MTAB 8795:Total2|age:14|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|fraction:unsorted whole organism|organism part:whole organism|sample name:E MTAB 8795:Total2|scientific name:Danio rerio|sex:not available|strain:Dual FUCCI                 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E MTAB 8795:Total2 s Total2 s CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Experimental Factor: fraction:unsorted whole organism OTHER TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   ERP120006 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 25 14SomiteTotal2_TATAGC_L003_R1_001.fastq.gz fastq 457981740.0 10177372.0 E MTAB 8795:Total2 0:45 1:0 A:108846441;C:95327665;G:163111561;T:90654528;N:41545 45 0     108846441 95327665 163111561 90654528 41545 ERX3918376 ERS4309134 ERA2381432 UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive 1 0.00612   0.00144   0.99387   0.66666   45   T   under 1.2% mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   United Kingdom 2020-02-13 Segmentation Embryo Whole Organism All anatomical structures
9805 9805 ERR3909551 ERX3918375 ERS4309133 ERP120006 PRJEB36776 CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E-MTAB-8795 Transcriptome Analysis The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics. ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 13   Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Total1 SAMEA6544758 UNIVERSITY OF BIRMINGHAM ENA FIRST PUBLIC:2020 06 19T17:05:18Z|ENA LAST UPDATE:2020 02 13T15:36:56Z|External Id:SAMEA6544758|INSDC center name:UNIVERSITY OF BIRMINGHAM|INSDC first public:2020 06 19T17:05:18Z|INSDC last update:2020 02 13T15:36:56Z|INSDC status:public|Submitter Id:E MTAB 8795:Total1|age:14|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|fraction:unsorted whole organism|organism part:whole organism|sample name:E MTAB 8795:Total1|scientific name:Danio rerio|sex:not available|strain:Dual FUCCI                 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E MTAB 8795:Total1 s Total1 s CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Experimental Factor: fraction:unsorted whole organism OTHER TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   ERP120006 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 25 14SomiteTotal1_GTATAC_L003_R1_001.fastq.gz fastq 778934655.0 17309659.0 E MTAB 8795:Total1 0:45 1:0 A:175694794;C:165046556;G:285795545;T:152324198;N:73562 45 0     175694794 165046556 285795545 152324198 73562 ERX3918375 ERS4309133 ERA2381432 UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive 1 0.0048   0.00098   0.99492   0.69892   45   T   under 1.2% mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   United Kingdom 2020-02-13 Segmentation Embryo Whole Organism All anatomical structures
9806 9806 ERR3909550 ERX3918374 ERS4309132 ERP120006 PRJEB36776 CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E-MTAB-8795 Transcriptome Analysis The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics. ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 13   Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Red3 SAMEA6544757 UNIVERSITY OF BIRMINGHAM ENA FIRST PUBLIC:2020 06 19T17:05:18Z|ENA LAST UPDATE:2020 02 13T15:36:56Z|External Id:SAMEA6544757|INSDC center name:UNIVERSITY OF BIRMINGHAM|INSDC first public:2020 06 19T17:05:18Z|INSDC last update:2020 02 13T15:36:56Z|INSDC status:public|Submitter Id:E MTAB 8795:Red3|age:14|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|fraction:G1 slow cycling|organism part:whole organism|sample name:E MTAB 8795:Red3|scientific name:Danio rerio|sex:not available|strain:Dual FUCCI                 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E MTAB 8795:Red3 s Red3 s CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Experimental Factor: fraction:G1 slow cycling OTHER TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   ERP120006 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 25 14SomiteRed3_CACGAT_L003_R1_001.fastq.gz fastq 980271990.0 21783822.0 E MTAB 8795:Red3 0:45 1:0 A:231772782;C:201265416;G:341867307;T:205267905;N:98580 45 0     231772782 201265416 341867307 205267905 98580 ERX3918374 ERS4309132 ERA2381432 UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive 1 0.0047   0.00138   0.99366   0.64343   45   T   under 1.2% mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   United Kingdom 2020-02-13 Segmentation Embryo Whole Organism All anatomical structures
9807 9807 ERR3909549 ERX3918373 ERS4309131 ERP120006 PRJEB36776 CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E-MTAB-8795 Transcriptome Analysis The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics. ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 13   Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Red2 SAMEA6544756 UNIVERSITY OF BIRMINGHAM ENA FIRST PUBLIC:2020 06 19T17:05:18Z|ENA LAST UPDATE:2020 02 13T15:36:56Z|External Id:SAMEA6544756|INSDC center name:UNIVERSITY OF BIRMINGHAM|INSDC first public:2020 06 19T17:05:18Z|INSDC last update:2020 02 13T15:36:56Z|INSDC status:public|Submitter Id:E MTAB 8795:Red2|age:14|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|fraction:G1 slow cycling|organism part:whole organism|sample name:E MTAB 8795:Red2|scientific name:Danio rerio|sex:not available|strain:Dual FUCCI                 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E MTAB 8795:Red2 s Red2 s CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Experimental Factor: fraction:G1 slow cycling OTHER TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   ERP120006 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 25 14SomiteRed2_ATCGTG_L003_R1_001.fastq.gz fastq 755095185.0 16779893.0 E MTAB 8795:Red2 0:45 1:0 A:173488674;C:161696782;G:267896203;T:151943387;N:70139 45 0     173488674 161696782 267896203 151943387 70139 ERX3918373 ERS4309131 ERA2381432 UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive 1 0.00548   0.00113   0.99415   0.65826   45   T   under 1.2% mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   United Kingdom 2020-02-13 Segmentation Embryo Whole Organism All anatomical structures
9808 9808 ERR3909548 ERX3918372 ERS4309130 ERP120006 PRJEB36776 CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E-MTAB-8795 Transcriptome Analysis The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics. ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 13   Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Red1 SAMEA6544755 UNIVERSITY OF BIRMINGHAM ENA FIRST PUBLIC:2020 06 19T17:05:18Z|ENA LAST UPDATE:2020 02 13T15:36:56Z|External Id:SAMEA6544755|INSDC center name:UNIVERSITY OF BIRMINGHAM|INSDC first public:2020 06 19T17:05:18Z|INSDC last update:2020 02 13T15:36:56Z|INSDC status:public|Submitter Id:E MTAB 8795:Red1|age:14|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|fraction:G1 slow cycling|organism part:whole organism|sample name:E MTAB 8795:Red1|scientific name:Danio rerio|sex:not available|strain:Dual FUCCI                 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E MTAB 8795:Red1 s Red1 s CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Experimental Factor: fraction:G1 slow cycling OTHER TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   ERP120006 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 25 14SomiteRed1_ACAGAT_L003_R1_001.fastq.gz fastq 755180370.0 16781786.0 E MTAB 8795:Red1 0:45 1:0 A:179369537;C:157573419;G:260889303;T:157277751;N:70360 45 0     179369537 157573419 260889303 157277751 70360 ERX3918372 ERS4309130 ERA2381432 UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive 1 0.00451   0.00099   0.99314   0.66248   45   T   under 1.2% mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   United Kingdom 2020-02-13 Segmentation Embryo Whole Organism All anatomical structures
9809 9809 ERR3909547 ERX3918371 ERS4309129 ERP120006 PRJEB36776 CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E-MTAB-8795 Transcriptome Analysis The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics. ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 13   Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Green3 SAMEA6544754 UNIVERSITY OF BIRMINGHAM ENA FIRST PUBLIC:2020 06 19T17:05:18Z|ENA LAST UPDATE:2020 02 13T15:36:56Z|External Id:SAMEA6544754|INSDC center name:UNIVERSITY OF BIRMINGHAM|INSDC first public:2020 06 19T17:05:18Z|INSDC last update:2020 02 13T15:36:56Z|INSDC status:public|Submitter Id:E MTAB 8795:Green3|age:14|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|fraction:S/G2/M rapid cycling|organism part:whole organism|sample name:E MTAB 8795:Green3|scientific name:Danio rerio|sex:not available|strain:Dual FUCCI                 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E MTAB 8795:Green3 s Green3 s CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Experimental Factor: fraction:S/G2/M rapid cycling OTHER TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   ERP120006 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 25 14SomiteGreen3_GAGTGA_L003_R1_001.fastq.gz fastq 819288855.0 18206419.0 E MTAB 8795:Green3 0:45 1:0 A:189173618;C:170597494;G:286250625;T:173188944;N:78174 45 0     189173618 170597494 286250625 173188944 78174 ERX3918371 ERS4309129 ERA2381432 UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive 1 0.00439   0.001   0.99377   0.68367   45   T   under 1.2% mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   United Kingdom 2020-02-13 Segmentation Embryo Whole Organism All anatomical structures
9810 9810 ERR3909546 ERX3918370 ERS4309128 ERP120006 PRJEB36776 CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E-MTAB-8795 Transcriptome Analysis The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics. ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 13   Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Green2 SAMEA6544753 UNIVERSITY OF BIRMINGHAM ENA FIRST PUBLIC:2020 06 19T17:05:18Z|ENA LAST UPDATE:2020 02 13T15:36:56Z|External Id:SAMEA6544753|INSDC center name:UNIVERSITY OF BIRMINGHAM|INSDC first public:2020 06 19T17:05:18Z|INSDC last update:2020 02 13T15:36:56Z|INSDC status:public|Submitter Id:E MTAB 8795:Green2|age:14|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|fraction:S/G2/M rapid cycling|organism part:whole organism|sample name:E MTAB 8795:Green2|scientific name:Danio rerio|sex:not available|strain:Dual FUCCI                 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E MTAB 8795:Green2 s Green2 s CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Experimental Factor: fraction:S/G2/M rapid cycling OTHER TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   ERP120006 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 25 14SomiteGreen2_CTGACG_L003_R1_001.fastq.gz fastq 697971375.0 15510475.0 E MTAB 8795:Green2 0:45 1:0 A:160028926;C:147075253;G:245773112;T:145025474;N:68610 45 0     160028926 147075253 245773112 145025474 68610 ERX3918370 ERS4309128 ERA2381432 UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive 1 0.00489   0.00085   0.99586   0.80163   45   T   under 1.2% mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   United Kingdom 2020-02-13 Segmentation Embryo Whole Organism All anatomical structures
9811 9811 ERR3909545 ERX3918369 ERS4309127 ERP120006 PRJEB36776 CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E-MTAB-8795 Transcriptome Analysis The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics. ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 13   Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Green1 SAMEA6544752 UNIVERSITY OF BIRMINGHAM ENA FIRST PUBLIC:2020 06 19T17:05:18Z|ENA LAST UPDATE:2020 02 13T15:36:56Z|External Id:SAMEA6544752|INSDC center name:UNIVERSITY OF BIRMINGHAM|INSDC first public:2020 06 19T17:05:18Z|INSDC last update:2020 02 13T15:36:56Z|INSDC status:public|Submitter Id:E MTAB 8795:Green1|age:14|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|fraction:S/G2/M rapid cycling|organism part:whole organism|sample name:E MTAB 8795:Green1|scientific name:Danio rerio|sex:not available|strain:Dual FUCCI                 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E MTAB 8795:Green1 s Green1 s CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Experimental Factor: fraction:S/G2/M rapid cycling OTHER TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   ERP120006 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 25 14SomiteGreen1_CACTGA_L003_R1_001.fastq.gz fastq 826595640.0 18368792.0 E MTAB 8795:Green1 0:45 1:0 A:193728088;C:171605661;G:287824557;T:173352680;N:84654 45 0     193728088 171605661 287824557 173352680 84654 ERX3918369 ERS4309127 ERA2381432 UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive 1 0.00505   0.00101   0.99287   0.58198   45   T   under 1.2% mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   United Kingdom 2020-02-13 Segmentation Embryo Whole Organism All anatomical structures
25295 25295 SRR25764045 SRX21486723 SRS18719024 SRP457105 PRJNA1009809 Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [Ribo Seq] GSE241753 Other Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. parent bioproject:PRJNA1009800 pubmed:39402326   WT bud 10 hpf Ribo seq rep1 GSM7734770   source name:Gastrula|strain:TLAB strain|tissue:Gastrula|developmental stage:Bud 10 hpf|treatment:100 µg/ml CHX 100 µg/ml TIG|geo loc name:missing|collection date:missing WT bud 10 hpf Ribo seq rep1 We identified the A site location in each mapped read with Scikit ribo [Fang et al. 2018] which uses a random forest with recursive feature selection and a generalized linear model for accurate A site prediction based on matched ribosome profiling and RNA Seq datasets. Kallisto 0.44.0 with parameters b 100 single l 180 s 20 t 40 was used to quantify transcript abundances in Transcripts Per Million TPM from RNA Seq data based on the reference set of MANE annotated transcripts see Codon usage analysis for description of this annotation. To avoid memory errors due to the large size of the human genome and the presence of multiple transcript isoforms all RNAfold dependencies in Scikit ribo were omitted and the index was built separately for each chromosome. To make the hg38 GTF compatible with Scikit ribo transcript/UTR annotations were removed. For each transcript the start codon in the first exon and the stop codon in the last exon were adjusted to represent transcript start and end coordinates taking into account the gene strand. To estimate codon dwell times short 20 23 nt and long 28 33 nt ribosome footprints were analyzed separately. rRNA filtered reads were aligned to GRCz11.108 using STAR v2.6.1c [Dobin et al. 2013] the following options: outFilterMultimapNmax 1 seedSearchStartLmax 15 outSAMtype BAM SortedByCoordinate outFilterMismatchNmax 2 alignEndsType EndToEnd quantMode TranscriptomeSAM outSAMattributes NH HI AS nM NM MD We identified the A site location in each mapped read with Scikit ribo [Fang et al. 2018] which uses a random forest with recursive feature selection and a generalized linear model for accurate A site prediction based on matched ribosome profiling and RNA Seq datasets. Kallisto 0.44.0 with parameters b 100 single l 180 s 20 t 40 was used to quantify transcript abundances in Transcripts Per Million TPM from RNA Seq data based on the reference set of MANE annotated transcripts see Codon usage analysis for description of this annotation. To avoid memory err… Gastrula unperturbed growth conditions in E3 medium for zebrafish embryos. 200 whole embryos were flash frozen in liquid nitrogen and subsequently lysed in footprint lysis buffer containing 100 µg/ml CHX and 100 µg/ml TIG 0.1% NP 40 10 µg/ml aprotinin 20 µM leupeptin 2.5 µM pepstatin A 0.5 mM AEBSF and 1x Phosphatase Inhibitor Cocktail. Samples were vortexed vigorously triturated through a 26G gauge needle and spun down for 7 minutes at 16 000xg/ 4°C. Supernatant was transferred to a new tube. 20 µg RNA in 200 µl polysome lysis buffer were digested with 50 U RNase I for 45 minutes at 2 000 rpm/22°C. post incubation on ice for 5 minutes extracts were pre cleared by centrifugation for 5 minutes at 3 000 g/ 4°C. Ribosomes were pelleted through 3 ml of a sucrose cushion 1 M sucrose 20 mM Tris pH=8.0 140 mM KCl 5 mM MgCl2 1 mM DTT by spinning the layered solutions in the Type 70 Ti rotor for 120 minutes at 50 000 rpm/ 4°C. Ribosome pellets were rinsed once dissolved in 200 µl drug free polysome lysis buffer and incubated with 200 U hiPSC or 300 U NPC RNase I for 45 minutes at 2 000 rpm/22°C. Ribosome footprint libraries were prepared essentially as described McGlincy and Ingolia 2017; Wu 2019 with minor modifications. RNase I digestion was stopped by addition of 100 U Superase In and extracts were loaded on a sucrose cushion. The pellet was dissolved in 400 µl LiDS/LET lysis buffer and RNA was extracted with the acid phenol protocol. Fragments in the range of 19 to 32 nucleotides were isolated by gel size selection with T4 PNK and ligated to pre adenylated adapters containing 5 random nucleotides at their 5’ ends McGlinzy 2017 with T4 RNA Ligase 2 truncated KQ. Adapter ligated RNA was subjected to rRNA depletion using the Ribo Seq riboPOOL h/m/r depletion kit siTOOLs for CHX only samples and legacy RiboZero Gold kit Illumina for CHX+TIG samples The rRNA depleted footprints were reverse transcribed with Protoscript II and cDNA was circularized with recombinant TS2126 RNA ligase 1 commercially available as CircLigase. Libraries were constructed from circularized cDNA with KAP… Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle. strain:TLAB strain|tissue:Gastrula|developmental stage:Bud 10 hpf|treatment:100 µg/ml CHX 100 µg/ml TIG GSM7734770 GSM7734770: WT bud 10 hpf Ribo seq rep1; Danio rerio; OTHER GSM7734770 r1 GSM7734770 1 200 whole embryos were flash frozen in liquid nitrogen and subsequently lysed in footprint lysis buffer containing 100 µg/ml CHX and 100 µg/ml TIG 0.1% NP 40 10 µg/ml aprotinin 20 µM leupeptin 2.5 µM pepstatin A 0.5 mM AEBSF and 1x Phosphatase Inhibitor Cocktail. Samples were vortexed vigorously triturated through a 26G gauge needle and spun down for 7 minutes at 16 000xg/ 4°C. Supernatant was transferred to a new tube. 20 µg RNA in 200 µl polysome lysis buffer were digested with 50 U RNase I for 45 minutes at 2 000 rpm/22°C. post incubation on ice for 5 minutes extracts were pre cleared by centrifugation for 5 minutes at 3 000 g/ 4°C. Ribosomes were pelleted through 3 ml of a sucrose cushion 1 M sucrose 20 mM Tris pH=8.0 140 mM KCl 5 mM MgCl2 1 mM DTT by spinning the layered solutions in the Type 70 Ti rotor for 120 minutes at 50 000 rpm/ 4°C. Ribosome pellets were rinsed once dissolved in 200 µl drug free polysome lysis buffer and incubated with 200 U hiPSC or 300 U NPC RNase I for 45 minutes at 2 000 rpm/22°C. Ribosome footprint libraries were prepared essentially as described McGlincy and Ingolia 2017; Wu 2019 with minor modifications. RNase I digestion was stopped by addition of 100 U Superase In and extracts were loaded on a sucrose cushion. The pellet was dissolved in 400 µl LiDS/LET lysis buffer and RNA was extracted with the acid phenol protocol. Fragments in the range of 19 to 32 nucleotides were isolated by gel size selection with T4 PNK and ligated to pre adenylated adapters containing 5 random nucleotides at their five prime ends McGlinzy 2017 with T4 RNA Ligase 2 truncated KQ. Adapter ligated RNA was subjected to rRNA depletion using the Ribo Seq riboPOOL h/m/r depletion kit siTOOLs for CHX only samples and legacy RiboZero Gold kit Illumina for CHX+TIG samples The rRNA depleted footprints were reverse transcribed with Protoscript II and cDNA was circularized with recombinant TS2126 RNA ligase 1 commercially available as CircLigase. Libraries were constructed from circularized cDNA …   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   SRP457105     WT_ribo_bud_1.fastq.gz fastq 1476985703.0 55745002.0 GSM7734770 r1 0:26.50 A:266369385;C:466461341;G:473469631;T:270671671;N:13675 26       266369385 466461341 473469631 270671671 13675 SRX21486723 SRS18719024 SRA1700409 Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry Max Planck Institute of Biochemistry 1 0.773   0.14121   0.82242   0.78464   30   B   usable mapping rate illumina nextseq 5prime rrna_depletion ribozero bulk unknown unknown   Germany 2023-08-28 Gastrula Embryo Whole Organism All anatomical structures
25296 25296 SRR25764046 SRX21486722 SRS18719023 SRP457105 PRJNA1009809 Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [Ribo Seq] GSE241753 Other Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. parent bioproject:PRJNA1009800 pubmed:39402326   WT sphere 4 hpf Ribo seq rep1 GSM7734769   source name:Blastula|strain:TLAB strain|tissue:Blastula|developmental stage:Sphere 4 hpf|treatment:100 µg/ml CHX 100 µg/ml TIG|geo loc name:missing|collection date:missing WT sphere 4 hpf Ribo seq rep1 We identified the A site location in each mapped read with Scikit ribo [Fang et al. 2018] which uses a random forest with recursive feature selection and a generalized linear model for accurate A site prediction based on matched ribosome profiling and RNA Seq datasets. Kallisto 0.44.0 with parameters b 100 single l 180 s 20 t 40 was used to quantify transcript abundances in Transcripts Per Million TPM from RNA Seq data based on the reference set of MANE annotated transcripts see Codon usage analysis for description of this annotation. To avoid memory errors due to the large size of the human genome and the presence of multiple transcript isoforms all RNAfold dependencies in Scikit ribo were omitted and the index was built separately for each chromosome. To make the hg38 GTF compatible with Scikit ribo transcript/UTR annotations were removed. For each transcript the start codon in the first exon and the stop codon in the last exon were adjusted to represent transcript start and end coordinates taking into account the gene strand. To estimate codon dwell times short 20 23 nt and long 28 33 nt ribosome footprints were analyzed separately. rRNA filtered reads were aligned to GRCz11.108 using STAR v2.6.1c [Dobin et al. 2013] the following options: outFilterMultimapNmax 1 seedSearchStartLmax 15 outSAMtype BAM SortedByCoordinate outFilterMismatchNmax 2 alignEndsType EndToEnd quantMode TranscriptomeSAM outSAMattributes NH HI AS nM NM MD We identified the A site location in each mapped read with Scikit ribo [Fang et al. 2018] which uses a random forest with recursive feature selection and a generalized linear model for accurate A site prediction based on matched ribosome profiling and RNA Seq datasets. Kallisto 0.44.0 with parameters b 100 single l 180 s 20 t 40 was used to quantify transcript abundances in Transcripts Per Million TPM from RNA Seq data based on the reference set of MANE annotated transcripts see Codon usage analysis for description of this annotation. To avoid memory err… Blastula unperturbed growth conditions in E3 medium for zebrafish embryos. 200 whole embryos were flash frozen in liquid nitrogen and subsequently lysed in footprint lysis buffer containing 100 µg/ml CHX and 100 µg/ml TIG 0.1% NP 40 10 µg/ml aprotinin 20 µM leupeptin 2.5 µM pepstatin A 0.5 mM AEBSF and 1x Phosphatase Inhibitor Cocktail. Samples were vortexed vigorously triturated through a 26G gauge needle and spun down for 7 minutes at 16 000xg/ 4°C. Supernatant was transferred to a new tube. 20 µg RNA in 200 µl polysome lysis buffer were digested with 50 U RNase I for 45 minutes at 2 000 rpm/22°C. post incubation on ice for 5 minutes extracts were pre cleared by centrifugation for 5 minutes at 3 000 g/ 4°C. Ribosomes were pelleted through 3 ml of a sucrose cushion 1 M sucrose 20 mM Tris pH=8.0 140 mM KCl 5 mM MgCl2 1 mM DTT by spinning the layered solutions in the Type 70 Ti rotor for 120 minutes at 50 000 rpm/ 4°C. Ribosome pellets were rinsed once dissolved in 200 µl drug free polysome lysis buffer and incubated with 200 U hiPSC or 300 U NPC RNase I for 45 minutes at 2 000 rpm/22°C. Ribosome footprint libraries were prepared essentially as described McGlincy and Ingolia 2017; Wu 2019 with minor modifications. RNase I digestion was stopped by addition of 100 U Superase In and extracts were loaded on a sucrose cushion. The pellet was dissolved in 400 µl LiDS/LET lysis buffer and RNA was extracted with the acid phenol protocol. Fragments in the range of 19 to 32 nucleotides were isolated by gel size selection with T4 PNK and ligated to pre adenylated adapters containing 5 random nucleotides at their 5’ ends McGlinzy 2017 with T4 RNA Ligase 2 truncated KQ. Adapter ligated RNA was subjected to rRNA depletion using the Ribo Seq riboPOOL h/m/r depletion kit siTOOLs for CHX only samples and legacy RiboZero Gold kit Illumina for CHX+TIG samples The rRNA depleted footprints were reverse transcribed with Protoscript II and cDNA was circularized with recombinant TS2126 RNA ligase 1 commercially available as CircLigase. Libraries were constructed from circularized cDNA with KAP… Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle. strain:TLAB strain|tissue:Blastula|developmental stage:Sphere 4 hpf|treatment:100 µg/ml CHX 100 µg/ml TIG GSM7734769 GSM7734769: WT sphere 4 hpf Ribo seq rep1; Danio rerio; OTHER GSM7734769 r1 GSM7734769 1 200 whole embryos were flash frozen in liquid nitrogen and subsequently lysed in footprint lysis buffer containing 100 µg/ml CHX and 100 µg/ml TIG 0.1% NP 40 10 µg/ml aprotinin 20 µM leupeptin 2.5 µM pepstatin A 0.5 mM AEBSF and 1x Phosphatase Inhibitor Cocktail. Samples were vortexed vigorously triturated through a 26G gauge needle and spun down for 7 minutes at 16 000xg/ 4°C. Supernatant was transferred to a new tube. 20 µg RNA in 200 µl polysome lysis buffer were digested with 50 U RNase I for 45 minutes at 2 000 rpm/22°C. post incubation on ice for 5 minutes extracts were pre cleared by centrifugation for 5 minutes at 3 000 g/ 4°C. Ribosomes were pelleted through 3 ml of a sucrose cushion 1 M sucrose 20 mM Tris pH=8.0 140 mM KCl 5 mM MgCl2 1 mM DTT by spinning the layered solutions in the Type 70 Ti rotor for 120 minutes at 50 000 rpm/ 4°C. Ribosome pellets were rinsed once dissolved in 200 µl drug free polysome lysis buffer and incubated with 200 U hiPSC or 300 U NPC RNase I for 45 minutes at 2 000 rpm/22°C. Ribosome footprint libraries were prepared essentially as described McGlincy and Ingolia 2017; Wu 2019 with minor modifications. RNase I digestion was stopped by addition of 100 U Superase In and extracts were loaded on a sucrose cushion. The pellet was dissolved in 400 µl LiDS/LET lysis buffer and RNA was extracted with the acid phenol protocol. Fragments in the range of 19 to 32 nucleotides were isolated by gel size selection with T4 PNK and ligated to pre adenylated adapters containing 5 random nucleotides at their five prime ends McGlinzy 2017 with T4 RNA Ligase 2 truncated KQ. Adapter ligated RNA was subjected to rRNA depletion using the Ribo Seq riboPOOL h/m/r depletion kit siTOOLs for CHX only samples and legacy RiboZero Gold kit Illumina for CHX+TIG samples The rRNA depleted footprints were reverse transcribed with Protoscript II and cDNA was circularized with recombinant TS2126 RNA ligase 1 commercially available as CircLigase. Libraries were constructed from circularized cDNA …   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   SRP457105     WT_ribo_sphere_1.fastq.gz fastq 1336027898.0 47907512.0 GSM7734769 r1 0:27.89 A:229038284;C:439455963;G:429428292;T:238088512;N:16847 27       229038284 439455963 429428292 238088512 16847 SRX21486722 SRS18719023 SRA1700409 Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry Max Planck Institute of Biochemistry 1 0.85867   0.20418   0.8776   0.79481   24   B   usable mapping rate illumina nextseq 5prime rrna_depletion ribozero bulk unknown unknown   Germany 2023-08-28 Blastula Embryo Whole Organism All anatomical structures
29739 29739 SRR27467672 SRX23139234 SRS20090275 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           Dome mock R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 5 hpf mock rep2 EV04009 EV04009 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV04009.R1.fastq.gz fastq 609590940.0 4354221.0 EV04009.R1.fastq.gz 0:140 A:155062144;C:147628702;G:168099121;T:138772205;N:28768 140       155062144 147628702 168099121 138772205 28768 SRX23139234 SRS20090275 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.0   0.0   1.0       140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Blastula Embryo Whole Organism All anatomical structures
29740 29740 SRR27467673 SRX23139233 SRS20090278 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           1K cell BS R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 3 hpf BS rep2 EV04008 EV04008 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV04008.R1.fastq.gz fastq 675505180.0 4825037.0 EV04008.R1.fastq.gz 0:140 A:178823976;C:121648962;G:198428643;T:176572292;N:31307 140       178823976 121648962 198428643 176572292 31307 SRX23139233 SRS20090278 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.0   0.0   1.0       140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Blastula Embryo Whole Organism All anatomical structures
29741 29741 SRR27467674 SRX23139232 SRS20090272 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           1K cell DM R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 3 hpf DM rep2 EV04007 EV04007 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV04007.R1.fastq.gz fastq 702064440.0 5014746.0 EV04007.R1.fastq.gz 0:140 A:176719694;C:166467163;G:207893965;T:150951950;N:31668 140       176719694 166467163 207893965 150951950 31668 SRX23139232 SRS20090272 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 2e-05   0.0   0.99997   1.0   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Blastula Embryo Whole Organism All anatomical structures
29742 29742 SRR27467675 SRX23139231 SRS20090271 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           1K cell mock R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 3 hpf mock rep2 EV04006 EV04006 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV04006.R1.fastq.gz fastq 664790700.0 4748505.0 EV04006.R1.fastq.gz 0:140 A:172014219;C:146545691;G:200358431;T:145840649;N:31710 140       172014219 146545691 200358431 145840649 31710 SRX23139231 SRS20090271 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 3e-05   0.0   0.99993   1.0   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Blastula Embryo Whole Organism All anatomical structures
29743 29743 SRR27467676 SRX23139230 SRS20090273 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           4 cell DM R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 1 hpf DM rep2 EV04004 EV04004 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV04004.R1.fastq.gz fastq 895671560.0 6397654.0 EV04004.R1.fastq.gz 0:140 A:206443066;C:147067097;G:365386937;T:176734600;N:39860 140       206443066 147067097 365386937 176734600 39860 SRX23139230 SRS20090273 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.0   0.0   1.0       140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Cleavage Embryo Whole Organism All anatomical structures
29744 29744 SRR27467677 SRX23139229 SRS20090274 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           4 cell mock R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 1 hpf mock rep2 EV04003 EV04003 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV04003.R1.fastq.gz fastq 664112120.0 4743658.0 EV04003.R1.fastq.gz 0:140 A:163711695;C:142612940;G:211194350;T:146562626;N:30509 140       163711695 142612940 211194350 146562626 30509 SRX23139229 SRS20090274 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 2e-05   0.0   0.99997   1.0   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Cleavage Embryo Whole Organism All anatomical structures
29747 29747 SRR27467680 SRX23139226 SRS20090267 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           24h BS R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:24 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 24 hpf BS rep2 EV03009 EV03009 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV03009.R1.fastq.gz fastq 168931280.0 2222780.0 EV03009.R1.fastq.gz 0:76 A:49803604;C:36479774;G:37758990;T:44874154;N:14758 76       49803604 36479774 37758990 44874154 14758 SRX23139226 SRS20090267 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.00034   0.0002   0.99965   0.5   76   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Pharyngula Embryo Whole Organism All anatomical structures
29748 29748 SRR27467681 SRX23139225 SRS20090266 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           24h DM R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:24 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 24 hpf DM rep2 EV03008 EV03008 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV03008.R1.fastq.gz fastq 200878792.0 2643142.0 EV03008.R1.fastq.gz 0:76 A:46955288;C:54746275;G:55887832;T:43270561;N:18836 76       46955288 54746275 55887832 43270561 18836 SRX23139225 SRS20090266 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.29408   0.00737   0.91823   0.54549   76   B   usable mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Pharyngula Embryo Whole Organism All anatomical structures
29749 29749 SRR27467682 SRX23139224 SRS20090269 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           24h mock R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:24 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 24 hpf mock rep2 EV03007 EV03007 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV03007.R1.fastq.gz fastq 175642840.0 2311090.0 EV03007.R1.fastq.gz 0:76 A:44745275;C:48908904;G:44862157;T:37111895;N:14609 76       44745275 48908904 44862157 37111895 14609 SRX23139224 SRS20090269 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.06887   0.00273   0.96623   0.48721   76   B   usable mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Pharyngula Embryo Whole Organism All anatomical structures
29750 29750 SRR27467683 SRX23139223 SRS20090265 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           Bud BS R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:10 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 10 hpf BS rep2 EV04014 EV04014 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV04014.R1.fastq.gz fastq 774901260.0 5535009.0 EV04014.R1.fastq.gz 0:140 A:193865579;C:138861953;G:251102013;T:191036071;N:35644 140       193865579 138861953 251102013 191036071 35644 SRX23139223 SRS20090265 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.0   0.0   1.0       140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Gastrula Embryo Whole Organism All anatomical structures
29751 29751 SRR27467684 SRX23139222 SRS20090264 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           Bud DM R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:10 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 10 hpf DM rep2 EV04013 EV04013 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV04013.R1.fastq.gz fastq 666372840.0 4759806.0 EV04013.R1.fastq.gz 0:140 A:172923134;C:142243998;G:211584978;T:139591020;N:29710 140       172923134 142243998 211584978 139591020 29710 SRX23139222 SRS20090264 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 3e-05   0.0   0.99991   1.0   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Gastrula Embryo Whole Organism All anatomical structures
29752 29752 SRR27467685 SRX23139221 SRS20090262 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           Bud mock R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:10 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 10 hpf mock rep2 EV04012 EV04012 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV04012.R1.fastq.gz fastq 628769540.0 4491211.0 EV04012.R1.fastq.gz 0:140 A:160925901;C:143204697;G:183224867;T:141385307;N:28768 140       160925901 143204697 183224867 141385307 28768 SRX23139221 SRS20090262 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 1e-05   0.0   0.99997   1.0   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Gastrula Embryo Whole Organism All anatomical structures
29753 29753 SRR27467686 SRX23139220 SRS20090263 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           Dome BS R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 5 hpf BS rep2 EV04011 EV04011 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV04011.R1.fastq.gz fastq 720913200.0 5149380.0 EV04011.R1.fastq.gz 0:140 A:185414155;C:126110104;G:238649631;T:170706590;N:32720 140       185414155 126110104 238649631 170706590 32720 SRX23139220 SRS20090263 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.0   0.0   1.0       140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Blastula Embryo Whole Organism All anatomical structures
29754 29754 SRR27467687 SRX23139219 SRS20090259 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           Dome DM R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 5 hpf DM rep2 EV04010 EV04010 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV04010.R1.fastq.gz fastq 443650200.0 3168930.0 EV04010.R1.fastq.gz 0:140 A:114663509;C:102512276;G:135709753;T:90744641;N:20021 140       114663509 102512276 135709753 90744641 20021 SRX23139219 SRS20090259 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 1e-05   0.0   0.99997   1.0   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Blastula Embryo Whole Organism All anatomical structures
29757 29757 SRR27437477 SRX23109820 SRS20064574 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           1K cell mock R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 3 hpf mock rep3 EV07007 EV07007 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV07007.R1.fastq.gz fastq 479994620.0 3428533.0 EV07007.R1.fastq.gz 0:140 A:124628886;C:116843590;G:123136721;T:115372734;N:12689 140       124628886 116843590 123136721 115372734 12689 SRX23109820 SRS20064574 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 6e-05   1e-05   0.99989   1.0   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Blastula Embryo Whole Organism All anatomical structures
29758 29758 SRR27437478 SRX23109819 SRS20064573 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           4 cell BS R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 1 hpf BS rep3 EV07006 EV07006 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV07006.R1.fastq.gz fastq 2584527680.0 18460912.0 EV07006.R1.fastq.gz 0:140 A:685107500;C:367766834;G:717359848;T:814224206;N:69292 140       685107500 367766834 717359848 814224206 69292 SRX23109819 SRS20064573 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 2e-05   1e-05   1.0       140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Cleavage Embryo Whole Organism All anatomical structures
29759 29759 SRR27437479 SRX23109818 SRS20064571 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           4 cell DM R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 1 hpf DM rep3 EV07005 EV07005 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV07005.R1.fastq.gz fastq 713829480.0 5098782.0 EV07005.R1.fastq.gz 0:140 A:183575304;C:168886779;G:213156258;T:148191838;N:19301 140       183575304 168886779 213156258 148191838 19301 SRX23109818 SRS20064571 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 5e-05   0.0   0.99989   1.0   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Cleavage Embryo Whole Organism All anatomical structures
29760 29760 SRR27437480 SRX23109817 SRS20064572 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           4 cell mock R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 1 hpf mock rep3 EV07004 EV07004 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV07004.R1.fastq.gz fastq 517336680.0 3695262.0 EV07004.R1.fastq.gz 0:140 A:136783049;C:131207858;G:139873280;T:109458276;N:14217 140       136783049 131207858 139873280 109458276 14217 SRX23109817 SRS20064572 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 7e-05   0.0   0.99981   0.7   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Cleavage Embryo Whole Organism All anatomical structures
29764 29764 SRR27437484 SRX23109813 SRS20064567 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           24h BS R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:24 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 24 hpf BS rep3 EV07018 EV07018 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV07018.R1.fastq.gz fastq 887731180.0 6340937.0 EV07018.R1.fastq.gz 0:140 A:204102176;C:148262233;G:350287017;T:185056779;N:22975 140       204102176 148262233 350287017 185056779 22975 SRX23109813 SRS20064567 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.0   0.0   1.0       140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Pharyngula Embryo Whole Organism All anatomical structures
29766 29766 SRR27437486 SRX23109811 SRS20064565 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           24h DM R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:24 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 24 hpf DM rep3 EV07017 EV07017 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV07017.R1.fastq.gz fastq 466089960.0 3329214.0 EV07017.R1.fastq.gz 0:140 A:117818387;C:108651920;G:144753443;T:94853810;N:12400 140       117818387 108651920 144753443 94853810 12400 SRX23109811 SRS20064565 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.0   0.0   1.0       140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Pharyngula Embryo Whole Organism All anatomical structures
29767 29767 SRR27437487 SRX23109810 SRS20064563 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           24h mock R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:24 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 24 hpf mock rep3 EV07016 EV07016 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV07016.R1.fastq.gz fastq 638674120.0 4561958.0 EV07016.R1.fastq.gz 0:140 A:159572532;C:147135537;G:186885553;T:145063254;N:17244 140       159572532 147135537 186885553 145063254 17244 SRX23109810 SRS20064563 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 4e-05   0.0   0.99993   0.0   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Pharyngula Embryo Whole Organism All anatomical structures
29768 29768 SRR27437488 SRX23109809 SRS20064564 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           Bud BS R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:10 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 10 hpf BS rep3 EV07015 EV07015 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV07015.R1.fastq.gz fastq 598389400.0 4274210.0 EV07015.R1.fastq.gz 0:140 A:150315140;C:106310211;G:186765596;T:154982225;N:16228 140       150315140 106310211 186765596 154982225 16228 SRX23109809 SRS20064564 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.0   0.0   1.0       140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Gastrula Embryo Whole Organism All anatomical structures
29769 29769 SRR27437489 SRX23109808 SRS20064562 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           Bud DM R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:10 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 10 hpf DM rep3 EV07014 EV07014 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV07014.R1.fastq.gz fastq 739056780.0 5278977.0 EV07014.R1.fastq.gz 0:140 A:197948890;C:178761090;G:200265458;T:162060992;N:20350 140       197948890 178761090 200265458 162060992 20350 SRX23109808 SRS20064562 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 3e-05   0.0   0.99995   0.5   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Gastrula Embryo Whole Organism All anatomical structures
29770 29770 SRR27437490 SRX23109807 SRS20064561 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           Bud mock R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:10 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 10 hpf mock rep3 EV07013 EV07013 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV07013.R1.fastq.gz fastq 844338040.0 6030986.0 EV07013.R1.fastq.gz 0:140 A:217780710;C:182517044;G:251974206;T:192043675;N:22405 140       217780710 182517044 251974206 192043675 22405 SRX23109807 SRS20064561 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 4e-05   0.0   0.99993   1.0   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Gastrula Embryo Whole Organism All anatomical structures
29771 29771 SRR27437491 SRX23109806 SRS20064560 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           Dome BS R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 5 hpf BS rep3 EV07011 EV07011 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV07011.R1.fastq.gz fastq 893528580.0 6382347.0 EV07011.R1.fastq.gz 0:140 A:240101890;C:155985797;G:262065322;T:235351334;N:24237 140       240101890 155985797 262065322 235351334 24237 SRX23109806 SRS20064560 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.0   0.0   1.0       140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Blastula Embryo Whole Organism All anatomical structures
29772 29772 SRR27437492 SRX23109805 SRS20064559 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           Dome DM R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 5 hpf DM rep3 EV07012 EV07012 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV07012.R1.fastq.gz fastq 797662600.0 5697590.0 EV07012.R1.fastq.gz 0:140 A:201908589;C:182656132;G:249672167;T:163404182;N:21530 140       201908589 182656132 249672167 163404182 21530 SRX23109805 SRS20064559 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 3e-05   0.0   0.99991   0.75   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Blastula Embryo Whole Organism All anatomical structures
29773 29773 SRR27437493 SRX23109804 SRS20064558 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           Dome mock R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 5 hpf mock rep3 EV07010 EV07010 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV07010.R1.fastq.gz fastq 467593280.0 3339952.0 EV07010.R1.fastq.gz 0:140 A:122604957;C:118747514;G:124074466;T:102153374;N:12969 140       122604957 118747514 124074466 102153374 12969 SRX23109804 SRS20064558 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 4e-05   0.0   0.99993   1.0   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Blastula Embryo Whole Organism All anatomical structures
29774 29774 SRR27437494 SRX23109803 SRS20064557 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           1K cell BS R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 3 hpf BS rep3 EV07008 EV07008 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV07008.R1.fastq.gz fastq 705682040.0 5040586.0 EV07008.R1.fastq.gz 0:140 A:194506527;C:127442743;G:192893716;T:190818958;N:20096 140       194506527 127442743 192893716 190818958 20096 SRX23109803 SRS20064557 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.0   0.0   1.0       140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Blastula Embryo Whole Organism All anatomical structures
29775 29775 SRR27437495 SRX23109802 SRS20064556 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           1K cell DM R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 3 hpf DM rep3 EV07009 EV07009 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV07009.R1.fastq.gz fastq 380716280.0 2719402.0 EV07009.R1.fastq.gz 0:140 A:95351632;C:89558330;G:115625953;T:80169603;N:10762 140       95351632 89558330 115625953 80169603 10762 SRX23109802 SRS20064556 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 6e-05   1e-05   0.99991   0.75   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Blastula Embryo Whole Organism All anatomical structures
29778 29778 SRR27435863 SRX23108233 SRS20063070 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           1K cell mock R4   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 3 hpf mock rep4 EV08010 EV08010 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV08010.R1.fastq.gz fastq 678729520.0 4848068.0 EV08010.R1.fastq.gz 0:140 A:170672553;C:182320916;G:171865707;T:153824163;N:46181 140       170672553 182320916 171865707 153824163 46181 SRX23108233 SRS20063070 SRA1780265 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.0006   4e-05   0.99878   0.79069   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-05 Blastula Embryo Whole Organism All anatomical structures
29779 29779 SRR27435864 SRX23108232 SRS20063068 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           4 cell BS R4   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 1 hpf BS rep4 EV08009 EV08009 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV08009.R1.fastq.gz fastq 756964460.0 5406889.0 EV08009.R1.fastq.gz 0:140 A:191381054;C:111783194;G:185694475;T:268052883;N:52854 140       191381054 111783194 185694475 268052883 52854 SRX23108232 SRS20063068 SRA1780265 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 1e-05   0.0   0.99997   1.0   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-05 Cleavage Embryo Whole Organism All anatomical structures
29780 29780 SRR27435865 SRX23108231 SRS20063069 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           4 cell DM R4   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 1 hpf DM rep4 EV08008 EV08008 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV08008.R1.fastq.gz fastq 751794680.0 5369962.0 EV08008.R1.fastq.gz 0:140 A:194845808;C:197389162;G:194749636;T:164756481;N:53593 140       194845808 197389162 194749636 164756481 53593 SRX23108231 SRS20063069 SRA1780265 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.00124   0.00029   0.99853   0.77083   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-05 Cleavage Embryo Whole Organism All anatomical structures
29781 29781 SRR27435866 SRX23108230 SRS20063066 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           4 cell mock R4   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 1 hpf mock rep4 EV08007 EV08007 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV08007.R1.fastq.gz fastq 761961760.0 5442584.0 EV08007.R1.fastq.gz 0:140 A:194053323;C:191169414;G:194452160;T:182234253;N:52610 140       194053323 191169414 194452160 182234253 52610 SRX23108230 SRS20063066 SRA1780265 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.00242   0.00062   0.99803   0.81818   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-05 Cleavage Embryo Whole Organism All anatomical structures
29785 29785 SRR27435870 SRX23108226 SRS20063064 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           24h BS R4   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:24 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 24 hpf BS rep4 EV08021 EV08021 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV08021.R1.fastq.gz fastq 747571860.0 5339799.0 EV08021.R1.fastq.gz 0:140 A:185666613;C:121868156;G:181153824;T:258830310;N:52957 140       185666613 121868156 181153824 258830310 52957 SRX23108226 SRS20063064 SRA1780265 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.0   0.0   1.0       140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-05 Pharyngula Embryo Whole Organism All anatomical structures
29787 29787 SRR27435872 SRX23108224 SRS20063061 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           24h DM R4   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:24 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 24 hpf DM rep4 EV08020 EV08020 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV08020.R1.fastq.gz fastq 775090400.0 5536360.0 EV08020.R1.fastq.gz 0:140 A:198131068;C:205114604;G:198783890;T:173006366;N:54472 140       198131068 205114604 198783890 173006366 54472 SRX23108224 SRS20063061 SRA1780265 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.00056   4e-05   0.9989   0.71052   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-05 Pharyngula Embryo Whole Organism All anatomical structures
29788 29788 SRR27435873 SRX23108223 SRS20063060 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           24h mock R4   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:24 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 24 hpf mock rep4 EV08019 EV08019 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV08019.R1.fastq.gz fastq 763233240.0 5451666.0 EV08019.R1.fastq.gz 0:140 A:189362337;C:199268270;G:198509945;T:176040551;N:52137 140       189362337 199268270 198509945 176040551 52137 SRX23108223 SRS20063060 SRA1780265 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.00036   6e-05   0.99939   0.85365   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-05 Pharyngula Embryo Whole Organism All anatomical structures
29789 29789 SRR27435874 SRX23108222 SRS20063057 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           Bud BS R4   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:10 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 10 hpf BS rep4 EV08018 EV08018 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV08018.R1.fastq.gz fastq 809203080.0 5780022.0 EV08018.R1.fastq.gz 0:140 A:209714496;C:130623600;G:197912909;T:270895413;N:56662 140       209714496 130623600 197912909 270895413 56662 SRX23108222 SRS20063057 SRA1780265 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.0   0.0   1.0       140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-05 Gastrula Embryo Whole Organism All anatomical structures
29790 29790 SRR27435875 SRX23108221 SRS20063059 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           Bud DM R4   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:10 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 10 hpf DM rep4 EV08017 EV08017 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV08017.R1.fastq.gz fastq 722137500.0 5158125.0 EV08017.R1.fastq.gz 0:140 A:176408094;C:195907583;G:188487109;T:161283055;N:51659 140       176408094 195907583 188487109 161283055 51659 SRX23108221 SRS20063059 SRA1780265 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.00053   3e-05   0.999   0.70422   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-05 Gastrula Embryo Whole Organism All anatomical structures
29791 29791 SRR27435876 SRX23108220 SRS20063058 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           Bud mock R4   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:10 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 10 hpf mock rep4 EV08016 EV08016 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV08016.R1.fastq.gz fastq 827605660.0 5911469.0 EV08016.R1.fastq.gz 0:140 A:204173663;C:224596562;G:206999037;T:191779555;N:56843 140       204173663 224596562 206999037 191779555 56843 SRX23108220 SRS20063058 SRA1780265 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.00037   2e-05   0.99908   0.7037   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-05 Gastrula Embryo Whole Organism All anatomical structures
29792 29792 SRR27435877 SRX23108219 SRS20063056 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           Dome BS R4   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 5 hpf BS rep4 EV08015 EV08015 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV08015.R1.fastq.gz fastq 804598200.0 5747130.0 EV08015.R1.fastq.gz 0:140 A:215467427;C:134937180;G:189531758;T:264604493;N:57342 140       215467427 134937180 189531758 264604493 57342 SRX23108219 SRS20063056 SRA1780265 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 2e-05   0.0   0.99995   1.0   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-05 Blastula Embryo Whole Organism All anatomical structures
29793 29793 SRR27435878 SRX23108218 SRS20063055 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           Dome DM R4   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 5 hpf DM rep4 EV08014 EV08014 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV08014.R1.fastq.gz fastq 662443740.0 4731741.0 EV08014.R1.fastq.gz 0:140 A:164941700;C:167025964;G:177255084;T:153175163;N:45829 140       164941700 167025964 177255084 153175163 45829 SRX23108218 SRS20063055 SRA1780265 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.00069   0.0001   0.9992   0.83076   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-05 Blastula Embryo Whole Organism All anatomical structures
29794 29794 SRR27435879 SRX23108217 SRS20063052 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           Dome mock R4   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 5 hpf mock rep4 EV08013 EV08013 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV08013.R1.fastq.gz fastq 794760540.0 5676861.0 EV08013.R1.fastq.gz 0:140 A:197361776;C:210230329;G:205734036;T:181380205;N:54194 140       197361776 210230329 205734036 181380205 54194 SRX23108217 SRS20063052 SRA1780265 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.00066   9e-05   0.99894   0.78378   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-05 Blastula Embryo Whole Organism All anatomical structures
29795 29795 SRR27435880 SRX23108216 SRS20063054 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           1K cell BS R4   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 3 hpf BS rep4 EV08012 EV08012 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV08012.R1.fastq.gz fastq 722593200.0 5161380.0 EV08012.R1.fastq.gz 0:140 A:188475497;C:119550806;G:173208825;T:241306038;N:52034 140       188475497 119550806 173208825 241306038 52034 SRX23108216 SRS20063054 SRA1780265 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.0   0.0   1.0       140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-05 Blastula Embryo Whole Organism All anatomical structures
29796 29796 SRR27435881 SRX23108215 SRS20063053 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           1K cell DM R4   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 3 hpf DM rep4 EV08011 EV08011 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV08011.R1.fastq.gz fastq 753783380.0 5384167.0 EV08011.R1.fastq.gz 0:140 A:190029713;C:193734250;G:194752855;T:175212145;N:54417 140       190029713 193734250 194752855 175212145 54417 SRX23108215 SRS20063053 SRA1780265 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.00076   5e-05   0.99859   0.70873   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-05 Blastula Embryo Whole Organism All anatomical structures
35567 35567 SRR32928199 SRX28203119 SRS24552825 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 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.enzymatic.P01.F01.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:6|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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: expt2 broad sequencing of many cells at low depth 48hpf enzymatic dissociation replicate 6 100 100 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     expt2.broad.48.enzymatic.P01.F01.fq.gz fastq 800436.0 9529.0 expt2.broad.48.enzymatic.P01.F01.fq.gz 0:84 A:247920;C:168170;G:180799;T:203153;N:394 84       247920 168170 180799 203153 394 SRX28203119 SRS24552825 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 Hatching Embryo Whole Organism All anatomical structures
35568 35568 SRR32928200 SRX28203118 SRS24552823 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 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.enzymatic.P01.E01.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:5|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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: expt2 broad sequencing of many cells at low depth 48hpf enzymatic dissociation replicate 5 99 99 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     expt2.broad.48.enzymatic.P01.E01.fq.gz fastq 496356.0 5909.0 expt2.broad.48.enzymatic.P01.E01.fq.gz 0:84 A:156600;C:99183;G:113282;T:127036;N:255 84       156600 99183 113282 127036 255 SRX28203118 SRS24552823 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 Hatching Embryo Whole Organism All anatomical structures
35569 35569 SRR32928201 SRX28203117 SRS24552824 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 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.enzymatic.P01.D01.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:4|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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: expt2 broad sequencing of many cells at low depth 48hpf enzymatic dissociation replicate 4 98 98 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     expt2.broad.48.enzymatic.P01.D01.fq.gz fastq 2053800.0 24450.0 expt2.broad.48.enzymatic.P01.D01.fq.gz 0:84 A:668634;C:393806;G:431279;T:559022;N:1059 84       668634 393806 431279 559022 1059 SRX28203117 SRS24552824 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 Hatching Embryo Whole Organism All anatomical structures
35570 35570 SRR32928202 SRX28203116 SRS24552821 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 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.enzymatic.P01.C01.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:3|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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: expt2 broad sequencing of many cells at low depth 48hpf enzymatic dissociation replicate 3 97 97 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     expt2.broad.48.enzymatic.P01.C01.fq.gz fastq 2159052.0 25703.0 expt2.broad.48.enzymatic.P01.C01.fq.gz 0:84 A:837784;C:348085;G:463530;T:508544;N:1109 84       837784 348085 463530 508544 1109 SRX28203116 SRS24552821 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 Hatching Embryo Whole Organism All anatomical structures
35571 35571 SRR32928203 SRX28203115 SRS24552822 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 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.enzymatic.P01.B01.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:2|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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: expt2 broad sequencing of many cells at low depth 48hpf enzymatic dissociation replicate 2 96 96 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     expt2.broad.48.enzymatic.P01.B01.fq.gz fastq 3287508.0 39137.0 expt2.broad.48.enzymatic.P01.B01.fq.gz 0:84 A:1090202;C:644484;G:702124;T:848812;N:1886 84       1090202 644484 702124 848812 1886 SRX28203115 SRS24552822 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 Hatching Embryo Whole Organism All anatomical structures
35572 35572 SRR32928204 SRX28203114 SRS24552819 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 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.enzymatic.P01.A01.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:1|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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: expt2 broad sequencing of many cells at low depth 48hpf enzymatic dissociation replicate 1 95 95 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     expt2.broad.48.enzymatic.P01.A01.fq.gz fastq 6623400.0 78850.0 expt2.broad.48.enzymatic.P01.A01.fq.gz 0:84 A:2915935;C:1012732;G:1256523;T:1434621;N:3589 84       2915935 1012732 1256523 1434621 3589 SRX28203114 SRS24552819 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 Hatching Embryo Whole Organism All anatomical structures
35573 35573 SRR32928205 SRX28203113 SRS24552820 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 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.bead.P18.H02.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:16|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 16 94 94 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     expt2.broad.48.bead.P18.H02.fq.gz fastq 18079152.0 215228.0 expt2.broad.48.bead.P18.H02.fq.gz 0:84 A:6013555;C:3409380;G:3853431;T:4793252;N:9534 84       6013555 3409380 3853431 4793252 9534 SRX28203113 SRS24552820 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 Hatching Embryo Whole Organism All anatomical structures
35574 35574 SRR32928206 SRX28203112 SRS24552818 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 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.bead.P18.H01.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:15|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 15 93 93 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     expt2.broad.48.bead.P18.H01.fq.gz fastq 13210764.0 157271.0 expt2.broad.48.bead.P18.H01.fq.gz 0:84 A:4207727;C:2577088;G:2821128;T:3597752;N:7069 84       4207727 2577088 2821128 3597752 7069 SRX28203112 SRS24552818 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 Hatching Embryo Whole Organism All anatomical structures
35575 35575 SRR32928207 SRX28203111 SRS24552817 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 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.bead.P18.G02.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:14|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 14 92 92 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     expt2.broad.48.bead.P18.G02.fq.gz fastq 14834736.0 176604.0 expt2.broad.48.bead.P18.G02.fq.gz 0:84 A:5041294;C:2753273;G:3108141;T:3924037;N:7991 84       5041294 2753273 3108141 3924037 7991 SRX28203111 SRS24552817 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 Hatching Embryo Whole Organism All anatomical structures
35576 35576 SRR32928310 SRX28203110 SRS24552815 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 96hpf whole zebrafish embryo dissociated using enzymatic digestion.   expt3.96.enzymatic.P18.G12.fq.gz   seq depth:NA|Experiment id:3|dissociation method:enzymatic|replicate:7|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|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: expt3 96hpf enzymatic dissociation replicate 7 212 212 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     expt3.96.enzymatic.P18.G12.fq.gz fastq 25010412.0 297743.0 expt3.96.enzymatic.P18.G12.fq.gz 0:84 A:10964374;C:4064284;G:5105517;T:4873835;N:2402 84       10964374 4064284 5105517 4873835 2402 SRX28203110 SRS24552815 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 Larval Larval Whole Organism All anatomical structures
35577 35577 SRR32928208 SRX28203109 SRS24552816 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 96hpf whole zebrafish embryo dissociated using enzymatic digestion.   expt3.96.enzymatic.P18.F12.fq.gz   seq depth:NA|Experiment id:3|dissociation method:enzymatic|replicate:6|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|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: expt3 96hpf enzymatic dissociation replicate 6 211 211 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     expt3.96.enzymatic.P18.F12.fq.gz fastq 34833876.0 414689.0 expt3.96.enzymatic.P18.F12.fq.gz 0:84 A:15190499;C:5741220;G:7109697;T:6789172;N:3288 84       15190499 5741220 7109697 6789172 3288 SRX28203109 SRS24552816 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 Larval Larval Whole Organism All anatomical structures
35578 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
35579 35579 SRR32928210 SRX28203107 SRS24552812 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 96hpf whole zebrafish embryo dissociated using enzymatic digestion.   expt3.96.enzymatic.P18.E12.fq.gz   seq depth:NA|Experiment id:3|dissociation method:enzymatic|replicate:5|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|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: expt3 96hpf enzymatic dissociation replicate 5 210 210 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     expt3.96.enzymatic.P18.E12.fq.gz fastq 27839784.0 331426.0 expt3.96.enzymatic.P18.E12.fq.gz 0:84 A:11930285;C:4560929;G:5811743;T:5534159;N:2668 84       11930285 4560929 5811743 5534159 2668 SRX28203107 SRS24552812 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 Larval Larval Whole Organism All anatomical structures
35580 35580 SRR32928211 SRX28203106 SRS24552811 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 96hpf whole zebrafish embryo dissociated using enzymatic digestion.   expt3.96.enzymatic.P18.D12.fq.gz   seq depth:NA|Experiment id:3|dissociation method:enzymatic|replicate:4|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|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: expt3 96hpf enzymatic dissociation replicate 4 209 209 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     expt3.96.enzymatic.P18.D12.fq.gz fastq 27695556.0 329709.0 expt3.96.enzymatic.P18.D12.fq.gz 0:84 A:12091110;C:4491745;G:5609269;T:5500850;N:2582 84       12091110 4491745 5609269 5500850 2582 SRX28203106 SRS24552811 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 Larval Larval Whole Organism All anatomical structures
35581 35581 SRR32928212 SRX28203105 SRS24552813 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 96hpf whole zebrafish embryo dissociated using enzymatic digestion.   expt3.96.enzymatic.P18.C12.fq.gz   seq depth:NA|Experiment id:3|dissociation method:enzymatic|replicate:3|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|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: expt3 96hpf enzymatic dissociation replicate 3 208 208 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     expt3.96.enzymatic.P18.C12.fq.gz fastq 24844932.0 295773.0 expt3.96.enzymatic.P18.C12.fq.gz 0:84 A:10700258;C:4111418;G:5035794;T:4994990;N:2472 84       10700258 4111418 5035794 4994990 2472 SRX28203105 SRS24552813 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 Larval Larval Whole Organism All anatomical structures
35582 35582 SRR32928213 SRX28203104 SRS24552810 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 96hpf whole zebrafish embryo dissociated using enzymatic digestion.   expt3.96.enzymatic.P18.B12.fq.gz   seq depth:NA|Experiment id:3|dissociation method:enzymatic|replicate:2|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|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: expt3 96hpf enzymatic dissociation replicate 2 207 207 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     expt3.96.enzymatic.P18.B12.fq.gz fastq 10780812.0 128343.0 expt3.96.enzymatic.P18.B12.fq.gz 0:84 A:4635118;C:1860640;G:2120826;T:2163173;N:1055 84       4635118 1860640 2120826 2163173 1055 SRX28203104 SRS24552810 SRA2104467 University of Washington|Genome Sciences University of Washington 1 0.33865   0.22704   0.93659   0.55528   84   B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Larval Larval Whole Organism All anatomical structures
35583 35583 SRR32928214 SRX28203103 SRS24552809 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 96hpf whole zebrafish embryo dissociated using enzymatic digestion.   expt3.96.enzymatic.P18.A12.fq.gz   seq depth:NA|Experiment id:3|dissociation method:enzymatic|replicate:1|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|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: expt3 96hpf enzymatic dissociation replicate 1 206 206 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     expt3.96.enzymatic.P18.A12.fq.gz fastq 10534272.0 125408.0 expt3.96.enzymatic.P18.A12.fq.gz 0:84 A:4632079;C:1746502;G:2069269;T:2085448;N:974 84       4632079 1746502 2069269 2085448 974 SRX28203103 SRS24552809 SRA2104467 University of Washington|Genome Sciences University of Washington 1 0.33522   0.19264   0.93624   0.50295   84   B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Larval Larval Whole Organism All anatomical structures
35584 35584 SRR32928215 SRX28203102 SRS24552808 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 96hpf whole zebrafish embryo dissociated using bead homogenization.   expt3.96.bead.P18.H11.fq.gz   seq depth:NA|Experiment id:3|dissociation method:bead|replicate:8|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|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: expt3 96hpf bead dissociation replicate 8 205 205 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     expt3.96.bead.P18.H11.fq.gz fastq 235038972.0 2798083.0 expt3.96.bead.P18.H11.fq.gz 0:84 A:85855798;C:40354173;G:45974107;T:62832438;N:22456 84       85855798 40354173 45974107 62832438 22456 SRX28203102 SRS24552808 SRA2104467 University of Washington|Genome Sciences University of Washington 1 0.61865   0.46937   0.80791   0.46334   84   B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Larval Larval Whole Organism All anatomical structures
35585 35585 SRR32928216 SRX28203101 SRS24552807 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 96hpf whole zebrafish embryo dissociated using bead homogenization.   expt3.96.bead.P18.G11.fq.gz   seq depth:NA|Experiment id:3|dissociation method:bead|replicate:7|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|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: expt3 96hpf bead dissociation replicate 7 204 204 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     expt3.96.bead.P18.G11.fq.gz fastq 280436688.0 3338532.0 expt3.96.bead.P18.G11.fq.gz 0:84 A:105066150;C:48021700;G:54614521;T:72707589;N:26728 84       105066150 48021700 54614521 72707589 26728 SRX28203101 SRS24552807 SRA2104467 University of Washington|Genome Sciences University of Washington 1 0.59159   0.43599   0.80842   0.46679   84   B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Larval Larval Whole Organism All anatomical structures
35586 35586 SRR32928217 SRX28203100 SRS24552806 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 96hpf whole zebrafish embryo dissociated using bead homogenization.   expt3.96.bead.P18.F11.fq.gz   seq depth:NA|Experiment id:3|dissociation method:bead|replicate:6|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|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: expt3 96hpf bead dissociation replicate 6 203 203 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     expt3.96.bead.P18.F11.fq.gz fastq 286313832.0 3408498.0 expt3.96.bead.P18.F11.fq.gz 0:84 A:106784155;C:49395267;G:55919780;T:74187078;N:27552 84       106784155 49395267 55919780 74187078 27552 SRX28203100 SRS24552806 SRA2104467 University of Washington|Genome Sciences University of Washington 1 0.60245   0.44424   0.81124   0.48908   84   B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Larval Larval Whole Organism All anatomical structures
35587 35587 SRR32928218 SRX28203099 SRS24552804 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 96hpf whole zebrafish embryo dissociated using bead homogenization.   expt3.96.bead.P18.E11.fq.gz   seq depth:NA|Experiment id:3|dissociation method:bead|replicate:5|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|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: expt3 96hpf bead dissociation replicate 5 202 202 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     expt3.96.bead.P18.E11.fq.gz fastq 307881252.0 3665253.0 expt3.96.bead.P18.E11.fq.gz 0:84 A:115701302;C:52449337;G:59620790;T:80080256;N:29567 84       115701302 52449337 59620790 80080256 29567 SRX28203099 SRS24552804 SRA2104467 University of Washington|Genome Sciences University of Washington 1 0.5787   0.44122   0.81854   0.50262   84   B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Larval Larval Whole Organism All anatomical structures
35588 35588 SRR32928219 SRX28203098 SRS24552803 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 96hpf whole zebrafish embryo dissociated using bead homogenization.   expt3.96.bead.P18.D11.fq.gz   seq depth:NA|Experiment id:3|dissociation method:bead|replicate:4|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|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: expt3 96hpf bead dissociation replicate 4 201 201 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     expt3.96.bead.P18.D11.fq.gz fastq 300632640.0 3578960.0 expt3.96.bead.P18.D11.fq.gz 0:84 A:113779580;C:51205126;G:58283346;T:77335567;N:29021 84       113779580 51205126 58283346 77335567 29021 SRX28203098 SRS24552803 SRA2104467 University of Washington|Genome Sciences University of Washington 1 0.57846   0.43882   0.81925   0.50496   84   B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Larval Larval Whole Organism All anatomical structures
35589 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 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
35591 35591 SRR32928222 SRX28203095 SRS24552801 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 96hpf whole zebrafish embryo dissociated using bead homogenization.   expt3.96.bead.P18.C11.fq.gz   seq depth:NA|Experiment id:3|dissociation method:bead|replicate:3|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|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: expt3 96hpf bead dissociation replicate 3 200 200 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     expt3.96.bead.P18.C11.fq.gz fastq 269049312.0 3202968.0 expt3.96.bead.P18.C11.fq.gz 0:84 A:100635643;C:45939296;G:52190404;T:70258145;N:25824 84       100635643 45939296 52190404 70258145 25824 SRX28203095 SRS24552801 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 Larval Larval Whole Organism All anatomical structures
35592 35592 SRR32928223 SRX28203094 SRS24552799 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 96hpf whole zebrafish embryo dissociated using bead homogenization.   expt3.96.bead.P18.B11.fq.gz   seq depth:NA|Experiment id:3|dissociation method:bead|replicate:2|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|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: expt3 96hpf bead dissociation replicate 2 199 199 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     expt3.96.bead.P18.B11.fq.gz fastq 123292428.0 1467767.0 expt3.96.bead.P18.B11.fq.gz 0:84 A:45529584;C:21218529;G:24007853;T:32524700;N:11762 84       45529584 21218529 24007853 32524700 11762 SRX28203094 SRS24552799 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 Larval Larval Whole Organism All anatomical structures
35593 35593 SRR32928224 SRX28203093 SRS24552800 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 96hpf whole zebrafish embryo dissociated using bead homogenization.   expt3.96.bead.P18.A11.fq.gz   seq depth:NA|Experiment id:3|dissociation method:bead|replicate:1|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|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: expt3 96hpf bead dissociation replicate 1 198 198 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     expt3.96.bead.P18.A11.fq.gz fastq 277357248.0 3301872.0 expt3.96.bead.P18.A11.fq.gz 0:84 A:105979207;C:47015802;G:54386470;T:69949155;N:26614 84       105979207 47015802 54386470 69949155 26614 SRX28203093 SRS24552800 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 Larval Larval Whole Organism All anatomical structures
35594 35594 SRR32928225 SRX28203092 SRS24552798 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 72hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.   expt2.deep.72.enzymatic.P01.H03.fq.gz   seq depth:deep many umis|Experiment id:2|dissociation method:enzymatic|replicate:8|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:72 hpf|dev stage:72 hpf|collection date:2024 02 01|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: expt2 deep sequencing of limited cells 72hpf enzymatic dissociation replicate 8 197 197 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     expt2.deep.72.enzymatic.P01.H03.fq.gz fastq 3437364.0 40921.0 expt2.deep.72.enzymatic.P01.H03.fq.gz 0:84 A:1374051;C:578097;G:717673;T:766942;N:601 84       1374051 578097 717673 766942 601 SRX28203092 SRS24552798 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 Larval Larval Whole Organism All anatomical structures
35595 35595 SRR32928226 SRX28203091 SRS24552797 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 72hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.   expt2.deep.72.enzymatic.P01.G03.fq.gz   seq depth:deep many umis|Experiment id:2|dissociation method:enzymatic|replicate:7|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:72 hpf|dev stage:72 hpf|collection date:2024 02 01|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: expt2 deep sequencing of limited cells 72hpf enzymatic dissociation replicate 7 196 196 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     expt2.deep.72.enzymatic.P01.G03.fq.gz fastq 8559096.0 101894.0 expt2.deep.72.enzymatic.P01.G03.fq.gz 0:84 A:3252394;C:1515721;G:1860485;T:1929016;N:1480 84       3252394 1515721 1860485 1929016 1480 SRX28203091 SRS24552797 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 Larval Larval Whole Organism All anatomical structures
35596 35596 SRR32928227 SRX28203090 SRS24552795 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 72hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.   expt2.deep.72.enzymatic.P01.F03.fq.gz   seq depth:deep many umis|Experiment id:2|dissociation method:enzymatic|replicate:6|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:72 hpf|dev stage:72 hpf|collection date:2024 02 01|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: expt2 deep sequencing of limited cells 72hpf enzymatic dissociation replicate 6 195 195 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     expt2.deep.72.enzymatic.P01.F03.fq.gz fastq 86570988.0 1030607.0 expt2.deep.72.enzymatic.P01.F03.fq.gz 0:84 A:39076701;C:15258279;G:16117195;T:16103299;N:15514 84       39076701 15258279 16117195 16103299 15514 SRX28203090 SRS24552795 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 Larval Larval Whole Organism All anatomical structures
35597 35597 SRR32928228 SRX28203089 SRS24552796 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 72hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.   expt2.deep.72.enzymatic.P01.E03.fq.gz   seq depth:deep many umis|Experiment id:2|dissociation method:enzymatic|replicate:5|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:72 hpf|dev stage:72 hpf|collection date:2024 02 01|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: expt2 deep sequencing of limited cells 72hpf enzymatic dissociation replicate 5 194 194 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     expt2.deep.72.enzymatic.P01.E03.fq.gz fastq 21496020.0 255905.0 expt2.deep.72.enzymatic.P01.E03.fq.gz 0:84 A:7897723;C:3941227;G:4608642;T:5044562;N:3866 84       7897723 3941227 4608642 5044562 3866 SRX28203089 SRS24552796 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 Larval Larval Whole Organism All anatomical structures
35598 35598 SRR32928229 SRX28203088 SRS24552794 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 72hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.   expt2.deep.72.enzymatic.P01.D03.fq.gz   seq depth:deep many umis|Experiment id:2|dissociation method:enzymatic|replicate:4|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:72 hpf|dev stage:72 hpf|collection date:2024 02 01|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: expt2 deep sequencing of limited cells 72hpf enzymatic dissociation replicate 4 193 193 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     expt2.deep.72.enzymatic.P01.D03.fq.gz fastq 38955504.0 463756.0 expt2.deep.72.enzymatic.P01.D03.fq.gz 0:84 A:18141798;C:6097971;G:8057753;T:6650850;N:7132 84       18141798 6097971 8057753 6650850 7132 SRX28203088 SRS24552794 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 Larval Larval Whole Organism All anatomical structures
35599 35599 SRR32928230 SRX28203087 SRS24552793 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 72hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.   expt2.deep.72.enzymatic.P01.C03.fq.gz   seq depth:deep many umis|Experiment id:2|dissociation method:enzymatic|replicate:3|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:72 hpf|dev stage:72 hpf|collection date:2024 02 01|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: expt2 deep sequencing of limited cells 72hpf enzymatic dissociation replicate 3 192 192 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     expt2.deep.72.enzymatic.P01.C03.fq.gz fastq 51870336.0 617504.0 expt2.deep.72.enzymatic.P01.C03.fq.gz 0:84 A:17090212;C:9836274;G:12030231;T:12904330;N:9289 84       17090212 9836274 12030231 12904330 9289 SRX28203087 SRS24552793 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 Larval Larval Whole Organism All anatomical structures
35600 35600 SRR32928231 SRX28203086 SRS24552791 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 72hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.   expt2.deep.72.enzymatic.P01.B03.fq.gz   seq depth:deep many umis|Experiment id:2|dissociation method:enzymatic|replicate:2|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:72 hpf|dev stage:72 hpf|collection date:2024 02 01|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: expt2 deep sequencing of limited cells 72hpf enzymatic dissociation replicate 2 191 191 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     expt2.deep.72.enzymatic.P01.B03.fq.gz fastq 14069832.0 167498.0 expt2.deep.72.enzymatic.P01.B03.fq.gz 0:84 A:5389848;C:2403134;G:3075076;T:3199255;N:2519 84       5389848 2403134 3075076 3199255 2519 SRX28203086 SRS24552791 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 Larval Larval Whole Organism All anatomical structures
35601 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
35602 35602 SRR32928233 SRX28203084 SRS24552790 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 72hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.   expt2.deep.72.enzymatic.P01.A03.fq.gz   seq depth:deep many umis|Experiment id:2|dissociation method:enzymatic|replicate:1|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:72 hpf|dev stage:72 hpf|collection date:2024 02 01|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: expt2 deep sequencing of limited cells 72hpf enzymatic dissociation replicate 1 190 190 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     expt2.deep.72.enzymatic.P01.A03.fq.gz fastq 218177316.0 2597349.0 expt2.deep.72.enzymatic.P01.A03.fq.gz 0:84 A:102730118;C:32493129;G:39547427;T:43367265;N:39377 84       102730118 32493129 39547427 43367265 39377 SRX28203084 SRS24552790 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 Larval Larval Whole Organism All anatomical structures
35603 35603 SRR32928234 SRX28203083 SRS24552789 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 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.bead.P18.G01.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:13|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 13 91 91 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     expt2.broad.48.bead.P18.G01.fq.gz fastq 14202468.0 169077.0 expt2.broad.48.bead.P18.G01.fq.gz 0:84 A:4692822;C:2685182;G:2975257;T:3841545;N:7662 84       4692822 2685182 2975257 3841545 7662 SRX28203083 SRS24552789 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 Hatching Embryo Whole Organism All anatomical structures
35604 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
35605 35605 SRR32928236 SRX28203081 SRS24552788 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 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.bead.P18.F02.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:12|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 12 90 90 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     expt2.broad.48.bead.P18.F02.fq.gz fastq 16051728.0 191092.0 expt2.broad.48.bead.P18.F02.fq.gz 0:84 A:5221193;C:3079215;G:3420876;T:4321889;N:8555 84       5221193 3079215 3420876 4321889 8555 SRX28203081 SRS24552788 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 Hatching Embryo Whole Organism All anatomical structures
35606 35606 SRR32928237 SRX28203080 SRS24552786 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 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.bead.P18.F01.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:11|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 11 89 89 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     expt2.broad.48.bead.P18.F01.fq.gz fastq 19022388.0 226457.0 expt2.broad.48.bead.P18.F01.fq.gz 0:84 A:6375349;C:3646304;G:4032366;T:4958089;N:10280 84       6375349 3646304 4032366 4958089 10280 SRX28203080 SRS24552786 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 Hatching Embryo Whole Organism All anatomical structures
35607 35607 SRR32928238 SRX28203079 SRS24552785 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 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.bead.P18.E02.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:10|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 10 88 88 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     expt2.broad.48.bead.P18.E02.fq.gz fastq 17436720.0 207580.0 expt2.broad.48.bead.P18.E02.fq.gz 0:84 A:5912075;C:3260546;G:3682832;T:4572094;N:9173 84       5912075 3260546 3682832 4572094 9173 SRX28203079 SRS24552785 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 Hatching Embryo Whole Organism All anatomical structures
35608 35608 SRR32928239 SRX28203078 SRS24552783 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 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.bead.P18.E01.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:9|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 9 87 87 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     expt2.broad.48.bead.P18.E01.fq.gz fastq 12759768.0 151902.0 expt2.broad.48.bead.P18.E01.fq.gz 0:84 A:4143321;C:2424389;G:2695567;T:3489773;N:6718 84       4143321 2424389 2695567 3489773 6718 SRX28203078 SRS24552783 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 Hatching Embryo Whole Organism All anatomical structures
35609 35609 SRR32928240 SRX28203077 SRS24552784 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 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.bead.P18.D02.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:8|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 8 86 86 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     expt2.broad.48.bead.P18.D02.fq.gz fastq 17226132.0 205073.0 expt2.broad.48.bead.P18.D02.fq.gz 0:84 A:5722683;C:3229414;G:3698323;T:4566519;N:9193 84       5722683 3229414 3698323 4566519 9193 SRX28203077 SRS24552784 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 Hatching Embryo Whole Organism All anatomical structures
35610 35610 SRR32928241 SRX28203076 SRS24552782 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 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.bead.P18.D01.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:7|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 7 85 85 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     expt2.broad.48.bead.P18.D01.fq.gz fastq 14390124.0 171311.0 expt2.broad.48.bead.P18.D01.fq.gz 0:84 A:4584304;C:2823369;G:3092301;T:3882609;N:7541 84       4584304 2823369 3092301 3882609 7541 SRX28203076 SRS24552782 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 Hatching Embryo Whole Organism All anatomical structures
35611 35611 SRR32928242 SRX28203075 SRS24552781 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 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.bead.P18.C02.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:6|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 6 84 84 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     expt2.broad.48.bead.P18.C02.fq.gz fastq 18592560.0 221340.0 expt2.broad.48.bead.P18.C02.fq.gz 0:84 A:6370777;C:3468105;G:3988886;T:4754942;N:9850 84       6370777 3468105 3988886 4754942 9850 SRX28203075 SRS24552781 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 Hatching Embryo Whole Organism All anatomical structures

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;