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
8055,ERR022484,ERX008924,ERS017427,ERP000400,PRJEB2333,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E-MTAB-434,Other,,,,,E MTAB 434:ZF 2cells,SAMEA898400,Wellcome Sanger Institute,Alias:E MTAB 434:ZF 2cells|Broker name:ArrayExpress|Description:Protocols: Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 250 to 300 bp.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 03 10T17:55:05Z|INSDC last update:2018 03 08T15:25:14Z|INSDC status:public|SRA accession:ERS017427|Sample Name:ERS017427|Sex:mixed|StrainOrLine:Tuebingen|Title:ZF 2cells,,,,,,,,,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E MTAB 434:sequencing of Zebrafish embryo 2cells,RNA from Zebrafish embryo 2cells,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C.   Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down.   The libraries have fragment size of 250 to 300 bp.,Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:cell,FL-cDNA,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina Genome Analyzer II,,ERP000400,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16,4946_5.srf,srf,3947547008.0,25970704.0,E MTAB 434:4946 5.srf,0:76 1:76,A:1069302461;C:914233601;G:902631356;T:1055986090;N:5393500,76,76,,,1069302461,914233601,902631356,1055986090,5393500,ERX008924,ERS017427,ERA015179,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.93356,0.93346,0.03988,0.04022,0.79135,0.79198,0.48864,0.48464,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2011-03-10,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
9419,ERR273825,ERX248101,ERS092357,ERP001559,PRJEB3118,Zebrafish transcript profiling,Zebrafish_transcript_profiling-sc-2012-06-28T15:47:32Z-82,Transcriptome Analysis,Paired end sequence data from the Illumina Genome Analyzer was prepared from normal and mutant zebrafish embryos for transcript profiling.   This includes pilot studies for transcript indexing within the sequence reads.,,,,,SAMEA1888984,SC,ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 05 13T11:13:14Z|ENA LAST UPDATE:2018 03 08T15:36:21Z|External Id:SAMEA1888984|INSDC center name:SC|INSDC first public:2013 05 13T11:13:14Z|INSDC last update:2018 03 08T15:36:21Z|INSDC status:public|Submitter Id:hu2117 mutant vs wild type sc 2012 02 06T13:11:11Z 1107268|common name:zebrafish|sample description:3 prime end enriched mRNA from 3 morphological mutant hu2117 embryo samples and 3 matched sibling wild type samples. A 6 base indexing sequence is bases 5 to 10 of read 1 followed by polyT.|sample name:hu2117 mutant vs wild type sc 2012 02 06T13:11:11Z 1107268|scientific name:Danio rerio,,,,,,,,,1,SC EXP 6316 8,2387558,Illumina sequencing of library 2387558  constructed from sample accession ERS092357 for study accession ERP001559.,qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP001559,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2013 05 13|ENA LAST UPDATE:2018 11 16,6316_8.bam,bam,12715227300.0,84768182.0,SC RUN 6316 8,0:75 1:75,A:3986328155;C:1983554902;G:2466211000;T:4277430579;N:1702664,75,75,,,3986328155,1983554902,2466211000,4277430579,1702664,ERX248101,ERS092357,ERA212579,SC,Wellcome Sanger Institute,2,0.06657,0.60346,0.04569,0.19203,0.9767,0.82014,0.52373,0.4048,75,75,T,B,mate1 technical by mapping diff,illumina,hiseq_era,3prime,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2013-05-13,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
9420,ERR273824,ERX248100,ERS092356,ERP001559,PRJEB3118,Zebrafish transcript profiling,Zebrafish_transcript_profiling-sc-2012-06-28T15:47:32Z-82,Transcriptome Analysis,Paired end sequence data from the Illumina Genome Analyzer was prepared from normal and mutant zebrafish embryos for transcript profiling.   This includes pilot studies for transcript indexing within the sequence reads.,,,,,SAMEA1889000,SC,ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 05 13T11:13:13Z|ENA LAST UPDATE:2018 03 08T15:36:25Z|External Id:SAMEA1889000|INSDC center name:SC|INSDC first public:2013 05 13T11:13:13Z|INSDC last update:2018 03 08T15:36:25Z|INSDC status:public|Submitter Id:e48 mutant vs wild type sc 2012 02 06T13:11:09Z 1107267|common name:zebrafish|sample description:3 prime end enriched mRNA from 3 morphological mutant e48 embryo samples and 3 matched sibling wild type samples. A 6 base indexing sequence is bases 5 to 10 of read 1 followed by polyT.|sample name:e48 mutant vs wild type sc 2012 02 06T13:11:09Z 1107267|scientific name:Danio rerio,,,,,,,,,1,SC EXP 6316 7,2387557,Illumina sequencing of library 2387557  constructed from sample accession ERS092356 for study accession ERP001559.,qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP001559,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2013 05 13|ENA LAST UPDATE:2018 11 16,6316_7.bam,bam,17475932100.0,116506214.0,SC RUN 6316 7,0:75 1:75,A:5548228936;C:2693024343;G:3365940794;T:5867204994;N:1533033,75,75,,,5548228936,2693024343,3365940794,5867204994,1533033,ERX248100,ERS092356,ERA212579,SC,Wellcome Sanger Institute,2,0.05939,0.59457,0.04089,0.19671,0.98068,0.838,0.46304,0.62741,75,75,T,B,mate1 technical by mapping diff,illumina,hiseq_era,3prime,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2013-05-13,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
9421,ERR273823,ERX248099,ERS092354,ERP001559,PRJEB3118,Zebrafish transcript profiling,Zebrafish_transcript_profiling-sc-2012-06-28T15:47:32Z-82,Transcriptome Analysis,Paired end sequence data from the Illumina Genome Analyzer was prepared from normal and mutant zebrafish embryos for transcript profiling.   This includes pilot studies for transcript indexing within the sequence reads.,,,,,SAMEA1889008,SC,ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 05 13T11:13:13Z|ENA LAST UPDATE:2018 03 08T15:36:21Z|External Id:SAMEA1889008|INSDC center name:SC|INSDC first public:2013 05 13T11:13:13Z|INSDC last update:2018 03 08T15:36:21Z|INSDC status:public|Submitter Id:hu3332 mutant vs wild type sc 2012 02 06T13:11:07Z 1107265|common name:zebrafish|sample description:3 prime end enriched mRNA from 3 morphological mutant hu3332 embryo samples and 3 matched sibling wild type samples. A 6 base indexing sequence is bases 5 to 10 of read 1 followed by polyT.|sample name:hu3332 mutant vs wild type sc 2012 02 06T13:11:07Z 1107265|scientific name:Danio rerio,,,,,,,,,1,SC EXP 6316 5,2387555,Illumina sequencing of library 2387555  constructed from sample accession ERS092354 for study accession ERP001559.,qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP001559,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2013 05 13|ENA LAST UPDATE:2018 11 16,6316_5.bam,bam,13995917850.0,93306119.0,SC RUN 6316 5,0:75 1:75,A:4367273029;C:2176748810;G:2714026832;T:4736121060;N:1748119,75,75,,,4367273029,2176748810,2714026832,4736121060,1748119,ERX248099,ERS092354,ERA212579,SC,Wellcome Sanger Institute,2,0.06401,0.62019,0.04224,0.18728,0.97723,0.81071,0.461,0.55379,75,75,T,B,mate1 technical by mapping diff,illumina,hiseq_era,3prime,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2013-05-13,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
9422,ERR273822,ERX248098,ERS092063,ERP001559,PRJEB3118,Zebrafish transcript profiling,Zebrafish_transcript_profiling-sc-2012-06-28T15:47:32Z-82,Transcriptome Analysis,Paired end sequence data from the Illumina Genome Analyzer was prepared from normal and mutant zebrafish embryos for transcript profiling.   This includes pilot studies for transcript indexing within the sequence reads.,,,,,SAMEA1888996,SC,ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 05 13T11:13:13Z|ENA LAST UPDATE:2018 03 08T15:36:13Z|External Id:SAMEA1888996|INSDC center name:SC|INSDC first public:2013 05 13T11:13:13Z|INSDC last update:2018 03 08T15:36:13Z|INSDC status:public|Submitter Id:sa0058 mutant vs wild type sc 2012 02 06T13:05:07Z 265521|common name:zebrafish|sample description:33 prime end enriched mRNA from 3 morphological mutant sa0058 embryo samples and 3 matched sibling wild type samples. A 6 base indexing sequence is bases 5 to 10 of read 1 followed by polyT.|sample name:sa0058 mutant vs wild type sc 2012 02 06T13:05:07Z 265521|scientific name:Danio rerio,,,,,,,,,1,SC EXP 5287 7,449230,Illumina sequencing of library 449230  constructed from sample accession ERS092063 for study accession ERP001559.,qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina Genome Analyzer II,,ERP001559,Illumina Genome Analyzer II paired end sequencing,ENA FIRST PUBLIC:2013 05 13|ENA LAST UPDATE:2018 11 16,5287_7.bam,bam,2216402460.0,20522245.0,SC RUN 5287 7,0:54 1:54,A:646882787;C:346392353;G:394060191;T:827745173;N:1321956,54,54,,,646882787,346392353,394060191,827745173,1321956,ERX248098,ERS092063,ERA212579,SC,Wellcome Sanger Institute,2,0.02565,0.72009,0.01691,0.21429,0.98725,0.78944,0.62084,0.61278,54,54,T,B,mate1 technical by mapping diff,illumina,early_illumina,3prime,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2013-05-13,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
9892,ERR4172795,ERX4136409,ERS4580819,ERP121885,PRJEB38455,RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E-MTAB-9113,Transcriptome Analysis,RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 05 22,,Protocols: Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion,sibling 3,SAMEA6853229,Centre for Developmental Neurobiology King's College London,ENA FIRST PUBLIC:2020 12 01T04:08:08Z|ENA LAST UPDATE:2020 05 22T17:13:15Z|External Id:SAMEA6853229|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2020 12 01T04:08:08Z|INSDC last update:2020 05 22T17:13:15Z|INSDC status:public|Submitter Id:E MTAB 9113:sibling 3|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|sample name:E MTAB 9113:sibling 3|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E MTAB 9113:sibling 3 p,sibling 3 p,RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP121885,Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 06 19,UCLGNS1141-gfp-sibs-3_S6_R1.fastq.gz UCLGNS1141-gfp-sibs-3_S6_R2.fastq.gz,fastq fastq,,,E MTAB 9113:UCLGNS1141 gfp sibs 3 S6 R,0:81 1:81,A:1144578958;C:1113109875;G:1138809559;T:1117038434;N:213932,81,81,,,1144578958,1113109875,1138809559,1117038434,213932,ERX4136409,ERS4580819,ERA2625401,Centre for Developmental Neurobiology King,Centre for Developmental Neurobiology King,2,0.96684,0.96492,0.03244,0.0317,0.71236,0.71514,0.45871,0.46189,81,81,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2020-05-22,Multi-stage,Multi-stage,Embryo Imprecise,All anatomical structures
9893,ERR4172794,ERX4136408,ERS4580818,ERP121885,PRJEB38455,RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E-MTAB-9113,Transcriptome Analysis,RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 05 22,,Protocols: Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion,sibling 2,SAMEA6853228,Centre for Developmental Neurobiology King's College London,ENA FIRST PUBLIC:2020 12 01T04:08:08Z|ENA LAST UPDATE:2020 05 22T17:13:15Z|External Id:SAMEA6853228|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2020 12 01T04:08:08Z|INSDC last update:2020 05 22T17:13:15Z|INSDC status:public|Submitter Id:E MTAB 9113:sibling 2|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|sample name:E MTAB 9113:sibling 2|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E MTAB 9113:sibling 2 p,sibling 2 p,RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP121885,Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 06 19,UCLGNS1141-gfp-sibs-2_S4_R1.fastq.gz UCLGNS1141-gfp-sibs-2_S4_R2.fastq.gz,fastq fastq,,,E MTAB 9113:UCLGNS1141 gfp sibs 2 S4 R,0:81 1:81,A:1056280368;C:1036355469;G:1045429486;T:1035773622;N:189389,81,81,,,1056280368,1036355469,1045429486,1035773622,189389,ERX4136408,ERS4580818,ERA2625401,Centre for Developmental Neurobiology King,Centre for Developmental Neurobiology King,2,0.95511,0.95696,0.02941,0.02903,0.71492,0.71628,0.45765,0.46537,81,81,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2020-05-22,Multi-stage,Multi-stage,Embryo Imprecise,All anatomical structures
9894,ERR4172793,ERX4136407,ERS4580817,ERP121885,PRJEB38455,RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E-MTAB-9113,Transcriptome Analysis,RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 05 22,,Protocols: Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion,sibling 1,SAMEA6853227,Centre for Developmental Neurobiology King's College London,ENA FIRST PUBLIC:2020 12 01T04:08:08Z|ENA LAST UPDATE:2020 05 22T17:13:15Z|External Id:SAMEA6853227|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2020 12 01T04:08:08Z|INSDC last update:2020 05 22T17:13:15Z|INSDC status:public|Submitter Id:E MTAB 9113:sibling 1|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|sample name:E MTAB 9113:sibling 1|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E MTAB 9113:sibling 1 p,sibling 1 p,RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP121885,Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 06 19,UCLGNS1141-gfp-sibs-1_S2_R1.fastq.gz UCLGNS1141-gfp-sibs-1_S2_R2.fastq.gz,fastq fastq,,,E MTAB 9113:UCLGNS1141 gfp sibs 1 S2 R,0:81 1:81,A:1121176859;C:1093927654;G:1108608188;T:1101082277;N:209264,81,81,,,1121176859,1093927654,1108608188,1101082277,209264,ERX4136407,ERS4580817,ERA2625401,Centre for Developmental Neurobiology King,Centre for Developmental Neurobiology King,2,0.95795,0.96004,0.02885,0.02854,0.71648,0.71756,0.44348,0.43956,81,81,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2020-05-22,Multi-stage,Multi-stage,Embryo Imprecise,All anatomical structures
9895,ERR4172792,ERX4136406,ERS4580816,ERP121885,PRJEB38455,RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E-MTAB-9113,Transcriptome Analysis,RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 05 22,,Protocols: Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion,sfpq 3,SAMEA6853226,Centre for Developmental Neurobiology King's College London,ENA FIRST PUBLIC:2020 12 01T04:08:08Z|ENA LAST UPDATE:2020 05 22T17:13:15Z|External Id:SAMEA6853226|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2020 12 01T04:08:08Z|INSDC last update:2020 05 22T17:13:15Z|INSDC status:public|Submitter Id:E MTAB 9113:sfpq 3|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:sfpq / |sample name:E MTAB 9113:sfpq 3|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E MTAB 9113:sfpq 3 p,sfpq 3 p,RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion,Experimental Factor: genotype:sfpq / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP121885,Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 06 19,UCLGNS1141-gfp-neg_3_S5_R1.fastq.gz UCLGNS1141-gfp-neg_3_S5_R2.fastq.gz,fastq fastq,,,E MTAB 9113:UCLGNS1141 gfp neg 3 S5 R,0:81 1:81,A:845849249;C:772302798;G:911660213;T:787409272;N:154042,81,81,,,845849249,772302798,911660213,787409272,154042,ERX4136406,ERS4580816,ERA2625401,Centre for Developmental Neurobiology King,Centre for Developmental Neurobiology King,2,0.96298,0.95486,0.03415,0.03476,0.7167,0.73503,0.4665,0.45947,81,81,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2020-05-22,Multi-stage,Multi-stage,Embryo Imprecise,All anatomical structures
9896,ERR4172791,ERX4136405,ERS4580815,ERP121885,PRJEB38455,RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E-MTAB-9113,Transcriptome Analysis,RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 05 22,,Protocols: Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion,sfpq 2,SAMEA6853225,Centre for Developmental Neurobiology King's College London,ENA FIRST PUBLIC:2020 12 01T04:08:08Z|ENA LAST UPDATE:2020 05 22T17:13:15Z|External Id:SAMEA6853225|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2020 12 01T04:08:08Z|INSDC last update:2020 05 22T17:13:15Z|INSDC status:public|Submitter Id:E MTAB 9113:sfpq 2|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:sfpq / |sample name:E MTAB 9113:sfpq 2|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E MTAB 9113:sfpq 2 p,sfpq 2 p,RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion,Experimental Factor: genotype:sfpq / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP121885,Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 06 19,UCLGNS1141-gfp-neg-2_S3_R1.fastq.gz UCLGNS1141-gfp-neg-2_S3_R2.fastq.gz,fastq fastq,,,E MTAB 9113:UCLGNS1141 gfp neg 2 S3 R,0:81 1:81,A:961156886;C:917011292;G:942713581;T:936109877;N:157724,81,81,,,961156886,917011292,942713581,936109877,157724,ERX4136405,ERS4580815,ERA2625401,Centre for Developmental Neurobiology King,Centre for Developmental Neurobiology King,2,0.96276,0.96147,0.03436,0.03382,0.71892,0.72021,0.4581,0.46402,81,81,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2020-05-22,Multi-stage,Multi-stage,Embryo Imprecise,All anatomical structures
9897,ERR4172790,ERX4136404,ERS4580814,ERP121885,PRJEB38455,RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E-MTAB-9113,Transcriptome Analysis,RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 05 22,,Protocols: Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion,sfpq 1,SAMEA6853224,Centre for Developmental Neurobiology King's College London,ENA FIRST PUBLIC:2020 12 01T04:08:08Z|ENA LAST UPDATE:2020 05 22T17:13:15Z|External Id:SAMEA6853224|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2020 12 01T04:08:08Z|INSDC last update:2020 05 22T17:13:15Z|INSDC status:public|Submitter Id:E MTAB 9113:sfpq 1|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:sfpq / |sample name:E MTAB 9113:sfpq 1|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E MTAB 9113:sfpq 1 p,sfpq 1 p,RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion,Experimental Factor: genotype:sfpq / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP121885,Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 06 19,UCLGNS1141-gfp-neg-1_S1_R1.fastq.gz UCLGNS1141-gfp-neg-1_S1_R2.fastq.gz,fastq fastq,,,E MTAB 9113:UCLGNS1141 gfp neg 1 S1 R,0:81 1:81,A:1046317524;C:1014946275;G:1036910299;T:1023619857;N:185237,81,81,,,1046317524,1014946275,1036910299,1023619857,185237,ERX4136404,ERS4580814,ERA2625401,Centre for Developmental Neurobiology King,Centre for Developmental Neurobiology King,2,0.96015,0.96173,0.03114,0.03098,0.7175,0.71865,0.46666,0.46399,81,81,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2020-05-22,Multi-stage,Multi-stage,Embryo Imprecise,All anatomical structures
10285,ERR7132868,ERX6700306,ERS8071630,ERP132573,PRJEB48231,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,E-MTAB-11086,Transcriptome Analysis,RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs   5 µM nicotine  1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug  plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos  exposed to the drug between 1 dpf and 5 dpf.,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,,Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Oxy 6,SAMEA10418786,Cambridge Institute of Therapeutic Immunology & Infectious Disease,ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418786|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Oxy 6|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:6|sample name:E MTAB 11086:Oxy 6|sex:not available|strain:Tüpfel long fin TLF,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs,E MTAB 11086:Oxy 6 p,Oxy 6 p,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Experimental Factor: compound:oxycod1|Experimental Factor: dose:1.14,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP132573,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,SLX-19351.B11.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.B11.HMLG7DRXX.s_2.r_2.fq.gz,fastq fastq,2330698400.0,23306984.0,E MTAB 11086:SLX 19351.B11.HMLG7DRXX.s 2.r ,0:50 1:50,A:619569172;C:544582535;G:551543197;T:614938437;N:65059,50,50,,,619569172,544582535,551543197,614938437,65059,ERX6700306,ERS8071630,ERA6757821,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,2,0.9448,0.95044,0.1029,0.09965,0.67152,0.66864,0.46844,0.47553,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2022-01-24,Larval,Larval,Embryo Imprecise,All anatomical structures
10286,ERR7132867,ERX6700305,ERS8071629,ERP132573,PRJEB48231,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,E-MTAB-11086,Transcriptome Analysis,RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs   5 µM nicotine  1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug  plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos  exposed to the drug between 1 dpf and 5 dpf.,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,,Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Oxy 5,SAMEA10418785,Cambridge Institute of Therapeutic Immunology & Infectious Disease,ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418785|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Oxy 5|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:5|sample name:E MTAB 11086:Oxy 5|sex:not available|strain:Tüpfel long fin TLF,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs,E MTAB 11086:Oxy 5 p,Oxy 5 p,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Experimental Factor: compound:oxycod1|Experimental Factor: dose:1.14,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP132573,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,SLX-19351.H9.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.H9.HMLG7DRXX.s_2.r_2.fq.gz,fastq fastq,2005314000.0,20053140.0,E MTAB 11086:SLX 19351.H9.HMLG7DRXX.s 2.r ,0:50 1:50,A:533671597;C:466449227;G:473126638;T:532010412;N:56126,50,50,,,533671597,466449227,473126638,532010412,56126,ERX6700305,ERS8071629,ERA6757821,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,2,0.94406,0.94793,0.11192,0.10798,0.66184,0.66074,0.4603,0.4683,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2022-01-24,Larval,Larval,Embryo Imprecise,All anatomical structures
10287,ERR7132866,ERX6700304,ERS8071628,ERP132573,PRJEB48231,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,E-MTAB-11086,Transcriptome Analysis,RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs   5 µM nicotine  1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug  plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos  exposed to the drug between 1 dpf and 5 dpf.,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,,Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Oxy 4,SAMEA10418784,Cambridge Institute of Therapeutic Immunology & Infectious Disease,ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418784|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Oxy 4|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:4|sample name:E MTAB 11086:Oxy 4|sex:not available|strain:Tüpfel long fin TLF,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs,E MTAB 11086:Oxy 4 p,Oxy 4 p,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Experimental Factor: compound:oxycod1|Experimental Factor: dose:1.14,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP132573,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,SLX-19351.A9.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.A9.HMLG7DRXX.s_2.r_2.fq.gz,fastq fastq,2036392600.0,20363926.0,E MTAB 11086:SLX 19351.A9.HMLG7DRXX.s 2.r ,0:50 1:50,A:547586305;C:468797712;G:476477515;T:543474510;N:56558,50,50,,,547586305,468797712,476477515,543474510,56558,ERX6700304,ERS8071628,ERA6757821,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,2,0.94235,0.94873,0.11388,0.11054,0.67655,0.67294,0.47135,0.47234,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2022-01-24,Larval,Larval,Embryo Imprecise,All anatomical structures
10288,ERR7132865,ERX6700303,ERS8071627,ERP132573,PRJEB48231,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,E-MTAB-11086,Transcriptome Analysis,RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs   5 µM nicotine  1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug  plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos  exposed to the drug between 1 dpf and 5 dpf.,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,,Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Oxy 3,SAMEA10418783,Cambridge Institute of Therapeutic Immunology & Infectious Disease,ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418783|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Oxy 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:3|sample name:E MTAB 11086:Oxy 3|sex:not available|strain:Tüpfel long fin TLF,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs,E MTAB 11086:Oxy 3 p,Oxy 3 p,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Experimental Factor: compound:oxycod1|Experimental Factor: dose:1.14,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP132573,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,SLX-19351.B9.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.B9.HMLG7DRXX.s_2.r_2.fq.gz,fastq fastq,2409819000.0,24098190.0,E MTAB 11086:SLX 19351.B9.HMLG7DRXX.s 2.r ,0:50 1:50,A:641053989;C:561685242;G:569693271;T:637320302;N:66196,50,50,,,641053989,561685242,569693271,637320302,66196,ERX6700303,ERS8071627,ERA6757821,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,2,0.94407,0.94902,0.10789,0.10496,0.66478,0.66387,0.47154,0.47373,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2022-01-24,Larval,Larval,Embryo Imprecise,All anatomical structures
10289,ERR7132864,ERX6700302,ERS8071626,ERP132573,PRJEB48231,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,E-MTAB-11086,Transcriptome Analysis,RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs   5 µM nicotine  1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug  plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos  exposed to the drug between 1 dpf and 5 dpf.,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,,Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Oxy 2,SAMEA10418782,Cambridge Institute of Therapeutic Immunology & Infectious Disease,ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418782|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Oxy 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:2|sample name:E MTAB 11086:Oxy 2|sex:not available|strain:Tüpfel long fin TLF,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs,E MTAB 11086:Oxy 2 p,Oxy 2 p,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Experimental Factor: compound:oxycod1|Experimental Factor: dose:1.14,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP132573,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,SLX-19351.A11.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.A11.HMLG7DRXX.s_2.r_2.fq.gz,fastq fastq,2068575200.0,20685752.0,E MTAB 11086:SLX 19351.A11.HMLG7DRXX.s 2.r ,0:50 1:50,A:547986796;C:484533693;G:490663629;T:545334125;N:56957,50,50,,,547986796,484533693,490663629,545334125,56957,ERX6700302,ERS8071626,ERA6757821,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,2,0.94539,0.95188,0.10373,0.10116,0.66718,0.66584,0.46991,0.47611,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2022-01-24,Larval,Larval,Embryo Imprecise,All anatomical structures
10290,ERR7132863,ERX6700301,ERS8071625,ERP132573,PRJEB48231,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,E-MTAB-11086,Transcriptome Analysis,RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs   5 µM nicotine  1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug  plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos  exposed to the drug between 1 dpf and 5 dpf.,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,,Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Oxy 1,SAMEA10418781,Cambridge Institute of Therapeutic Immunology & Infectious Disease,ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418781|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Oxy 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:1|sample name:E MTAB 11086:Oxy 1|sex:not available|strain:Tüpfel long fin TLF,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs,E MTAB 11086:Oxy 1 p,Oxy 1 p,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Experimental Factor: compound:oxycod1|Experimental Factor: dose:1.14,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP132573,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,SLX-19351.G9.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.G9.HMLG7DRXX.s_2.r_2.fq.gz,fastq fastq,2101607900.0,21016079.0,E MTAB 11086:SLX 19351.G9.HMLG7DRXX.s 2.r ,0:50 1:50,A:557420271;C:491161431;G:497494262;T:555471610;N:60326,50,50,,,557420271,491161431,497494262,555471610,60326,ERX6700301,ERS8071625,ERA6757821,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,2,0.94378,0.94916,0.10779,0.10431,0.66507,0.66377,0.45477,0.4679,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2022-01-24,Larval,Larval,Embryo Imprecise,All anatomical structures
10291,ERR7132862,ERX6700300,ERS8071624,ERP132573,PRJEB48231,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,E-MTAB-11086,Transcriptome Analysis,RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs   5 µM nicotine  1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug  plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos  exposed to the drug between 1 dpf and 5 dpf.,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,,Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Nic 6,SAMEA10418780,Cambridge Institute of Therapeutic Immunology & Infectious Disease,ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418780|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Nic 6|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:6|sample name:E MTAB 11086:Nic 6|sex:not available|strain:Tüpfel long fin TLF,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs,E MTAB 11086:Nic 6 p,Nic 6 p,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Experimental Factor: compound:nicotine|Experimental Factor: dose:5,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP132573,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,SLX-19351.H11.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.H11.HMLG7DRXX.s_2.r_2.fq.gz,fastq fastq,2236235700.0,22362357.0,E MTAB 11086:SLX 19351.H11.HMLG7DRXX.s 2.r ,0:50 1:50,A:597573047;C:518264376;G:525314754;T:595021334;N:62189,50,50,,,597573047,518264376,525314754,595021334,62189,ERX6700300,ERS8071624,ERA6757821,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,2,0.94255,0.94893,0.11268,0.10955,0.66819,0.66687,0.46882,0.47485,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2022-01-24,Larval,Larval,Embryo Imprecise,All anatomical structures
10292,ERR7132861,ERX6700299,ERS8071623,ERP132573,PRJEB48231,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,E-MTAB-11086,Transcriptome Analysis,RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs   5 µM nicotine  1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug  plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos  exposed to the drug between 1 dpf and 5 dpf.,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,,Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Nic 5,SAMEA10418779,Cambridge Institute of Therapeutic Immunology & Infectious Disease,ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418779|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Nic 5|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:5|sample name:E MTAB 11086:Nic 5|sex:not available|strain:Tüpfel long fin TLF,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs,E MTAB 11086:Nic 5 p,Nic 5 p,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Experimental Factor: compound:nicotine|Experimental Factor: dose:5,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP132573,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,SLX-19351.D10.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.D10.HMLG7DRXX.s_2.r_2.fq.gz,fastq fastq,1904348300.0,19043483.0,E MTAB 11086:SLX 19351.D10.HMLG7DRXX.s 2.r ,0:50 1:50,A:506678821;C:443756285;G:450118827;T:503742221;N:52146,50,50,,,506678821,443756285,450118827,503742221,52146,ERX6700299,ERS8071623,ERA6757821,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,2,0.94468,0.95019,0.10313,0.10023,0.66762,0.66513,0.47749,0.47611,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2022-01-24,Larval,Larval,Embryo Imprecise,All anatomical structures
10293,ERR7132860,ERX6700298,ERS8071622,ERP132573,PRJEB48231,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,E-MTAB-11086,Transcriptome Analysis,RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs   5 µM nicotine  1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug  plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos  exposed to the drug between 1 dpf and 5 dpf.,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,,Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Nic 4,SAMEA10418778,Cambridge Institute of Therapeutic Immunology & Infectious Disease,ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418778|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Nic 4|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:4|sample name:E MTAB 11086:Nic 4|sex:not available|strain:Tüpfel long fin TLF,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs,E MTAB 11086:Nic 4 p,Nic 4 p,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Experimental Factor: compound:nicotine|Experimental Factor: dose:5,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP132573,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,SLX-19351.C10.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.C10.HMLG7DRXX.s_2.r_2.fq.gz,fastq fastq,2134565600.0,21345656.0,E MTAB 11086:SLX 19351.C10.HMLG7DRXX.s 2.r ,0:50 1:50,A:568799307;C:496480840;G:503115671;T:566109163;N:60619,50,50,,,568799307,496480840,503115671,566109163,60619,ERX6700298,ERS8071622,ERA6757821,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,2,0.94279,0.94878,0.11466,0.1122,0.66291,0.66176,0.46991,0.47168,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2022-01-24,Larval,Larval,Embryo Imprecise,All anatomical structures
10294,ERR7132859,ERX6700297,ERS8071621,ERP132573,PRJEB48231,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,E-MTAB-11086,Transcriptome Analysis,RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs   5 µM nicotine  1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug  plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos  exposed to the drug between 1 dpf and 5 dpf.,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,,Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Nic 3,SAMEA10418777,Cambridge Institute of Therapeutic Immunology & Infectious Disease,ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418777|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Nic 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:3|sample name:E MTAB 11086:Nic 3|sex:not available|strain:Tüpfel long fin TLF,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs,E MTAB 11086:Nic 3 p,Nic 3 p,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Experimental Factor: compound:nicotine|Experimental Factor: dose:5,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP132573,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,SLX-19351.B10.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.B10.HMLG7DRXX.s_2.r_2.fq.gz,fastq fastq,2409355400.0,24093554.0,E MTAB 11086:SLX 19351.B10.HMLG7DRXX.s 2.r ,0:50 1:50,A:643046449;C:559571909;G:567748411;T:638920943;N:67688,50,50,,,643046449,559571909,567748411,638920943,67688,ERX6700297,ERS8071621,ERA6757821,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,2,0.94305,0.94796,0.11097,0.10766,0.66149,0.65888,0.46643,0.47512,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2022-01-24,Larval,Larval,Embryo Imprecise,All anatomical structures
10295,ERR7132858,ERX6700296,ERS8071620,ERP132573,PRJEB48231,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,E-MTAB-11086,Transcriptome Analysis,RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs   5 µM nicotine  1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug  plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos  exposed to the drug between 1 dpf and 5 dpf.,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,,Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Nic 2,SAMEA10418776,Cambridge Institute of Therapeutic Immunology & Infectious Disease,ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418776|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Nic 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:2|sample name:E MTAB 11086:Nic 2|sex:not available|strain:Tüpfel long fin TLF,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs,E MTAB 11086:Nic 2 p,Nic 2 p,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Experimental Factor: compound:nicotine|Experimental Factor: dose:5,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP132573,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,SLX-19351.F10.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.F10.HMLG7DRXX.s_2.r_2.fq.gz,fastq fastq,2046910800.0,20469108.0,E MTAB 11086:SLX 19351.F10.HMLG7DRXX.s 2.r ,0:50 1:50,A:547096034;C:475610002;G:481041169;T:543104402;N:59193,50,50,,,547096034,475610002,481041169,543104402,59193,ERX6700296,ERS8071620,ERA6757821,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,2,0.94391,0.94965,0.10824,0.10557,0.66241,0.65963,0.47747,0.47375,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2022-01-24,Larval,Larval,Embryo Imprecise,All anatomical structures
10296,ERR7132857,ERX6700295,ERS8071619,ERP132573,PRJEB48231,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,E-MTAB-11086,Transcriptome Analysis,RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs   5 µM nicotine  1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug  plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos  exposed to the drug between 1 dpf and 5 dpf.,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,,Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Nic 1,SAMEA10418775,Cambridge Institute of Therapeutic Immunology & Infectious Disease,ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418775|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Nic 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:1|sample name:E MTAB 11086:Nic 1|sex:not available|strain:Tüpfel long fin TLF,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs,E MTAB 11086:Nic 1 p,Nic 1 p,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Experimental Factor: compound:nicotine|Experimental Factor: dose:5,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP132573,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,SLX-19351.G10.HMLG7DRXX.s_2.r_2.fq.gz SLX-19351.G10.HMLG7DRXX.s_2.r_1.fq.gz,fastq fastq,2001312600.0,20013126.0,E MTAB 11086:SLX 19351.G10.HMLG7DRXX.s 2.r ,0:50 1:50,A:535065614;C:463328218;G:468900497;T:533963156;N:55115,50,50,,,535065614,463328218,468900497,533963156,55115,ERX6700295,ERS8071619,ERA6757821,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,2,0.94179,0.9477,0.11455,0.11139,0.66697,0.66569,0.45749,0.47217,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2022-01-24,Larval,Larval,Embryo Imprecise,All anatomical structures
10297,ERR7132856,ERX6700294,ERS8071618,ERP132573,PRJEB48231,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,E-MTAB-11086,Transcriptome Analysis,RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs   5 µM nicotine  1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug  plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos  exposed to the drug between 1 dpf and 5 dpf.,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,,Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Cnt 6,SAMEA10418774,Cambridge Institute of Therapeutic Immunology & Infectious Disease,ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418774|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Cnt 6|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:6|sample name:E MTAB 11086:Cnt 6|sex:not available|strain:Tüpfel long fin TLF,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs,E MTAB 11086:Cnt 6 p,Cnt 6 p,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Experimental Factor: compound:n1,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP132573,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,SLX-19351.C11.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.C11.HMLG7DRXX.s_2.r_2.fq.gz,fastq fastq,2311609400.0,23116094.0,E MTAB 11086:SLX 19351.C11.HMLG7DRXX.s 2.r ,0:50 1:50,A:616569709;C:538286683;G:545161394;T:611525546;N:66068,50,50,,,616569709,538286683,545161394,611525546,66068,ERX6700294,ERS8071618,ERA6757821,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,2,0.94486,0.95028,0.1097,0.10661,0.66703,0.6644,0.47311,0.47453,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2022-01-24,Larval,Larval,Embryo Imprecise,All anatomical structures
10298,ERR7132855,ERX6700293,ERS8071617,ERP132573,PRJEB48231,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,E-MTAB-11086,Transcriptome Analysis,RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs   5 µM nicotine  1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug  plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos  exposed to the drug between 1 dpf and 5 dpf.,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,,Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Cnt 5,SAMEA10418773,Cambridge Institute of Therapeutic Immunology & Infectious Disease,ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418773|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Cnt 5|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:5|sample name:E MTAB 11086:Cnt 5|sex:not available|strain:Tüpfel long fin TLF,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs,E MTAB 11086:Cnt 5 p,Cnt 5 p,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Experimental Factor: compound:n1,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP132573,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,SLX-19351.G11.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.G11.HMLG7DRXX.s_2.r_2.fq.gz,fastq fastq,1590322800.0,15903228.0,E MTAB 11086:SLX 19351.G11.HMLG7DRXX.s 2.r ,0:50 1:50,A:407583907;C:385496371;G:392945463;T:404250386;N:46673,50,50,,,407583907,385496371,392945463,404250386,46673,ERX6700293,ERS8071617,ERA6757821,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,2,0.94942,0.95571,0.10693,0.10576,0.69329,0.69063,0.46419,0.4826,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2022-01-24,Larval,Larval,Embryo Imprecise,All anatomical structures
10299,ERR7132854,ERX6700292,ERS8071616,ERP132573,PRJEB48231,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,E-MTAB-11086,Transcriptome Analysis,RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs   5 µM nicotine  1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug  plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos  exposed to the drug between 1 dpf and 5 dpf.,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,,Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Cnt 4,SAMEA10418772,Cambridge Institute of Therapeutic Immunology & Infectious Disease,ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418772|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Cnt 4|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:4|sample name:E MTAB 11086:Cnt 4|sex:not available|strain:Tüpfel long fin TLF,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs,E MTAB 11086:Cnt 4 p,Cnt 4 p,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Experimental Factor: compound:n1,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP132573,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,SLX-19351.C9.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.C9.HMLG7DRXX.s_2.r_2.fq.gz,fastq fastq,2079441500.0,20794415.0,E MTAB 11086:SLX 19351.C9.HMLG7DRXX.s 2.r ,0:50 1:50,A:555430147;C:483109623;G:489773903;T:551069513;N:58314,50,50,,,555430147,483109623,489773903,551069513,58314,ERX6700292,ERS8071616,ERA6757821,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,2,0.94258,0.9491,0.10928,0.10545,0.66561,0.66279,0.46967,0.47237,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2022-01-24,Larval,Larval,Embryo Imprecise,All anatomical structures
10300,ERR7132853,ERX6700291,ERS8071615,ERP132573,PRJEB48231,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,E-MTAB-11086,Transcriptome Analysis,RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs   5 µM nicotine  1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug  plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos  exposed to the drug between 1 dpf and 5 dpf.,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,,Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Cnt 3,SAMEA10418771,Cambridge Institute of Therapeutic Immunology & Infectious Disease,ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418771|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Cnt 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:3|sample name:E MTAB 11086:Cnt 3|sex:not available|strain:Tüpfel long fin TLF,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs,E MTAB 11086:Cnt 3 p,Cnt 3 p,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Experimental Factor: compound:n1,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP132573,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,SLX-19351.H10.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.H10.HMLG7DRXX.s_2.r_2.fq.gz,fastq fastq,2606680900.0,26066809.0,E MTAB 11086:SLX 19351.H10.HMLG7DRXX.s 2.r ,0:50 1:50,A:698010494;C:604285893;G:612505273;T:691805693;N:73547,50,50,,,698010494,604285893,612505273,691805693,73547,ERX6700291,ERS8071615,ERA6757821,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,2,0.94271,0.94917,0.11288,0.10987,0.67115,0.66827,0.4729,0.4736,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2022-01-24,Larval,Larval,Embryo Imprecise,All anatomical structures
10301,ERR7132852,ERX6700290,ERS8071614,ERP132573,PRJEB48231,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,E-MTAB-11086,Transcriptome Analysis,RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs   5 µM nicotine  1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug  plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos  exposed to the drug between 1 dpf and 5 dpf.,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,,Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Cnt 2,SAMEA10418770,Cambridge Institute of Therapeutic Immunology & Infectious Disease,ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418770|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Cnt 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:2|sample name:E MTAB 11086:Cnt 2|sex:not available|strain:Tüpfel long fin TLF,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs,E MTAB 11086:Cnt 2 p,Cnt 2 p,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Experimental Factor: compound:n1,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP132573,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,SLX-19351.E11.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.E11.HMLG7DRXX.s_2.r_2.fq.gz,fastq fastq,2248468400.0,22484684.0,E MTAB 11086:SLX 19351.E11.HMLG7DRXX.s 2.r ,0:50 1:50,A:601914808;C:521501189;G:527610060;T:597380501;N:61842,50,50,,,601914808,521501189,527610060,597380501,61842,ERX6700290,ERS8071614,ERA6757821,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,2,0.94347,0.94939,0.11234,0.10984,0.66689,0.66342,0.46711,0.46831,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2022-01-24,Larval,Larval,Embryo Imprecise,All anatomical structures
10302,ERR7132851,ERX6700289,ERS8071613,ERP132573,PRJEB48231,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,E-MTAB-11086,Transcriptome Analysis,RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs   5 µM nicotine  1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug  plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos  exposed to the drug between 1 dpf and 5 dpf.,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,,Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Cnt 1,SAMEA10418769,Cambridge Institute of Therapeutic Immunology & Infectious Disease,ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418769|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Cnt 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:1|sample name:E MTAB 11086:Cnt 1|sex:not available|strain:Tüpfel long fin TLF,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs,E MTAB 11086:Cnt 1 p,Cnt 1 p,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Experimental Factor: compound:n1,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP132573,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,SLX-19351.D11.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.D11.HMLG7DRXX.s_2.r_2.fq.gz,fastq fastq,1958517300.0,19585173.0,E MTAB 11086:SLX 19351.D11.HMLG7DRXX.s 2.r ,0:50 1:50,A:523101436;C:454540970;G:459925156;T:520895141;N:54597,50,50,,,523101436,454540970,459925156,520895141,54597,ERX6700289,ERS8071613,ERA6757821,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,2,0.94413,0.95047,0.10482,0.10253,0.67044,0.66782,0.47233,0.4771,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2022-01-24,Larval,Larval,Embryo Imprecise,All anatomical structures
10303,ERR7132850,ERX6700288,ERS8071612,ERP132573,PRJEB48231,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,E-MTAB-11086,Transcriptome Analysis,RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs   5 µM nicotine  1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug  plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos  exposed to the drug between 1 dpf and 5 dpf.,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,,Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Amp 6,SAMEA10418768,Cambridge Institute of Therapeutic Immunology & Infectious Disease,ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418768|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Amp 6|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:6|sample name:E MTAB 11086:Amp 6|sex:not available|strain:Tüpfel long fin TLF,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs,E MTAB 11086:Amp 6 p,Amp 6 p,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Experimental Factor: compound:amphetamine|Experimental Factor: dose:25,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP132573,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,SLX-19351.E9.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.E9.HMLG7DRXX.s_2.r_2.fq.gz,fastq fastq,1712505000.0,17125050.0,E MTAB 11086:SLX 19351.E9.HMLG7DRXX.s 2.r ,0:50 1:50,A:455641002;C:398314392;G:404466444;T:454036255;N:46907,50,50,,,455641002,398314392,404466444,454036255,46907,ERX6700288,ERS8071612,ERA6757821,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,2,0.94358,0.94966,0.10681,0.1037,0.66665,0.66373,0.46688,0.47225,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2022-01-24,Larval,Larval,Embryo Imprecise,All anatomical structures
10304,ERR7132849,ERX6700287,ERS8071611,ERP132573,PRJEB48231,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,E-MTAB-11086,Transcriptome Analysis,RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs   5 µM nicotine  1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug  plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos  exposed to the drug between 1 dpf and 5 dpf.,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,,Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Amp 5,SAMEA10418767,Cambridge Institute of Therapeutic Immunology & Infectious Disease,ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418767|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Amp 5|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:5|sample name:E MTAB 11086:Amp 5|sex:not available|strain:Tüpfel long fin TLF,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs,E MTAB 11086:Amp 5 p,Amp 5 p,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Experimental Factor: compound:amphetamine|Experimental Factor: dose:25,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP132573,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,SLX-19351.A10.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.A10.HMLG7DRXX.s_2.r_2.fq.gz,fastq fastq,2007519200.0,20075192.0,E MTAB 11086:SLX 19351.A10.HMLG7DRXX.s 2.r ,0:50 1:50,A:534568558;C:467539630;G:473805079;T:531550688;N:55245,50,50,,,534568558,467539630,473805079,531550688,55245,ERX6700287,ERS8071611,ERA6757821,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,2,0.94408,0.9499,0.10888,0.10604,0.66797,0.66458,0.46039,0.46669,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2022-01-24,Larval,Larval,Embryo Imprecise,All anatomical structures
10305,ERR7132848,ERX6700286,ERS8071610,ERP132573,PRJEB48231,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,E-MTAB-11086,Transcriptome Analysis,RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs   5 µM nicotine  1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug  plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos  exposed to the drug between 1 dpf and 5 dpf.,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,,Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Amp 4,SAMEA10418766,Cambridge Institute of Therapeutic Immunology & Infectious Disease,ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418766|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Amp 4|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:4|sample name:E MTAB 11086:Amp 4|sex:not available|strain:Tüpfel long fin TLF,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs,E MTAB 11086:Amp 4 p,Amp 4 p,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Experimental Factor: compound:amphetamine|Experimental Factor: dose:25,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP132573,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,SLX-19351.F11.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.F11.HMLG7DRXX.s_2.r_2.fq.gz,fastq fastq,1845345300.0,18453453.0,E MTAB 11086:SLX 19351.F11.HMLG7DRXX.s 2.r ,0:50 1:50,A:490920758;C:430637266;G:435667744;T:488067453;N:52079,50,50,,,490920758,430637266,435667744,488067453,52079,ERX6700286,ERS8071610,ERA6757821,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,2,0.94484,0.9504,0.10472,0.10237,0.66618,0.66336,0.46903,0.47774,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2022-01-24,Larval,Larval,Embryo Imprecise,All anatomical structures
10306,ERR7132847,ERX6700285,ERS8071609,ERP132573,PRJEB48231,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,E-MTAB-11086,Transcriptome Analysis,RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs   5 µM nicotine  1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug  plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos  exposed to the drug between 1 dpf and 5 dpf.,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,,Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Amp 3,SAMEA10418765,Cambridge Institute of Therapeutic Immunology & Infectious Disease,ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418765|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Amp 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:3|sample name:E MTAB 11086:Amp 3|sex:not available|strain:Tüpfel long fin TLF,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs,E MTAB 11086:Amp 3 p,Amp 3 p,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Experimental Factor: compound:amphetamine|Experimental Factor: dose:25,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP132573,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,SLX-19351.F9.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.F9.HMLG7DRXX.s_2.r_2.fq.gz,fastq fastq,2195415300.0,21954153.0,E MTAB 11086:SLX 19351.F9.HMLG7DRXX.s 2.r ,0:50 1:50,A:583956682;C:511927452;G:518373455;T:581095379;N:62332,50,50,,,583956682,511927452,518373455,581095379,62332,ERX6700285,ERS8071609,ERA6757821,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,2,0.94571,0.95178,0.10567,0.10288,0.6688,0.66661,0.4677,0.47288,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2022-01-24,Larval,Larval,Embryo Imprecise,All anatomical structures
10307,ERR7132846,ERX6700284,ERS8071608,ERP132573,PRJEB48231,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,E-MTAB-11086,Transcriptome Analysis,RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs   5 µM nicotine  1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug  plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos  exposed to the drug between 1 dpf and 5 dpf.,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,,Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Amp 2,SAMEA10418764,Cambridge Institute of Therapeutic Immunology & Infectious Disease,ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418764|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Amp 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:2|sample name:E MTAB 11086:Amp 2|sex:not available|strain:Tüpfel long fin TLF,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs,E MTAB 11086:Amp 2 p,Amp 2 p,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Experimental Factor: compound:amphetamine|Experimental Factor: dose:25,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP132573,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,SLX-19351.D9.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.D9.HMLG7DRXX.s_2.r_2.fq.gz,fastq fastq,2093635000.0,20936350.0,E MTAB 11086:SLX 19351.D9.HMLG7DRXX.s 2.r ,0:50 1:50,A:556451381;C:488314672;G:495691630;T:553118514;N:58803,50,50,,,556451381,488314672,495691630,553118514,58803,ERX6700284,ERS8071608,ERA6757821,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,2,0.94407,0.95012,0.11198,0.10872,0.66651,0.66352,0.46901,0.47198,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2022-01-24,Larval,Larval,Embryo Imprecise,All anatomical structures
10308,ERR7132845,ERX6700283,ERS8071607,ERP132573,PRJEB48231,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,E-MTAB-11086,Transcriptome Analysis,RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs   5 µM nicotine  1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug  plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos  exposed to the drug between 1 dpf and 5 dpf.,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,,Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Amp 1,SAMEA10418763,Cambridge Institute of Therapeutic Immunology & Infectious Disease,ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418763|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Amp 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:1|sample name:E MTAB 11086:Amp 1|sex:not available|strain:Tüpfel long fin TLF,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs,E MTAB 11086:Amp 1 p,Amp 1 p,RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period  larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet  beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.,Experimental Factor: compound:amphetamine|Experimental Factor: dose:25,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP132573,Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs,ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24,SLX-19351.E10.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.E10.HMLG7DRXX.s_2.r_2.fq.gz,fastq fastq,2254130000.0,22541300.0,E MTAB 11086:SLX 19351.E10.HMLG7DRXX.s 2.r ,0:50 1:50,A:599784010;C:525655199;G:531849347;T:596777643;N:63801,50,50,,,599784010,525655199,531849347,596777643,63801,ERX6700283,ERS8071607,ERA6757821,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive,2,0.94449,0.95026,0.10608,0.10323,0.66758,0.66257,0.46869,0.47045,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2022-01-24,Larval,Larval,Embryo Imprecise,All anatomical structures
11245,ERR10851251,ERX10296231,ERS14601258,ERP144652,PRJEB59599,Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41,E-MTAB-12577,Transcriptome Analysis,Comparison between wildtype and Gata2b heterozygous zebrafish HSPCs,ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17,,Protocols: Embryos were dissociated using Collagenase 1  2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified,WT3 cd41pflt1p48hpf,SAMEA112483908,Department of Hematology cancer institute ErasmusMC,ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17|External Id:SAMEA112483908|INSDC center alias:Department of Hematology cancer institute ErasmusMC|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC first public:2023 02 17T00:21:53Z|INSDC last update:2023 02 17T00:21:53Z|INSDC status:public|Submitter Id:E MTAB 12577:WT3 cd41pflt1p48hpf|age:48|broker name:ArrayExpress|cell type:hematopoietic stem cell|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|immunophenotype:CD41:GFP+ Flt1:RFP+|individual:pools of 3 embryos 1|organism part:liver|sample name:E MTAB 12577:WT3 cd41pflt1p48hpf|scientific name:Danio rerio|strain:TgCD41:GFP TgFlt1:RFP WT,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41,E MTAB 12577:WT3 cd41pflt1p48hpf p,WT3 cd41pflt1p48hpf p,Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41,Embryos were dissociated using Collagenase 1  2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP144652,Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41,ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17,WT3_cd41pflt1p48hpf_R1.fastq.gz WT3_cd41pflt1p48hpf_R2.fastq.gz,fastq fastq,2865896816.0,14187608.0,E MTAB 12577:WT3 cd41pflt1p48hpf R,0:101 1:101,A:766433553;C:631932872;G:660672891;T:806849737;N:7763,101,101,,,766433553,631932872,660672891,806849737,7763,ERX10296231,ERS14601258,ERA20429817,Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive,Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive,2,0.90501,0.85042,0.09405,0.09335,0.87286,0.87943,0.48423,0.47904,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,Netherlands,2023-02-17,Hatching,Embryo,Embryo Imprecise,All anatomical structures
11246,ERR10851250,ERX10296230,ERS14601257,ERP144652,PRJEB59599,Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41,E-MTAB-12577,Transcriptome Analysis,Comparison between wildtype and Gata2b heterozygous zebrafish HSPCs,ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17,,Protocols: Embryos were dissociated using Collagenase 1  2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified,WT2 cd41pflt1p48hpf,SAMEA112483907,Department of Hematology cancer institute ErasmusMC,ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17|External Id:SAMEA112483907|INSDC center alias:Department of Hematology cancer institute ErasmusMC|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC first public:2023 02 17T00:21:53Z|INSDC last update:2023 02 17T00:21:53Z|INSDC status:public|Submitter Id:E MTAB 12577:WT2 cd41pflt1p48hpf|age:48|broker name:ArrayExpress|cell type:hematopoietic stem cell|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|immunophenotype:CD41:GFP+ Flt1:RFP+|individual:pools of 3 embryos 5|organism part:liver|sample name:E MTAB 12577:WT2 cd41pflt1p48hpf|scientific name:Danio rerio|strain:TgCD41:GFP TgFlt1:RFP WT,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41,E MTAB 12577:WT2 cd41pflt1p48hpf p,WT2 cd41pflt1p48hpf p,Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41,Embryos were dissociated using Collagenase 1  2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP144652,Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41,ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17,WT2_cd41pflt1p48hpf_R1.fastq.gz WT2_cd41pflt1p48hpf_R2.fastq.gz,fastq fastq,2929743360.0,14503680.0,E MTAB 12577:WT2 cd41pflt1p48hpf R,0:101 1:101,A:803775344;C:639485652;G:661899077;T:824575679;N:7608,101,101,,,803775344,639485652,661899077,824575679,7608,ERX10296230,ERS14601257,ERA20429817,Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive,Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive,2,0.94558,0.90768,0.09379,0.09399,0.79058,0.79833,0.48216,0.47743,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,Netherlands,2023-02-17,Hatching,Embryo,Embryo Imprecise,All anatomical structures
11247,ERR10851249,ERX10296229,ERS14601256,ERP144652,PRJEB59599,Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41,E-MTAB-12577,Transcriptome Analysis,Comparison between wildtype and Gata2b heterozygous zebrafish HSPCs,ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17,,Protocols: Embryos were dissociated using Collagenase 1  2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified,WT1 cd41pflt1p48hpf,SAMEA112483906,Department of Hematology cancer institute ErasmusMC,ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17|External Id:SAMEA112483906|INSDC center alias:Department of Hematology cancer institute ErasmusMC|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC first public:2023 02 17T00:21:53Z|INSDC last update:2023 02 17T00:21:53Z|INSDC status:public|Submitter Id:E MTAB 12577:WT1 cd41pflt1p48hpf|age:48|broker name:ArrayExpress|cell type:hematopoietic stem cell|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|immunophenotype:CD41:GFP+ Flt1:RFP+|individual:pools of 3 embryos 4|organism part:liver|sample name:E MTAB 12577:WT1 cd41pflt1p48hpf|scientific name:Danio rerio|strain:TgCD41:GFP TgFlt1:RFP WT,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41,E MTAB 12577:WT1 cd41pflt1p48hpf p,WT1 cd41pflt1p48hpf p,Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41,Embryos were dissociated using Collagenase 1  2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP144652,Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41,ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17,WT1_cd41pflt1p48hpf_R1.fastq.gz WT1_cd41pflt1p48hpf_R2.fastq.gz,fastq fastq,3248647426.0,16082413.0,E MTAB 12577:WT1 cd41pflt1p48hpf R,0:101 1:101,A:883030193;C:725566673;G:750551574;T:889489774;N:9212,101,101,,,883030193,725566673,750551574,889489774,9212,ERX10296229,ERS14601256,ERA20429817,Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive,Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive,2,0.91568,0.8915,0.09819,0.09602,0.86634,0.8706,0.48887,0.48731,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,Netherlands,2023-02-17,Hatching,Embryo,Embryo Imprecise,All anatomical structures
11248,ERR10851248,ERX10296228,ERS14601255,ERP144652,PRJEB59599,Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41,E-MTAB-12577,Transcriptome Analysis,Comparison between wildtype and Gata2b heterozygous zebrafish HSPCs,ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17,,Protocols: Embryos were dissociated using Collagenase 1  2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified,Het3 cd41pflt1p48hpf,SAMEA112483905,Department of Hematology cancer institute ErasmusMC,ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17|External Id:SAMEA112483905|INSDC center alias:Department of Hematology cancer institute ErasmusMC|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC first public:2023 02 17T00:21:53Z|INSDC last update:2023 02 17T00:21:53Z|INSDC status:public|Submitter Id:E MTAB 12577:Het3 cd41pflt1p48hpf|age:48|broker name:ArrayExpress|cell type:hematopoietic stem cell|common name:zebrafish|developmental stage:embryo|genotype:Gata2b +/ |immunophenotype:CD41:GFP+ Flt1:RFP+|individual:pools of 3 embryos 3|organism part:liver|sample name:E MTAB 12577:Het3 cd41pflt1p48hpf|scientific name:Danio rerio|strain:TgCD41:GFP TgFlt1:RFP Gata2b KO,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41,E MTAB 12577:Het3 cd41pflt1p48hpf p,Het3 cd41pflt1p48hpf p,Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41,Embryos were dissociated using Collagenase 1  2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified,Experimental Factor: genotype:Gata2b +/ ,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP144652,Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41,ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17,Het3_cd41pflt1p48hpf_R1.fastq.gz Het3_cd41pflt1p48hpf_R2.fastq.gz,fastq fastq,2826011512.0,13990156.0,E MTAB 12577:Het3 cd41pflt1p48hpf R,0:101 1:101,A:777245323;C:622387331;G:640520737;T:785850577;N:7544,101,101,,,777245323,622387331,640520737,785850577,7544,ERX10296228,ERS14601255,ERA20429817,Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive,Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive,2,0.92716,0.90121,0.10896,0.10895,0.76739,0.77628,0.47007,0.46569,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,Netherlands,2023-02-17,Hatching,Embryo,Embryo Imprecise,All anatomical structures
11249,ERR10851247,ERX10296227,ERS14601254,ERP144652,PRJEB59599,Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41,E-MTAB-12577,Transcriptome Analysis,Comparison between wildtype and Gata2b heterozygous zebrafish HSPCs,ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17,,Protocols: Embryos were dissociated using Collagenase 1  2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified,Het2 cd41pflt1p48hpf,SAMEA112483904,Department of Hematology cancer institute ErasmusMC,ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17|External Id:SAMEA112483904|INSDC center alias:Department of Hematology cancer institute ErasmusMC|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC first public:2023 02 17T00:21:53Z|INSDC last update:2023 02 17T00:21:53Z|INSDC status:public|Submitter Id:E MTAB 12577:Het2 cd41pflt1p48hpf|age:48|broker name:ArrayExpress|cell type:hematopoietic stem cell|common name:zebrafish|developmental stage:embryo|genotype:Gata2b +/ |immunophenotype:CD41:GFP+ Flt1:RFP+|individual:pools of 3 embryos 2|organism part:liver|sample name:E MTAB 12577:Het2 cd41pflt1p48hpf|scientific name:Danio rerio|strain:TgCD41:GFP TgFlt1:RFP Gata2b KO,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41,E MTAB 12577:Het2 cd41pflt1p48hpf p,Het2 cd41pflt1p48hpf p,Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41,Embryos were dissociated using Collagenase 1  2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified,Experimental Factor: genotype:Gata2b +/ ,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP144652,Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41,ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17,Het2_cd41pflt1p48hpf_R1.fastq.gz Het2_cd41pflt1p48hpf_R2.fastq.gz,fastq fastq,2999149954.0,14847277.0,E MTAB 12577:Het2 cd41pflt1p48hpf R,0:101 1:101,A:822247269;C:656610849;G:681974696;T:838308917;N:8223,101,101,,,822247269,656610849,681974696,838308917,8223,ERX10296227,ERS14601254,ERA20429817,Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive,Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive,2,0.94678,0.91473,0.10277,0.10053,0.76686,0.77684,0.46042,0.47202,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,Netherlands,2023-02-17,Hatching,Embryo,Embryo Imprecise,All anatomical structures
11250,ERR10851246,ERX10296226,ERS14601253,ERP144652,PRJEB59599,Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41,E-MTAB-12577,Transcriptome Analysis,Comparison between wildtype and Gata2b heterozygous zebrafish HSPCs,ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17,,Protocols: Embryos were dissociated using Collagenase 1  2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified,Het1 cd41pflt1p48hpf,SAMEA112483903,Department of Hematology cancer institute ErasmusMC,ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17|External Id:SAMEA112483903|INSDC center alias:Department of Hematology cancer institute ErasmusMC|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC first public:2023 02 17T00:21:53Z|INSDC last update:2023 02 17T00:21:53Z|INSDC status:public|Submitter Id:E MTAB 12577:Het1 cd41pflt1p48hpf|age:48|broker name:ArrayExpress|cell type:hematopoietic stem cell|common name:zebrafish|developmental stage:embryo|genotype:Gata2b +/ |immunophenotype:CD41:GFP+ Flt1:RFP+|individual:pools of 3 embryos 1|organism part:liver|sample name:E MTAB 12577:Het1 cd41pflt1p48hpf|scientific name:Danio rerio|strain:TgCD41:GFP TgFlt1:RFP Gata2b KO,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41,E MTAB 12577:Het1 cd41pflt1p48hpf p,Het1 cd41pflt1p48hpf p,Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41,Embryos were dissociated using Collagenase 1  2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified,Experimental Factor: genotype:Gata2b +/ ,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP144652,Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41,ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17,Het1_cd41pflt1p48hpf_R1.fastq.gz Het1_cd41pflt1p48hpf_R2.fastq.gz,fastq fastq,36682350994.0,181595797.0,E MTAB 12577:Het1 cd41pflt1p48hpf R,0:101 1:101,A:10130106739;C:7969045717;G:8373740062;T:10209360741;N:97735,101,101,,,10130106739,7969045717,8373740062,10209360741,97735,ERX10296226,ERS14601253,ERA20429817,Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive,Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive,2,0.94302,0.91104,0.11873,0.11597,0.7554,0.76579,0.48813,0.47764,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,Netherlands,2023-02-17,Hatching,Embryo,Embryo Imprecise,All anatomical structures
11723,ERR11422840,ERX10830011,ERS15422295,ERP147133,PRJEB62042,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E-MTAB-12934,Transcriptome Analysis,RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos.,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,,Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,srpk3 hom ttn1 het 1,SAMEA113427169,QMUL,ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427169|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 hom ttn1 het 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3  / ; ttn.1 +/ |individual:pool of 3 embryos 1|organism part:embryo|replicate:1|sample name:E MTAB 12934:srpk3 hom ttn1 het 1|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin,,,,,,,,,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E MTAB 12934:srpk3 hom ttn1 het 1 p,srpk3 hom ttn1 het 1 p,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,Experimental Factor: genotype:srpk3  / ; ttn.1 +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP147133,Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,SLX-21419.C4.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.C4.HV2TTDRXY.s_2.r_2.fq.gz,fastq fastq,5201588100.0,17338627.0,E MTAB 12934:SLX 21419.C4.HV2TTDRXY.s 2.r ,0:150 1:150,A:1395812979;C:1209220590;G:1233107747;T:1363200419;N:246365,150,150,,,1395812979,1209220590,1233107747,1363200419,246365,ERX10830011,ERS15422295,ERA23329494,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2024-02-09,Larval,Larval,Embryo Imprecise,All anatomical structures
11724,ERR11422856,ERX10830027,ERS15422311,ERP147133,PRJEB62042,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E-MTAB-12934,Transcriptome Analysis,RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos.,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,,Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,srpk3 wt ttn1 het 8,SAMEA113427185,QMUL,ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427185|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 wt ttn1 het 8|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 +/+; ttn.1 +/ |individual:pool of 3 embryos 8|organism part:embryo|replicate:8|sample name:E MTAB 12934:srpk3 wt ttn1 het 8|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin,,,,,,,,,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E MTAB 12934:srpk3 wt ttn1 het 8 p,srpk3 wt ttn1 het 8 p,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,Experimental Factor: genotype:srpk3 +/+; ttn.1 +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP147133,Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,SLX-21419.C5.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.C5.HV2TTDRXY.s_2.r_2.fq.gz,fastq fastq,6243031800.0,20810106.0,E MTAB 12934:SLX 21419.C5.HV2TTDRXY.s 2.r ,0:150 1:150,A:1678428066;C:1448795147;G:1483028868;T:1632478253;N:301466,150,150,,,1678428066,1448795147,1483028868,1632478253,301466,ERX10830027,ERS15422311,ERA23329494,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2024-02-09,Larval,Larval,Embryo Imprecise,All anatomical structures
11725,ERR11422863,ERX10830034,ERS15422318,ERP147133,PRJEB62042,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E-MTAB-12934,Transcriptome Analysis,RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos.,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,,Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,srpk3 wt ttn1 wt 7,SAMEA113427192,QMUL,ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427192|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 wt ttn1 wt 7|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 +/+; ttn.1 +/+|individual:pool of 3 embryos 7|organism part:embryo|replicate:7|sample name:E MTAB 12934:srpk3 wt ttn1 wt 7|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin,,,,,,,,,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E MTAB 12934:srpk3 wt ttn1 wt 7 p,srpk3 wt ttn1 wt 7 p,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,Experimental Factor: genotype:srpk3 +/+; ttn.1 +/+,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP147133,Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,SLX-21419.G3.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.G3.HV2TTDRXY.s_2.r_2.fq.gz,fastq fastq,7924538100.0,26415127.0,E MTAB 12934:SLX 21419.G3.HV2TTDRXY.s 2.r ,0:150 1:150,A:2128544326;C:1844570027;G:1875605207;T:2075443615;N:374925,150,150,,,2128544326,1844570027,1875605207,2075443615,374925,ERX10830034,ERS15422318,ERA23329494,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2024-02-09,Larval,Larval,Embryo Imprecise,All anatomical structures
11726,ERR11422862,ERX10830033,ERS15422317,ERP147133,PRJEB62042,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E-MTAB-12934,Transcriptome Analysis,RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos.,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,,Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,srpk3 wt ttn1 wt 6,SAMEA113427191,QMUL,ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427191|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 wt ttn1 wt 6|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 +/+; ttn.1 +/+|individual:pool of 3 embryos 6|organism part:embryo|replicate:6|sample name:E MTAB 12934:srpk3 wt ttn1 wt 6|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin,,,,,,,,,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E MTAB 12934:srpk3 wt ttn1 wt 6 p,srpk3 wt ttn1 wt 6 p,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,Experimental Factor: genotype:srpk3 +/+; ttn.1 +/+,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP147133,Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,SLX-21419.D5.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.D5.HV2TTDRXY.s_2.r_2.fq.gz,fastq fastq,8652848700.0,28842829.0,E MTAB 12934:SLX 21419.D5.HV2TTDRXY.s 2.r ,0:150 1:150,A:2323784475;C:2011287942;G:2055678520;T:2261686116;N:411647,150,150,,,2323784475,2011287942,2055678520,2261686116,411647,ERX10830033,ERS15422317,ERA23329494,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2024-02-09,Larval,Larval,Embryo Imprecise,All anatomical structures
11727,ERR11422852,ERX10830023,ERS15422307,ERP147133,PRJEB62042,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E-MTAB-12934,Transcriptome Analysis,RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos.,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,,Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,srpk3 wt ttn1 het 1,SAMEA113427181,QMUL,ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427181|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 wt ttn1 het 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 +/+; ttn.1 +/ |individual:pool of 3 embryos 1|organism part:embryo|replicate:1|sample name:E MTAB 12934:srpk3 wt ttn1 het 1|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin,,,,,,,,,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E MTAB 12934:srpk3 wt ttn1 het 1 p,srpk3 wt ttn1 het 1 p,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,Experimental Factor: genotype:srpk3 +/+; ttn.1 +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP147133,Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,SLX-21419.E3.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.E3.HV2TTDRXY.s_2.r_2.fq.gz,fastq fastq,5595162300.0,18650541.0,E MTAB 12934:SLX 21419.E3.HV2TTDRXY.s 2.r ,0:150 1:150,A:1500582422;C:1301393746;G:1326420086;T:1466508237;N:257809,150,150,,,1500582422,1301393746,1326420086,1466508237,257809,ERX10830023,ERS15422307,ERA23329494,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2024-02-09,Larval,Larval,Embryo Imprecise,All anatomical structures
11728,ERR11422841,ERX10830012,ERS15422296,ERP147133,PRJEB62042,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E-MTAB-12934,Transcriptome Analysis,RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos.,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,,Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,srpk3 hom ttn1 het 10,SAMEA113427170,QMUL,ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427170|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 hom ttn1 het 10|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3  / ; ttn.1 +/ |individual:pool of 3 embryos 10|organism part:embryo|replicate:10|sample name:E MTAB 12934:srpk3 hom ttn1 het 10|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin,,,,,,,,,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E MTAB 12934:srpk3 hom ttn1 het 10 p,srpk3 hom ttn1 het 10 p,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,Experimental Factor: genotype:srpk3  / ; ttn.1 +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP147133,Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,SLX-21419.F2.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.F2.HV2TTDRXY.s_2.r_2.fq.gz,fastq fastq,6163159800.0,20543866.0,E MTAB 12934:SLX 21419.F2.HV2TTDRXY.s 2.r ,0:150 1:150,A:1651051246;C:1435397149;G:1465377920;T:1611039390;N:294095,150,150,,,1651051246,1435397149,1465377920,1611039390,294095,ERX10830012,ERS15422296,ERA23329494,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2024-02-09,Larval,Larval,Embryo Imprecise,All anatomical structures
11729,ERR11422858,ERX10830029,ERS15422313,ERP147133,PRJEB62042,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E-MTAB-12934,Transcriptome Analysis,RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos.,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,,Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,srpk3 wt ttn1 wt 2,SAMEA113427187,QMUL,ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427187|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 wt ttn1 wt 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 +/+; ttn.1 +/+|individual:pool of 3 embryos 2|organism part:embryo|replicate:2|sample name:E MTAB 12934:srpk3 wt ttn1 wt 2|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin,,,,,,,,,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E MTAB 12934:srpk3 wt ttn1 wt 2 p,srpk3 wt ttn1 wt 2 p,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,Experimental Factor: genotype:srpk3 +/+; ttn.1 +/+,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP147133,Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,SLX-21419.E4.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.E4.HV2TTDRXY.s_2.r_2.fq.gz,fastq fastq,4948755000.0,16495850.0,E MTAB 12934:SLX 21419.E4.HV2TTDRXY.s 2.r ,0:150 1:150,A:1328315519;C:1150664187;G:1172962823;T:1296576134;N:236337,150,150,,,1328315519,1150664187,1172962823,1296576134,236337,ERX10830029,ERS15422313,ERA23329494,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2024-02-09,Larval,Larval,Embryo Imprecise,All anatomical structures
11730,ERR11422853,ERX10830024,ERS15422308,ERP147133,PRJEB62042,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E-MTAB-12934,Transcriptome Analysis,RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos.,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,,Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,srpk3 wt ttn1 het 2,SAMEA113427182,QMUL,ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427182|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 wt ttn1 het 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 +/+; ttn.1 +/ |individual:pool of 3 embryos 2|organism part:embryo|replicate:2|sample name:E MTAB 12934:srpk3 wt ttn1 het 2|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin,,,,,,,,,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E MTAB 12934:srpk3 wt ttn1 het 2 p,srpk3 wt ttn1 het 2 p,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,Experimental Factor: genotype:srpk3 +/+; ttn.1 +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP147133,Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,SLX-21419.A5.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.A5.HV2TTDRXY.s_2.r_2.fq.gz,fastq fastq,5172515100.0,17241717.0,E MTAB 12934:SLX 21419.A5.HV2TTDRXY.s 2.r ,0:150 1:150,A:1390660856;C:1200693628;G:1226597252;T:1354312680;N:250684,150,150,,,1390660856,1200693628,1226597252,1354312680,250684,ERX10830024,ERS15422308,ERA23329494,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2024-02-09,Larval,Larval,Embryo Imprecise,All anatomical structures
11731,ERR11422842,ERX10830013,ERS15422297,ERP147133,PRJEB62042,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E-MTAB-12934,Transcriptome Analysis,RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos.,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,,Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,srpk3 hom ttn1 het 2,SAMEA113427171,QMUL,ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427171|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 hom ttn1 het 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3  / ; ttn.1 +/ |individual:pool of 3 embryos 2|organism part:embryo|replicate:2|sample name:E MTAB 12934:srpk3 hom ttn1 het 2|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin,,,,,,,,,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E MTAB 12934:srpk3 hom ttn1 het 2 p,srpk3 hom ttn1 het 2 p,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,Experimental Factor: genotype:srpk3  / ; ttn.1 +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP147133,Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,SLX-21419.B3.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.B3.HV2TTDRXY.s_2.r_2.fq.gz,fastq fastq,7596727500.0,25322425.0,E MTAB 12934:SLX 21419.B3.HV2TTDRXY.s 2.r ,0:150 1:150,A:2040744877;C:1765753859;G:1800431343;T:1989434039;N:363382,150,150,,,2040744877,1765753859,1800431343,1989434039,363382,ERX10830013,ERS15422297,ERA23329494,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2024-02-09,Larval,Larval,Embryo Imprecise,All anatomical structures
11732,ERR11422854,ERX10830025,ERS15422309,ERP147133,PRJEB62042,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E-MTAB-12934,Transcriptome Analysis,RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos.,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,,Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,srpk3 wt ttn1 het 3,SAMEA113427183,QMUL,ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427183|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 wt ttn1 het 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 +/+; ttn.1 +/ |individual:pool of 3 embryos 3|organism part:embryo|replicate:3|sample name:E MTAB 12934:srpk3 wt ttn1 het 3|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin,,,,,,,,,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E MTAB 12934:srpk3 wt ttn1 het 3 p,srpk3 wt ttn1 het 3 p,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,Experimental Factor: genotype:srpk3 +/+; ttn.1 +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP147133,Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,SLX-21419.B4.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.B4.HV2TTDRXY.s_2.r_2.fq.gz,fastq fastq,4147455600.0,13824852.0,E MTAB 12934:SLX 21419.B4.HV2TTDRXY.s 2.r ,0:150 1:150,A:1111933168;C:965101703;G:986324158;T:1083898570;N:198001,150,150,,,1111933168,965101703,986324158,1083898570,198001,ERX10830025,ERS15422309,ERA23329494,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2024-02-09,Larval,Larval,Embryo Imprecise,All anatomical structures
11733,ERR11422855,ERX10830026,ERS15422310,ERP147133,PRJEB62042,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E-MTAB-12934,Transcriptome Analysis,RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos.,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,,Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,srpk3 wt ttn1 het 7,SAMEA113427184,QMUL,ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427184|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 wt ttn1 het 7|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 +/+; ttn.1 +/ |individual:pool of 3 embryos 7|organism part:embryo|replicate:7|sample name:E MTAB 12934:srpk3 wt ttn1 het 7|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin,,,,,,,,,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E MTAB 12934:srpk3 wt ttn1 het 7 p,srpk3 wt ttn1 het 7 p,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,Experimental Factor: genotype:srpk3 +/+; ttn.1 +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP147133,Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,SLX-21419.C3.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.C3.HV2TTDRXY.s_2.r_2.fq.gz,fastq fastq,7815347400.0,26051158.0,E MTAB 12934:SLX 21419.C3.HV2TTDRXY.s 2.r ,0:150 1:150,A:2105543787;C:1810060936;G:1848658748;T:2050709339;N:374590,150,150,,,2105543787,1810060936,1848658748,2050709339,374590,ERX10830026,ERS15422310,ERA23329494,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2024-02-09,Larval,Larval,Embryo Imprecise,All anatomical structures
11734,ERR11422847,ERX10830018,ERS15422302,ERP147133,PRJEB62042,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E-MTAB-12934,Transcriptome Analysis,RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos.,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,,Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,srpk3 hom ttn1 wt 4,SAMEA113427176,QMUL,ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427176|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 hom ttn1 wt 4|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3  / ; ttn.1 +/+|individual:pool of 3 embryos 4|organism part:embryo|replicate:4|sample name:E MTAB 12934:srpk3 hom ttn1 wt 4|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin,,,,,,,,,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E MTAB 12934:srpk3 hom ttn1 wt 4 p,srpk3 hom ttn1 wt 4 p,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,Experimental Factor: genotype:srpk3  / ; ttn.1 +/+,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP147133,Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,SLX-21419.F4.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.F4.HV2TTDRXY.s_2.r_2.fq.gz,fastq fastq,5552048400.0,18506828.0,E MTAB 12934:SLX 21419.F4.HV2TTDRXY.s 2.r ,0:150 1:150,A:1494691750;C:1287655327;G:1313223405;T:1456215647;N:262271,150,150,,,1494691750,1287655327,1313223405,1456215647,262271,ERX10830018,ERS15422302,ERA23329494,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2024-02-09,Larval,Larval,Embryo Imprecise,All anatomical structures
11735,ERR11422843,ERX10830014,ERS15422298,ERP147133,PRJEB62042,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E-MTAB-12934,Transcriptome Analysis,RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos.,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,,Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,srpk3 hom ttn1 het 7,SAMEA113427172,QMUL,ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427172|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 hom ttn1 het 7|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3  / ; ttn.1 +/ |individual:pool of 3 embryos 7|organism part:embryo|replicate:7|sample name:E MTAB 12934:srpk3 hom ttn1 het 7|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin,,,,,,,,,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E MTAB 12934:srpk3 hom ttn1 het 7 p,srpk3 hom ttn1 het 7 p,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,Experimental Factor: genotype:srpk3  / ; ttn.1 +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP147133,Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,SLX-21419.G2.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.G2.HV2TTDRXY.s_2.r_2.fq.gz,fastq fastq,6130593900.0,20435313.0,E MTAB 12934:SLX 21419.G2.HV2TTDRXY.s 2.r ,0:150 1:150,A:1646268883;C:1426071699;G:1453474221;T:1604484627;N:294470,150,150,,,1646268883,1426071699,1453474221,1604484627,294470,ERX10830014,ERS15422298,ERA23329494,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2024-02-09,Larval,Larval,Embryo Imprecise,All anatomical structures
11736,ERR11422857,ERX10830028,ERS15422312,ERP147133,PRJEB62042,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E-MTAB-12934,Transcriptome Analysis,RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos.,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,,Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,srpk3 wt ttn1 het 9,SAMEA113427186,QMUL,ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427186|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 wt ttn1 het 9|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 +/+; ttn.1 +/ |individual:pool of 3 embryos 9|organism part:embryo|replicate:9|sample name:E MTAB 12934:srpk3 wt ttn1 het 9|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin,,,,,,,,,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E MTAB 12934:srpk3 wt ttn1 het 9 p,srpk3 wt ttn1 het 9 p,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,Experimental Factor: genotype:srpk3 +/+; ttn.1 +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP147133,Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,SLX-21419.A3.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.A3.HV2TTDRXY.s_2.r_2.fq.gz,fastq fastq,7955802600.0,26519342.0,E MTAB 12934:SLX 21419.A3.HV2TTDRXY.s 2.r ,0:150 1:150,A:2139048525;C:1844468923;G:1881094685;T:2090808427;N:382040,150,150,,,2139048525,1844468923,1881094685,2090808427,382040,ERX10830028,ERS15422312,ERA23329494,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2024-02-09,Larval,Larval,Embryo Imprecise,All anatomical structures
11737,ERR11422844,ERX10830015,ERS15422299,ERP147133,PRJEB62042,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E-MTAB-12934,Transcriptome Analysis,RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos.,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,,Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,srpk3 hom ttn1 het 8,SAMEA113427173,QMUL,ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427173|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 hom ttn1 het 8|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3  / ; ttn.1 +/ |individual:pool of 3 embryos 8|organism part:embryo|replicate:8|sample name:E MTAB 12934:srpk3 hom ttn1 het 8|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin,,,,,,,,,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E MTAB 12934:srpk3 hom ttn1 het 8 p,srpk3 hom ttn1 het 8 p,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,Experimental Factor: genotype:srpk3  / ; ttn.1 +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP147133,Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,SLX-21419.H2.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.H2.HV2TTDRXY.s_2.r_2.fq.gz,fastq fastq,4707444000.0,15691480.0,E MTAB 12934:SLX 21419.H2.HV2TTDRXY.s 2.r ,0:150 1:150,A:1266769556;C:1091810198;G:1114454117;T:1234185729;N:224400,150,150,,,1266769556,1091810198,1114454117,1234185729,224400,ERX10830015,ERS15422299,ERA23329494,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2024-02-09,Larval,Larval,Embryo Imprecise,All anatomical structures
11738,ERR11422850,ERX10830021,ERS15422305,ERP147133,PRJEB62042,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E-MTAB-12934,Transcriptome Analysis,RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos.,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,,Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,srpk3 hom ttn1 wt 7,SAMEA113427179,QMUL,ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427179|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 hom ttn1 wt 7|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3  / ; ttn.1 +/+|individual:pool of 3 embryos 7|organism part:embryo|replicate:7|sample name:E MTAB 12934:srpk3 hom ttn1 wt 7|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin,,,,,,,,,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E MTAB 12934:srpk3 hom ttn1 wt 7 p,srpk3 hom ttn1 wt 7 p,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,Experimental Factor: genotype:srpk3  / ; ttn.1 +/+,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP147133,Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,SLX-21419.G4.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.G4.HV2TTDRXY.s_2.r_2.fq.gz,fastq fastq,6262379700.0,20874599.0,E MTAB 12934:SLX 21419.G4.HV2TTDRXY.s 2.r ,0:150 1:150,A:1681113096;C:1456657472;G:1485545256;T:1638760380;N:303496,150,150,,,1681113096,1456657472,1485545256,1638760380,303496,ERX10830021,ERS15422305,ERA23329494,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2024-02-09,Larval,Larval,Embryo Imprecise,All anatomical structures
11739,ERR11422846,ERX10830017,ERS15422301,ERP147133,PRJEB62042,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E-MTAB-12934,Transcriptome Analysis,RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos.,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,,Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,srpk3 hom ttn1 wt 1,SAMEA113427175,QMUL,ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427175|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 hom ttn1 wt 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3  / ; ttn.1 +/+|individual:pool of 3 embryos 1|organism part:embryo|replicate:1|sample name:E MTAB 12934:srpk3 hom ttn1 wt 1|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin,,,,,,,,,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E MTAB 12934:srpk3 hom ttn1 wt 1 p,srpk3 hom ttn1 wt 1 p,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,Experimental Factor: genotype:srpk3  / ; ttn.1 +/+,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP147133,Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,SLX-21419.A4.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.A4.HV2TTDRXY.s_2.r_2.fq.gz,fastq fastq,6071901300.0,20239671.0,E MTAB 12934:SLX 21419.A4.HV2TTDRXY.s 2.r ,0:150 1:150,A:1629141748;C:1412963306;G:1441970376;T:1587528201;N:297669,150,150,,,1629141748,1412963306,1441970376,1587528201,297669,ERX10830017,ERS15422301,ERA23329494,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2024-02-09,Larval,Larval,Embryo Imprecise,All anatomical structures
11740,ERR11422860,ERX10830031,ERS15422315,ERP147133,PRJEB62042,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E-MTAB-12934,Transcriptome Analysis,RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos.,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,,Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,srpk3 wt ttn1 wt 4,SAMEA113427189,QMUL,ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427189|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 wt ttn1 wt 4|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 +/+; ttn.1 +/+|individual:pool of 3 embryos 4|organism part:embryo|replicate:4|sample name:E MTAB 12934:srpk3 wt ttn1 wt 4|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin,,,,,,,,,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E MTAB 12934:srpk3 wt ttn1 wt 4 p,srpk3 wt ttn1 wt 4 p,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,Experimental Factor: genotype:srpk3 +/+; ttn.1 +/+,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP147133,Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,SLX-21419.H4.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.H4.HV2TTDRXY.s_2.r_2.fq.gz,fastq fastq,8552416200.0,28508054.0,E MTAB 12934:SLX 21419.H4.HV2TTDRXY.s 2.r ,0:150 1:150,A:2292742388;C:1992671634;G:2031906776;T:2234679447;N:415955,150,150,,,2292742388,1992671634,2031906776,2234679447,415955,ERX10830031,ERS15422315,ERA23329494,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2024-02-09,Larval,Larval,Embryo Imprecise,All anatomical structures
11741,ERR11422851,ERX10830022,ERS15422306,ERP147133,PRJEB62042,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E-MTAB-12934,Transcriptome Analysis,RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos.,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,,Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,srpk3 hom ttn1 wt 8,SAMEA113427180,QMUL,ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427180|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 hom ttn1 wt 8|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3  / ; ttn.1 +/+|individual:pool of 3 embryos 8|organism part:embryo|replicate:8|sample name:E MTAB 12934:srpk3 hom ttn1 wt 8|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin,,,,,,,,,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E MTAB 12934:srpk3 hom ttn1 wt 8 p,srpk3 hom ttn1 wt 8 p,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,Experimental Factor: genotype:srpk3  / ; ttn.1 +/+,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP147133,Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,SLX-21419.D4.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.D4.HV2TTDRXY.s_2.r_2.fq.gz,fastq fastq,4693977900.0,15646593.0,E MTAB 12934:SLX 21419.D4.HV2TTDRXY.s 2.r ,0:150 1:150,A:1260530822;C:1090058889;G:1111595821;T:1231573984;N:218384,150,150,,,1260530822,1090058889,1111595821,1231573984,218384,ERX10830022,ERS15422306,ERA23329494,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2024-02-09,Larval,Larval,Embryo Imprecise,All anatomical structures
11742,ERR11422849,ERX10830020,ERS15422304,ERP147133,PRJEB62042,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E-MTAB-12934,Transcriptome Analysis,RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos.,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,,Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,srpk3 hom ttn1 wt 6,SAMEA113427178,QMUL,ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427178|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 hom ttn1 wt 6|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3  / ; ttn.1 +/+|individual:pool of 3 embryos 6|organism part:embryo|replicate:6|sample name:E MTAB 12934:srpk3 hom ttn1 wt 6|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin,,,,,,,,,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E MTAB 12934:srpk3 hom ttn1 wt 6 p,srpk3 hom ttn1 wt 6 p,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,Experimental Factor: genotype:srpk3  / ; ttn.1 +/+,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP147133,Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,SLX-21419.E2.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.E2.HV2TTDRXY.s_2.r_2.fq.gz,fastq fastq,8212296300.0,27374321.0,E MTAB 12934:SLX 21419.E2.HV2TTDRXY.s 2.r ,0:150 1:150,A:2208490788;C:1905530286;G:1945454560;T:2152431537;N:389129,150,150,,,2208490788,1905530286,1945454560,2152431537,389129,ERX10830020,ERS15422304,ERA23329494,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2024-02-09,Larval,Larval,Embryo Imprecise,All anatomical structures
11743,ERR11422845,ERX10830016,ERS15422300,ERP147133,PRJEB62042,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E-MTAB-12934,Transcriptome Analysis,RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos.,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,,Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,srpk3 hom ttn1 het 9,SAMEA113427174,QMUL,ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427174|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 hom ttn1 het 9|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3  / ; ttn.1 +/ |individual:pool of 3 embryos 9|organism part:embryo|replicate:9|sample name:E MTAB 12934:srpk3 hom ttn1 het 9|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin,,,,,,,,,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E MTAB 12934:srpk3 hom ttn1 het 9 p,srpk3 hom ttn1 het 9 p,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,Experimental Factor: genotype:srpk3  / ; ttn.1 +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP147133,Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,SLX-21419.H3.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.H3.HV2TTDRXY.s_2.r_2.fq.gz,fastq fastq,6498128700.0,21660429.0,E MTAB 12934:SLX 21419.H3.HV2TTDRXY.s 2.r ,0:150 1:150,A:1747443944;C:1508729516;G:1535387292;T:1706266342;N:301606,150,150,,,1747443944,1508729516,1535387292,1706266342,301606,ERX10830016,ERS15422300,ERA23329494,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2024-02-09,Larval,Larval,Embryo Imprecise,All anatomical structures
11744,ERR11422861,ERX10830032,ERS15422316,ERP147133,PRJEB62042,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E-MTAB-12934,Transcriptome Analysis,RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos.,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,,Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,srpk3 wt ttn1 wt 5,SAMEA113427190,QMUL,ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427190|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 wt ttn1 wt 5|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 +/+; ttn.1 +/+|individual:pool of 3 embryos 5|organism part:embryo|replicate:5|sample name:E MTAB 12934:srpk3 wt ttn1 wt 5|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin,,,,,,,,,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E MTAB 12934:srpk3 wt ttn1 wt 5 p,srpk3 wt ttn1 wt 5 p,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,Experimental Factor: genotype:srpk3 +/+; ttn.1 +/+,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP147133,Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,SLX-21419.B5.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.B5.HV2TTDRXY.s_2.r_2.fq.gz,fastq fastq,5670094800.0,18900316.0,E MTAB 12934:SLX 21419.B5.HV2TTDRXY.s 2.r ,0:150 1:150,A:1520345271;C:1320386106;G:1349261719;T:1479832706;N:268998,150,150,,,1520345271,1320386106,1349261719,1479832706,268998,ERX10830032,ERS15422316,ERA23329494,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2024-02-09,Larval,Larval,Embryo Imprecise,All anatomical structures
11745,ERR11422848,ERX10830019,ERS15422303,ERP147133,PRJEB62042,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E-MTAB-12934,Transcriptome Analysis,RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos.,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,,Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,srpk3 hom ttn1 wt 5,SAMEA113427177,QMUL,ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427177|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 hom ttn1 wt 5|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3  / ; ttn.1 +/+|individual:pool of 3 embryos 5|organism part:embryo|replicate:5|sample name:E MTAB 12934:srpk3 hom ttn1 wt 5|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin,,,,,,,,,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E MTAB 12934:srpk3 hom ttn1 wt 5 p,srpk3 hom ttn1 wt 5 p,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,Experimental Factor: genotype:srpk3  / ; ttn.1 +/+,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP147133,Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,SLX-21419.D3.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.D3.HV2TTDRXY.s_2.r_2.fq.gz,fastq fastq,4627365300.0,15424551.0,E MTAB 12934:SLX 21419.D3.HV2TTDRXY.s 2.r ,0:150 1:150,A:1240390225;C:1077656611;G:1099301867;T:1209799382;N:217215,150,150,,,1240390225,1077656611,1099301867,1209799382,217215,ERX10830019,ERS15422303,ERA23329494,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2024-02-09,Larval,Larval,Embryo Imprecise,All anatomical structures
11746,ERR11422859,ERX10830030,ERS15422314,ERP147133,PRJEB62042,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E-MTAB-12934,Transcriptome Analysis,RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos.,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,,Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,srpk3 wt ttn1 wt 3,SAMEA113427188,QMUL,ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427188|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 wt ttn1 wt 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 +/+; ttn.1 +/+|individual:pool of 3 embryos 3|organism part:embryo|replicate:3|sample name:E MTAB 12934:srpk3 wt ttn1 wt 3|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin,,,,,,,,,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,E MTAB 12934:srpk3 wt ttn1 wt 3 p,srpk3 wt ttn1 wt 3 p,RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet  the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB  Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.,Experimental Factor: genotype:srpk3 +/+; ttn.1 +/+,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP147133,Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein,ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09,SLX-21419.F3.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.F3.HV2TTDRXY.s_2.r_2.fq.gz,fastq fastq,6046705800.0,20155686.0,E MTAB 12934:SLX 21419.F3.HV2TTDRXY.s 2.r ,0:150 1:150,A:1628067770;C:1402636688;G:1430886037;T:1584821803;N:293502,150,150,,,1628067770,1402636688,1430886037,1584821803,293502,ERX10830030,ERS15422314,ERA23329494,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2024-02-09,Larval,Larval,Embryo Imprecise,All anatomical structures
11753,ERR11758614,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S25_L001_R1_001.fastq.gz FliTp124hpf_S25_L001_R2_001.fastq.gz,fastq fastq,226833768.0,1800268.0,E MTAB 13196:FliTp124hpf S25 L001,0:28 1:98,A:65319978;C:50920193;G:49999849;T:60474280;N:119468,28,98,,,65319978,50920193,49999849,60474280,119468,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00122,0.88236,0.00056,0.09684,0.9978,0.89309,0.424,0.44186,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11754,ERR11758619,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S27_L001_R1_001.fastq.gz FliTp124hpf_S27_L001_R2_001.fastq.gz,fastq fastq,261098334.0,2072209.0,E MTAB 13196:FliTp124hpf S27 L001,0:28 1:98,A:76098436;C:58031830;G:57099955;T:69729759;N:138354,28,98,,,76098436,58031830,57099955,69729759,138354,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00109,0.87641,0.00062,0.0976,0.99837,0.90065,0.45555,0.48712,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11755,ERR11758589,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S16_L005_R1_001.fastq.gz FliTp124hpf_S16_L005_R2_001.fastq.gz,fastq fastq,1168367130.0,9272755.0,E MTAB 13196:FliTp124hpf S16 L005,0:28 1:98,A:323651598;C:269884286;G:268030176;T:306695030;N:106040,28,98,,,323651598,269884286,268030176,306695030,106040,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00491,0.90853,0.00131,0.07851,0.99019,0.84331,0.41536,0.48076,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11756,ERR11758638,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S22_L001_R1_001.fastq.gz FliTp124hpf_S22_L001_R2_001.fastq.gz,fastq fastq,864786636.0,6863386.0,E MTAB 13196:FliTp124hpf S22 L001,0:28 1:98,A:241767760;C:198370882;G:198049093;T:226508751;N:90150,28,98,,,241767760,198370882,198049093,226508751,90150,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00375,0.89002,0.00114,0.0769,0.99237,0.84563,0.41796,0.48995,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11757,ERR11758599,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S15_L005_R1_001.fastq.gz FliTp124hpf_S15_L005_R2_001.fastq.gz,fastq fastq,1795799502.0,14252377.0,E MTAB 13196:FliTp124hpf S15 L005,0:28 1:98,A:500590460;C:413239086;G:410401125;T:471402890;N:165941,28,98,,,500590460,413239086,410401125,471402890,165941,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00492,0.91242,0.0012,0.08044,0.99007,0.84668,0.42778,0.49291,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11758,ERR11758601,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S26_L001_R1_001.fastq.gz FliTp124hpf_S26_L001_R2_001.fastq.gz,fastq fastq,266141358.0,2112233.0,E MTAB 13196:FliTp124hpf S26 L001,0:28 1:98,A:76996100;C:59592346;G:58963461;T:70457732;N:131719,28,98,,,76996100,59592346,58963461,70457732,131719,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00106,0.88422,0.00046,0.09358,0.99782,0.89449,0.47826,0.48948,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11759,ERR11758630,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S14_L005_R1_001.fastq.gz FliTp124hpf_S14_L005_R2_001.fastq.gz,fastq fastq,1812847428.0,14387678.0,E MTAB 13196:FliTp124hpf S14 L005,0:28 1:98,A:502956890;C:417865079;G:416595454;T:475266679;N:163326,28,98,,,502956890,417865079,416595454,475266679,163326,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00483,0.91317,0.00123,0.07918,0.99036,0.84143,0.40704,0.4819,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11760,ERR11758603,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S13_L005_R1_001.fastq.gz FliTp124hpf_S13_L005_R2_001.fastq.gz,fastq fastq,1544281830.0,12256205.0,E MTAB 13196:FliTp124hpf S13 L005,0:28 1:98,A:428008915;C:356252081;G:354333187;T:405545992;N:141655,28,98,,,428008915,356252081,354333187,405545992,141655,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00507,0.91025,0.00138,0.07858,0.98987,0.84295,0.41793,0.4891,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11761,ERR11758613,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S21_L001_R1_001.fastq.gz FliTp124hpf_S21_L001_R2_001.fastq.gz,fastq fastq,761441436.0,6043186.0,E MTAB 13196:FliTp124hpf S21 L001,0:28 1:98,A:212876877;C:174700212;G:174244892;T:199537401;N:82054,28,98,,,212876877,174700212,174244892,199537401,82054,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00334,0.88899,0.00106,0.07762,0.99322,0.84476,0.42792,0.48783,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11762,ERR11758645,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S23_L001_R1_001.fastq.gz FliTp124hpf_S23_L001_R2_001.fastq.gz,fastq fastq,873938772.0,6936022.0,E MTAB 13196:FliTp124hpf S23 L001,0:28 1:98,A:245075115;C:199879929;G:199312177;T:229576663;N:94888,28,98,,,245075115,199879929,199312177,229576663,94888,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00361,0.88671,0.00104,0.07855,0.99255,0.84723,0.41141,0.4885,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11763,ERR11758598,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S28_L001_R1_001.fastq.gz FliTp124hpf_S28_L001_R2_001.fastq.gz,fastq fastq,164465532.0,1305282.0,E MTAB 13196:FliTp124hpf S28 L001,0:28 1:98,A:47319366;C:37063279;G:36394680;T:43602586;N:85621,28,98,,,47319366,37063279,36394680,43602586,85621,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00117,0.88222,0.00058,0.09358,0.99799,0.89217,0.54867,0.48545,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11764,ERR11758593,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S24_L001_R1_001.fastq.gz FliTp124hpf_S24_L001_R2_001.fastq.gz,fastq fastq,558365976.0,4431476.0,E MTAB 13196:FliTp124hpf S24 L001,0:28 1:98,A:156054630;C:128109738;G:127885708;T:146256146;N:59754,28,98,,,156054630,128109738,127885708,146256146,59754,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00345,0.8879,0.00104,0.07718,0.99322,0.84364,0.38266,0.49193,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11765,ERR11758635,ERX11157720,ERS16172938,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 wt 22hpf,SAMEA114192245,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192245|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 wt 22hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 wt 22hpf|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 wt 22hpf p,etv2 wt 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2Kaede_WT_S6_L001_R1_001.fastq.gz Etv2Kaede_WT_S6_L001_R2_001.fastq.gz,fastq fastq,1144014102.0,9079477.0,E MTAB 13196:Etv2Kaede WT S6 L001,0:28 1:98,A:316366230;C:260322813;G:259447166;T:307680623;N:197270,28,98,,,316366230,260322813,259447166,307680623,197270,ERX11157720,ERS16172938,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00336,0.89267,0.00137,0.13734,0.99545,0.81957,0.3734,0.53458,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11766,ERR11758622,ERX11157720,ERS16172938,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 wt 22hpf,SAMEA114192245,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192245|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 wt 22hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 wt 22hpf|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 wt 22hpf p,etv2 wt 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2Kaede_WT_S8_L001_R2_001.fastq.gz Etv2Kaede_WT_S8_L001_R1_001.fastq.gz,fastq fastq,919270926.0,7295801.0,E MTAB 13196:Etv2Kaede WT S8 L001,0:28 1:98,A:259787542;C:207541571;G:206711907;T:245072713;N:157193,28,98,,,259787542,207541571,206711907,245072713,157193,ERX11157720,ERS16172938,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00358,0.88757,0.00137,0.15368,0.99551,0.83378,0.36405,0.53733,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11767,ERR11758644,ERX11157720,ERS16172938,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 wt 22hpf,SAMEA114192245,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192245|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 wt 22hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 wt 22hpf|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 wt 22hpf p,etv2 wt 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2Kaede_WT_S5_L001_R2_001.fastq.gz Etv2Kaede_WT_S5_L001_R1_001.fastq.gz,fastq fastq,877658166.0,6965541.0,E MTAB 13196:Etv2Kaede WT S5 L001,0:28 1:98,A:243057461;C:199464116;G:198654377;T:236322700;N:159512,28,98,,,243057461,199464116,198654377,236322700,159512,ERX11157720,ERS16172938,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00328,0.88916,0.00127,0.13782,0.99559,0.81925,0.38227,0.53623,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11768,ERR11758628,ERX11157720,ERS16172938,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 wt 22hpf,SAMEA114192245,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192245|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 wt 22hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 wt 22hpf|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 wt 22hpf p,etv2 wt 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2Kaede_WT_S7_L001_R1_001.fastq.gz Etv2Kaede_WT_S7_L001_R2_001.fastq.gz,fastq fastq,930443598.0,7384473.0,E MTAB 13196:Etv2Kaede WT S7 L001,0:28 1:98,A:258539610;C:211017108;G:209074684;T:251641766;N:170430,28,98,,,258539610,211017108,209074684,251641766,170430,ERX11157720,ERS16172938,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00355,0.88938,0.00148,0.14297,0.99569,0.83358,0.35626,0.53314,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11769,ERR11758631,ERX11157719,ERS16172937,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 15s,SAMEA114192244,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192244|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 15s|age:16.5|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:15 somite stage|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 15s|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 15s p,etv2 15s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2_Traver_S10_L001_R2_001.fastq.gz Etv2_Traver_S10_L001_R1_001.fastq.gz,fastq fastq,1947733326.0,15458201.0,E MTAB 13196:Etv2 Traver S10 L001,0:28 1:98,A:532150077;C:434208725;G:472140578;T:508906834;N:327112,28,98,,,532150077,434208725,472140578,508906834,327112,ERX11157719,ERS16172937,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00677,0.92596,0.00142,0.07895,0.98526,0.85123,0.42802,0.53518,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11770,ERR11758646,ERX11157719,ERS16172937,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 15s,SAMEA114192244,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192244|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 15s|age:16.5|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:15 somite stage|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 15s|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 15s p,etv2 15s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2_Traver_S28_L001_R2_001.fastq.gz Etv2_Traver_S28_L001_R1_001.fastq.gz,fastq fastq,1091426920.0,8801830.0,E MTAB 13196:Etv2 Traver S28 L001,0:26 1:98,A:302665480;C:247712584;G:269795015;T:271081940;N:171901,26,98,,,302665480,247712584,269795015,271081940,171901,ERX11157719,ERS16172937,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00585,0.90012,0.00149,0.07225,0.98746,0.84916,0.39007,0.54873,26,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11771,ERR11758602,ERX11157719,ERS16172937,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 15s,SAMEA114192244,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192244|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 15s|age:16.5|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:15 somite stage|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 15s|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 15s p,etv2 15s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2_Traver_S25_L001_R2_001.fastq.gz Etv2_Traver_S25_L001_R1_001.fastq.gz,fastq fastq,983616732.0,7932393.0,E MTAB 13196:Etv2 Traver S25 L001,0:26 1:98,A:272974243;C:222949925;G:242884450;T:244652916;N:155198,26,98,,,272974243,222949925,242884450,244652916,155198,ERX11157719,ERS16172937,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00571,0.90139,0.00143,0.07484,0.98756,0.85019,0.40119,0.54977,26,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11772,ERR11758647,ERX11157719,ERS16172937,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 15s,SAMEA114192244,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192244|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 15s|age:16.5|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:15 somite stage|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 15s|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 15s p,etv2 15s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2_Traver_S27_L001_R2_001.fastq.gz Etv2_Traver_S27_L001_R1_001.fastq.gz,fastq fastq,1162223232.0,9372768.0,E MTAB 13196:Etv2 Traver S27 L001,0:26 1:98,A:322910431;C:262934167;G:286614718;T:289578468;N:185448,26,98,,,322910431,262934167,286614718,289578468,185448,ERX11157719,ERS16172937,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00563,0.89924,0.00128,0.07464,0.98762,0.85064,0.38525,0.53889,26,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11773,ERR11758634,ERX11157719,ERS16172937,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 15s,SAMEA114192244,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192244|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 15s|age:16.5|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:15 somite stage|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 15s|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 15s p,etv2 15s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2_Traver_S12_L001_R2_001.fastq.gz Etv2_Traver_S12_L001_R1_001.fastq.gz,fastq fastq,1979462268.0,15710018.0,E MTAB 13196:Etv2 Traver S12 L001,0:28 1:98,A:539088187;C:442520328;G:480420115;T:517077908;N:355730,28,98,,,539088187,442520328,480420115,517077908,355730,ERX11157719,ERS16172937,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00707,0.9236,0.00137,0.07727,0.98451,0.85021,0.41845,0.56136,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11774,ERR11758642,ERX11157719,ERS16172937,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 15s,SAMEA114192244,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192244|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 15s|age:16.5|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:15 somite stage|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 15s|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 15s p,etv2 15s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2_Traver_S9_L001_R2_001.fastq.gz Etv2_Traver_S9_L001_R1_001.fastq.gz,fastq fastq,1809560214.0,14361589.0,E MTAB 13196:Etv2 Traver S9 L001,0:28 1:98,A:493206820;C:403886293;G:438502430;T:473641472;N:323199,28,98,,,493206820,403886293,438502430,473641472,323199,ERX11157719,ERS16172937,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00668,0.92354,0.00141,0.0785,0.98543,0.84938,0.43326,0.52002,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11775,ERR11758623,ERX11157719,ERS16172937,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 15s,SAMEA114192244,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192244|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 15s|age:16.5|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:15 somite stage|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 15s|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 15s p,etv2 15s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2_Traver_S26_L001_R2_001.fastq.gz Etv2_Traver_S26_L001_R1_001.fastq.gz,fastq fastq,1074533780.0,8665595.0,E MTAB 13196:Etv2 Traver S26 L001,0:26 1:98,A:298569273;C:243430874;G:265536499;T:266825982;N:171152,26,98,,,298569273,243430874,265536499,266825982,171152,ERX11157719,ERS16172937,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00579,0.90109,0.00136,0.07564,0.98788,0.85017,0.3554,0.54362,26,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11776,ERR11758596,ERX11157719,ERS16172937,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 15s,SAMEA114192244,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192244|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 15s|age:16.5|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:15 somite stage|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 15s|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 15s p,etv2 15s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2_Traver_S11_L001_R2_001.fastq.gz Etv2_Traver_S11_L001_R1_001.fastq.gz,fastq fastq,2167279758.0,17200633.0,E MTAB 13196:Etv2 Traver S11 L001,0:28 1:98,A:591928396;C:482735357;G:524267488;T:567952272;N:396245,28,98,,,591928396,482735357,524267488,567952272,396245,ERX11157719,ERS16172937,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00635,0.92351,0.00136,0.07835,0.9865,0.85204,0.41521,0.53672,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11777,ERR11758595,ERX11157718,ERS16172936,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl tb,SAMEA114192243,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl tb p,drl tb p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_tb_S36_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S36_L001_R1_001.fastq.gz,fastq fastq,211593816.0,1679316.0,E MTAB 13196:drl h2b dendra tb S36 L001,0:28 1:98,A:62689430;C:45809168;G:45709128;T:57272091;N:113999,28,98,,,62689430,45809168,45709128,57272091,113999,ERX11157718,ERS16172936,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00192,0.91331,0.00072,0.14588,0.99675,0.89292,0.51304,0.63144,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
11778,ERR11758629,ERX11157718,ERS16172936,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl tb,SAMEA114192243,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl tb p,drl tb p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_tb_S37_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S37_L001_R1_001.fastq.gz,fastq fastq,980164836.0,7779086.0,E MTAB 13196:drl h2b dendra tb S37 L001,0:28 1:98,A:281375011;C:216067640;G:222839674;T:259781180;N:101331,28,98,,,281375011,216067640,222839674,259781180,101331,ERX11157718,ERS16172936,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00817,0.89718,0.00237,0.12153,0.98912,0.82643,0.46403,0.64954,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
11779,ERR11758618,ERX11157718,ERS16172936,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl tb,SAMEA114192243,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl tb p,drl tb p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_tb_S39_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S39_L001_R1_001.fastq.gz,fastq fastq,12118302.0,96177.0,E MTAB 13196:drl h2b dendra tb S39 L001,0:28 1:98,A:3543790;C:2662872;G:2728134;T:3182383;N:1123,28,98,,,3543790,2662872,2728134,3182383,1123,ERX11157718,ERS16172936,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00786,0.88963,0.0025,0.12543,0.99403,0.88635,0.50098,0.64694,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
11780,ERR11758643,ERX11157718,ERS16172936,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl tb,SAMEA114192243,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl tb p,drl tb p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_tb_S5_L005_R2_001.fastq.gz drl_h2b-dendra_tb_S5_L005_R1_001.fastq.gz,fastq fastq,2061022698.0,16357323.0,E MTAB 13196:drl h2b dendra tb S5 L005,0:28 1:98,A:587730953;C:457631700;G:470283474;T:545196979;N:179592,28,98,,,587730953,457631700,470283474,545196979,179592,ERX11157718,ERS16172936,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.01192,0.91661,0.00336,0.12397,0.98518,0.82568,0.45692,0.65555,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
11781,ERR11758610,ERX11157718,ERS16172936,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl tb,SAMEA114192243,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl tb p,drl tb p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_tb_S38_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S38_L001_R1_001.fastq.gz,fastq fastq,924603120.0,7338120.0,E MTAB 13196:drl h2b dendra tb S38 L001,0:28 1:98,A:265987815;C:203824483;G:210024160;T:244670646;N:96016,28,98,,,265987815,203824483,210024160,244670646,96016,ERX11157718,ERS16172936,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00773,0.89881,0.00242,0.12145,0.98944,0.82948,0.50529,0.66568,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
11782,ERR11758641,ERX11157718,ERS16172936,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl tb,SAMEA114192243,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl tb p,drl tb p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_tb_S6_L005_R2_001.fastq.gz drl_h2b-dendra_tb_S6_L005_R1_001.fastq.gz,fastq fastq,1954661562.0,15513187.0,E MTAB 13196:drl h2b dendra tb S6 L005,0:28 1:98,A:558769608;C:433724557;G:445550100;T:516443984;N:173313,28,98,,,558769608,433724557,445550100,516443984,173313,ERX11157718,ERS16172936,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.0125,0.91697,0.00373,0.12359,0.98447,0.82558,0.4881,0.6456,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
11783,ERR11758591,ERX11157718,ERS16172936,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl tb,SAMEA114192243,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl tb p,drl tb p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_tb_S35_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S35_L001_R1_001.fastq.gz,fastq fastq,4717188.0,37438.0,E MTAB 13196:drl h2b dendra tb S35 L001,0:28 1:98,A:1419430;C:1014265;G:1016661;T:1264642;N:2190,28,98,,,1419430,1014265,1016661,1264642,2190,ERX11157718,ERS16172936,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.0012,0.65482,0.00054,0.10783,0.99953,0.97157,0.625,0.63689,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
11784,ERR11758606,ERX11157718,ERS16172936,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl tb,SAMEA114192243,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl tb p,drl tb p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_tb_S34_L001_R1_001.fastq.gz drl_h2b-dendra_tb_S34_L001_R2_001.fastq.gz,fastq fastq,303645636.0,2409886.0,E MTAB 13196:drl h2b dendra tb S34 L001,0:28 1:98,A:90748559;C:65369482;G:65969002;T:81405258;N:153335,28,98,,,90748559,65369482,65969002,81405258,153335,ERX11157718,ERS16172936,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00228,0.91262,0.00099,0.14666,0.99638,0.89006,0.47177,0.63109,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
11785,ERR11758640,ERX11157718,ERS16172936,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl tb,SAMEA114192243,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl tb p,drl tb p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_tb_S40_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S40_L001_R1_001.fastq.gz,fastq fastq,661361022.0,5248897.0,E MTAB 13196:drl h2b dendra tb S40 L001,0:28 1:98,A:190087869;C:145985661;G:150124621;T:175095762;N:67109,28,98,,,190087869,145985661,150124621,175095762,67109,ERX11157718,ERS16172936,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00785,0.89784,0.00251,0.12159,0.98948,0.83055,0.46095,0.64951,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
11786,ERR11758605,ERX11157718,ERS16172936,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl tb,SAMEA114192243,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl tb p,drl tb p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_tb_S7_L005_R2_001.fastq.gz drl_h2b-dendra_tb_S7_L005_R1_001.fastq.gz,fastq fastq,25157790.0,199665.0,E MTAB 13196:drl h2b dendra tb S7 L005,0:28 1:98,A:7330053;C:5600451;G:5635840;T:6589498;N:1948,28,98,,,7330053,5600451,5635840,6589498,1948,ERX11157718,ERS16172936,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.01201,0.91385,0.00341,0.12826,0.98595,0.85161,0.49226,0.64953,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
11787,ERR11758600,ERX11157718,ERS16172936,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl tb,SAMEA114192243,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl tb p,drl tb p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_tb_S8_L005_R2_001.fastq.gz drl_h2b-dendra_tb_S8_L005_R1_001.fastq.gz,fastq fastq,1422735804.0,11291554.0,E MTAB 13196:drl h2b dendra tb S8 L005,0:28 1:98,A:405788442;C:317299433;G:322206476;T:377317416;N:124037,28,98,,,405788442,317299433,322206476,377317416,124037,ERX11157718,ERS16172936,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.01226,0.91547,0.0037,0.12565,0.9849,0.83662,0.48279,0.64531,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Undetermined,Embryo,Embryo Imprecise,All anatomical structures