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 8056,ERR022486,ERX008922,ERS012705,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 308:Zebrafish embryo 1 dpf 2,SAMEA898401,Wellcome Sanger Institute,Age:1 days|Alias:E MTAB 308:Zebrafish embryo 1 dpf 2|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.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 08 19T15:57:35Z|INSDC last update:2018 03 08T15:25:04Z|INSDC status:public|InitialTimePoint:fertilization|OrganismPart:whole organism|SRA accession:ERS012705|Sample Name:ERS012705|Sex:unknown sex|StrainOrLine:Tuebingen|Title:Danio rerio,,,,,,,,,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 1 dpf,RNA from Zebrafish embryo 1 dpf,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: AGE:1 d|Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism,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 16,5141_3.srf,srf,4788693120.0,31504560.0,E MTAB 434:5141 3.srf,0:76 1:76,A:1329328273;C:1071568772;G:1063807333;T:1316891498;N:7097244,76,76,,,1329328273,1071568772,1063807333,1316891498,7097244,ERX008922,ERS012705,ERA015179,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.95867,0.95691,0.14543,0.14805,0.69753,0.70078,0.46273,0.47662,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2010-08-19,Pharyngula,Embryo,Whole Organism,All anatomical structures 39751,SRR2422954,SRX1092140,SRS987764,SRP060685,PRJNA289590,Danio rerio Raw sequence reads,PRJNA289590,Whole Genome Sequencing,The Goal of the study is to compare RNA expression especially splicing profiles in wildtype and U2af2 KD zebrafish,,,U2AFAB KD,U2AFA2B KD,U2A2FA and U2AF2B knockdown,,treatment:U2AF2A B morpholino|developmental stage:embryo|age:24 hours|strain:wildtype|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,U2AF2A and U2AF2B KD,U2AFAB KD,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020Application ReadForward11Application ReadReverse102,SRP060685,,,zebrafish_U2af2KD_2_2.fastq.gz zebrafish_U2af2KD_2_1.fastq.gz,fastq fastq,4010033906.0,19851653.0,u2afa u2afb kd,0:101 1:101,A:954988404;C:1049486839;G:1028325376;T:975960838;N:1272449,101,101,,,954988404,1049486839,1028325376,975960838,1272449,SRX1092140,SRS987764,SRA276795,Brown University|Fairbrother Lab,Brown University,2,0.88891,0.88704,0.22441,0.2245,0.73781,0.74111,0.60755,0.61314,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-09-19,Pharyngula,Embryo,Whole Organism,All anatomical structures 39752,SRR2422968,SRX1092139,SRS987762,SRP060685,PRJNA289590,Danio rerio Raw sequence reads,PRJNA289590,Whole Genome Sequencing,The Goal of the study is to compare RNA expression especially splicing profiles in wildtype and U2af2 KD zebrafish,,,U2AFB KD,U2AF2B KD,U2AF2B knockdown,,treatment:U2AF2B morpholino|developmental stage:embryo|age:24 hours|strain:wildtype|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,U2AF2B KD,U2AFB KD,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020Application ReadForward11Application ReadReverse102,SRP060685,,,zebrafish_U2af2KD_5_1.fastq.gz zebrafish_U2af2KD_5_2.fastq.gz,fastq fastq,3657236866.0,18105133.0,u2af2b kd,0:101 1:101,A:859906359;C:963846892;G:950183263;T:882292781;N:1007571,101,101,,,859906359,963846892,950183263,882292781,1007571,SRX1092139,SRS987762,SRA276795,Brown University|Fairbrother Lab,Brown University,2,0.87685,0.87325,0.21282,0.21347,0.74899,0.75166,0.65013,0.65163,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-09-19,Pharyngula,Embryo,Whole Organism,All anatomical structures 39753,SRR2422941,SRX1092136,SRS987760,SRP060685,PRJNA289590,Danio rerio Raw sequence reads,PRJNA289590,Whole Genome Sequencing,The Goal of the study is to compare RNA expression especially splicing profiles in wildtype and U2af2 KD zebrafish,,,Control1,Control1,Control1,,treatment:Control 1|developmental stage:embryo|age:24 hours|strain:wildtype|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,control 1,Control1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020Application ReadForward11Application ReadReverse102,SRP060685,,,zebrafish_U2af2KD_1_2.fastq.gz zebrafish_U2af2KD_1_1.fastq.gz,fastq fastq,5446154724.0,26961162.0,control1,0:101 1:101,A:1236792250;C:1484635192;G:1463483173;T:1259686822;N:1557287,101,101,,,1236792250,1484635192,1463483173,1259686822,1557287,SRX1092136,SRS987760,SRA276795,Brown University|Fairbrother Lab,Brown University,2,0.88645,0.88416,0.23061,0.23167,0.75872,0.75921,0.63459,0.63891,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-09-19,Pharyngula,Embryo,Whole Organism,All anatomical structures 39754,SRR2422967,SRX1092138,SRS987763,SRP060685,PRJNA289590,Danio rerio Raw sequence reads,PRJNA289590,Whole Genome Sequencing,The Goal of the study is to compare RNA expression especially splicing profiles in wildtype and U2af2 KD zebrafish,,,U2AFA KD,U2AF2A KD,U2AF2A knockdown,,treatment:U2AF2A morpholino|developmental stage:embryo|age:24 hours|strain:wildtype|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,U2AF A KD,U2AFA KD,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020Application ReadForward11Application ReadReverse102,SRP060685,,,zebrafish_U2af2KD_4_1.fastq.gz zebrafish_U2af2KD_4_2.fastq.gz,fastq fastq,7385905174.0,36563887.0,u2af2a kd,0:101 1:101,A:1742999157;C:1956220866;G:1920103000;T:1764198542;N:2383609,101,101,,,1742999157,1956220866,1920103000,1764198542,2383609,SRX1092138,SRS987763,SRA276795,Brown University|Fairbrother Lab,Brown University,2,0.74404,0.74051,0.14971,0.14762,0.76641,0.76757,0.56197,0.56515,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-09-19,Pharyngula,Embryo,Whole Organism,All anatomical structures 39755,SRR2422942,SRX1092137,SRS987761,SRP060685,PRJNA289590,Danio rerio Raw sequence reads,PRJNA289590,Whole Genome Sequencing,The Goal of the study is to compare RNA expression especially splicing profiles in wildtype and U2af2 KD zebrafish,,,Control2,Control2,Control2,,treatment:Control 2|developmental stage:embryo|age:24 hours|strain:wildtype|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,control 2,Control 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020Application ReadForward11Application ReadReverse102,SRP060685,,,zebrafish_U2af2KD_3_1.fastq.gz zebrafish_U2af2KD_3_2.fastq.gz,fastq fastq,4226478926.0,20923163.0,control2,0:101 1:101,A:1005765442;C:1098720686;G:1084955814;T:1035764094;N:1272890,101,101,,,1005765442,1098720686,1084955814,1035764094,1272890,SRX1092137,SRS987761,SRA276795,Brown University|Fairbrother Lab,Brown University,2,0.83225,0.83092,0.22325,0.22374,0.75396,0.75603,0.6203,0.61868,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-09-19,Pharyngula,Embryo,Whole Organism,All anatomical structures 39934,SRR2473238,SRX1270438,SRS1078341,SRP063952,PRJNA296414,SPOP mutation leads to genomic instability in prostate cancer,PRJNA296414,Transcriptome Analysis,Examination of the effects of morpholino based SPOP knockdown or ectopic expression of prostate cancer specific SPOP mutant F133V on the transcriptome of zebrafish embryos.,,,Danio rerio embryos ectopically expressing human SPOPwt.,,Danio rerio ectopic SPOPwt,,strain:AB/T|age:24 HPF|sex:pooled male and female|tissue:whole embryo|biomaterial provider:Yariv Houvras|BioSampleModel:Model organism or animal,,,,,,,,,SPOP mutation leads to genomic instability in prostate cancer,Danio rerio ectopic SPOPwt,1,SPOP mutation leads to genomic instability in prostate cancer RNA seq: Danio rerio ectopic SPOPwt,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,1020Application ReadForward11Application ReadReverse52,SRP063952,,,WT_CAGATC_L001_R1.fastq.gz WT_CAGATC_L001_R2.fastq.gz,fastq fastq,6185345892.0,60640646.0,Danio rerio ectopic SPOPwt,0:51 1:51,A:1647678166;C:1462773970;G:1416249443;T:1657464504;N:1179809,51,51,,,1647678166,1462773970,1416249443,1657464504,1179809,SRX1270438,SRS1078341,,,Weill Cornell Medical College,2,0.94598,0.94553,0.09216,0.0934,0.68789,0.69065,0.46814,0.47172,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-02-17,Pharyngula,Embryo,Whole Organism,All anatomical structures 39935,SRR2473236,SRX1270437,SRS1078340,SRP063952,PRJNA296414,SPOP mutation leads to genomic instability in prostate cancer,PRJNA296414,Transcriptome Analysis,Examination of the effects of morpholino based SPOP knockdown or ectopic expression of prostate cancer specific SPOP mutant F133V on the transcriptome of zebrafish embryos.,,,Danio rerio ectopically expressing SPOP F133V,,Danio rerio ectopic SPOP F133V,,strain:AB/T|age:24 HPF|sex:pooled male and female|tissue:whole embryo|biomaterial provider:Yariv Houvras|BioSampleModel:Model organism or animal,,,,,,,,,SPOP mutation leads to genomic instability in prostate cancer,Danio rerio ectopic SPOP F133V,1,SPOP mutation leads to genomic instability in prostate cancer RNA seq: Danio rerio ectopic SPOP F133V,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,1020Application ReadForward11Application ReadReverse52,SRP063952,,,Mut_GATCAG_L001_R2.fastq.gz Mut_GATCAG_L001_R1.fastq.gz,fastq fastq,6130528134.0,60103217.0,Danio rerio ectopic SPOP F133V,0:51 1:51,A:1630145057;C:1450811256;G:1409924927;T:1638457859;N:1189035,51,51,,,1630145057,1450811256,1409924927,1638457859,1189035,SRX1270437,SRS1078340,,,Weill Cornell Medical College,2,0.9444,0.94139,0.09809,0.0979,0.68487,0.68657,0.46751,0.47276,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-09-21,Pharyngula,Embryo,Whole Organism,All anatomical structures 39936,SRR2473235,SRX1270436,SRS1078339,SRP063952,PRJNA296414,SPOP mutation leads to genomic instability in prostate cancer,PRJNA296414,Transcriptome Analysis,Examination of the effects of morpholino based SPOP knockdown or ectopic expression of prostate cancer specific SPOP mutant F133V on the transcriptome of zebrafish embryos.,,,,,Danio rerio SPOP morpholino,,strain:AB/T|age:24 HPF|sex:pooled male and female|tissue:whole embryo|biomaterial provider:Yariv Houvras|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio SPOP morpholino,Danio rerio SPOP morpholino,1,SPOP mutation leads to genomic instability in prostate cancer RNA seq: Danio rerio SPOP morpholino,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,1020Application ReadForward11Application ReadReverse52,SRP063952,,,Mock_ACTTGA_L001_R1.fastq.gz Mock_ACTTGA_L001_R2.fastq.gz,fastq fastq,5693947938.0,55823019.0,Danio rerio SPOP morpholino,0:51 1:51,A:1513477521;C:1350461483;G:1305374194;T:1523527099;N:1107641,51,51,,,1513477521,1350461483,1305374194,1523527099,1107641,SRX1270436,SRS1078339,,,Weill Cornell Medical College,2,0.94534,0.94431,0.09368,0.0945,0.68941,0.69077,0.46543,0.46749,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-02-17,Pharyngula,Embryo,Whole Organism,All anatomical structures 46211,SRR6477199,SRX3567065,SRS2838997,SRP129892,PRJNA430431,RES complex is associated with intron definition and required for zebrafish early embryogenesis,PRJNA430431,Other,Pre mRNA splicing is a critical step of gene expression in eukaryotes. Transcriptome wide splicing patterns are complex and primarily regulated by a diverse set of recognition elements and associated RNA binding proteins. The retention and splicing RES complex is formed by three different proteins Bud13p Pml1p and Snu17p and is involved in splicing in yeast. However the importance of the RES complex for vertebrate splicing the intronic features associated with its activity and its role in development are unknown. In this study we have generated loss of function mutants for the three components of the RES complex in zebrafish and showed that they are required during early development. The mutants showed a marked neural phenotype with increased cell death in the brain and a decrease in differentiated neurons. Transcriptomic analysis of bud13 snip1 pml1 and rbmx2 snu17 mutants revealed a global defect in intron splicing with strong mis splicing of a subset of introns. We found these RES dependent introns were short rich in GC and flanked by GC depleted exons all of which are features associated with intron definition. Using these features we developed and validated a predictive model that classifies RES dependent introns. Altogether our study uncovers the essential role of the RES complex during vertebrate development and provides new insights into its function during splicing.,,,,RNAseq Bud13 Bud13 Sibling 30h,RNAseq Bud13 Bud13 Sib 30h AG01145,,strain:TU/AB|age:30.0|dev stage:30h|sex:pooled male and female|tissue:embryo|genotype:+/?|molecule:mRNA|selection:pA|replicate group:2|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq Bud13 Bud13 Sibling 30h,AG01145.2,AG01145.2,mRNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP129892,,,AG01145.2_R2.fastq.gz AG01145.2_R1.fastq.gz,fastq fastq,12323940056.0,81078553.0,AG01145.2 R1.fastq.gz,0:76 1:76,A:3425803431;C:2777524766;G:2722925333;T:3380952969;N:16733557,76,76,,,3425803431,2777524766,2722925333,3380952969,16733557,SRX3567065,SRS2838997,SRA647342,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.94345,0.94709,0.12521,0.12335,0.69165,0.69475,0.4685,0.47082,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-01-17,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures 46212,SRR6477200,SRX3567064,SRS2838996,SRP129892,PRJNA430431,RES complex is associated with intron definition and required for zebrafish early embryogenesis,PRJNA430431,Other,Pre mRNA splicing is a critical step of gene expression in eukaryotes. Transcriptome wide splicing patterns are complex and primarily regulated by a diverse set of recognition elements and associated RNA binding proteins. The retention and splicing RES complex is formed by three different proteins Bud13p Pml1p and Snu17p and is involved in splicing in yeast. However the importance of the RES complex for vertebrate splicing the intronic features associated with its activity and its role in development are unknown. In this study we have generated loss of function mutants for the three components of the RES complex in zebrafish and showed that they are required during early development. The mutants showed a marked neural phenotype with increased cell death in the brain and a decrease in differentiated neurons. Transcriptomic analysis of bud13 snip1 pml1 and rbmx2 snu17 mutants revealed a global defect in intron splicing with strong mis splicing of a subset of introns. We found these RES dependent introns were short rich in GC and flanked by GC depleted exons all of which are features associated with intron definition. Using these features we developed and validated a predictive model that classifies RES dependent introns. Altogether our study uncovers the essential role of the RES complex during vertebrate development and provides new insights into its function during splicing.,,,,RNAseq Bud13 Bud13 KO 30h,RNAseq Bud13 Bud13 KO 30h AG01144,,strain:TU/AB|age:30.0|dev stage:30h|sex:pooled male and female|tissue:embryo|genotype: / |molecule:mRNA|selection:pA|replicate group:1|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq Bud13 Bud13 KO 30h,AG01144.2,AG01144.2,mRNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP129892,,,AG01144.2_R1.fastq.gz AG01144.2_R2.fastq.gz,fastq fastq,12242377920.0,80541960.0,AG01144.2 R1.fastq.gz,0:76 1:76,A:3501235324;C:2524126832;G:2520934401;T:3679154562;N:16926801,76,76,,,3501235324,2524126832,2520934401,3679154562,16926801,SRX3567064,SRS2838996,SRA647342,Yale_Giraldez|Genetics,Yale_Giraldez_Group,2,0.93874,0.93814,0.2229,0.17671,0.71102,0.71234,0.48631,0.48352,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-06-23,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures 54192,SRR10095968,SRX6828141,SRS5370316,SRP221273,PRJNA564810,A Single Cell Transcriptome Atlas for Zebrafish Development,PRJNA564810,Other,The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis to launch an effort to define the diversity of cell types during zebrafish organogenesis and to examine the transcriptional profiles that produce each cell type over developmental time.,,,,,1b,,strain:Tgolig2:GFPvu12|age:1 dpf|sex:unknown|tissue:whole embryo|Replicate name:1b|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of whole zebrafish embryos,1b,1b,10X v2 chromium cDNA library,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP221273,,loader:latf load,olig2gfp24hb_S2_L001_R1_001.fastq olig2gfp24hb_S2_L001_R2_001.fastq olig2gfp24hb_S2_L002_R1_001.fastq olig2gfp24hb_S2_L002_R2_001.fastq olig2gfp24hb_S2_L003_R1_001.fastq olig2gfp24hb_S2_L003_R2_001.fastq olig2gfp24hb_S2_L004_R1_001.fastq olig2gfp24hb_S2_L004_R2_001.fastq olig2gfp24hb_S2_L005_R1_001.fastq olig2gfp24hb_S2_L005_R2_001.fastq olig2gfp24hb_S2_L006_R1_001.fastq olig2gfp24hb_S2_L006_R2_001.fastq olig2gfp24hb_S2_L007_R1_001.fastq olig2gfp24hb_S2_L007_R2_001.fastq olig2gfp24hb_S2_L008_R1_001.fastq olig2gfp24hb_S2_L008_R2_001.fastq,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,98193351273.0,617568247.0,1b.gz,0:26 1:133,A:27237053473;C:21828277485;G:22951157364;T:26162156154;N:14706797,26,133,,,27237053473,21828277485,22951157364,26162156154,14706797,SRX6828141,SRS5370316,SRA960102,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.01479,0.95138,0.00273,0.12104,0.97327,0.78293,0.39405,0.4998,26,133,T,B,sc-like readlen,illumina,hiseq_era,unknown,unknown,unknown,sc,single_cell_droplet,10x,,United States,2019-12-10,Pharyngula,Embryo,Whole Organism,All anatomical structures 54193,SRR10095969,SRX6828140,SRS5370315,SRP221273,PRJNA564810,A Single Cell Transcriptome Atlas for Zebrafish Development,PRJNA564810,Other,The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis to launch an effort to define the diversity of cell types during zebrafish organogenesis and to examine the transcriptional profiles that produce each cell type over developmental time.,,,,,1a,,strain:Tgolig2:GFPvu12|age:1 dpf|sex:unknown|tissue:whole embryo|Replicate name:1a|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of whole zebrafish embryos,1a,1a,10X v2 chromium cDNA library,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP221273,,loader:latf load,olig2gfp24ha_S1_L001_R1_001.fastq olig2gfp24ha_S1_L001_R2_001.fastq olig2gfp24ha_S1_L002_R1_001.fastq olig2gfp24ha_S1_L002_R2_001.fastq olig2gfp24ha_S1_L003_R1_001.fastq olig2gfp24ha_S1_L003_R2_001.fastq olig2gfp24ha_S1_L004_R1_001.fastq olig2gfp24ha_S1_L004_R2_001.fastq olig2gfp24ha_S1_L005_R1_001.fastq olig2gfp24ha_S1_L005_R2_001.fastq olig2gfp24ha_S1_L006_R1_001.fastq olig2gfp24ha_S1_L006_R2_001.fastq olig2gfp24ha_S1_L007_R1_001.fastq olig2gfp24ha_S1_L007_R2_001.fastq olig2gfp24ha_S1_L008_R1_001.fastq olig2gfp24ha_S1_L008_R2_001.fastq,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,99552249225.0,626114775.0,1a.gz,0:26 1:133,A:27540748865;C:22111148705;G:23108024457;T:26777444676;N:14882522,26,133,,,27540748865,22111148705,23108024457,26777444676,14882522,SRX6828140,SRS5370315,SRA960102,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.01166,0.95413,0.002,0.08635,0.9779,0.80034,0.44044,0.48046,26,133,T,B,sc-like readlen,illumina,hiseq_era,unknown,unknown,unknown,sc,single_cell_droplet,10x,,United States,2019-12-10,Pharyngula,Embryo,Whole Organism,All anatomical structures