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
34977,SRR32588734,SRX27895217,SRS24266222,SRP568323,PRJNA1232602,Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains,PRJNA1232602,Other,In this study  Iso Seq was performed on different zebrafish body organs  enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues  including the brain  testis  liver  eye  muscle  ovary  inner ear and kidney  to identify novel isoforms  tissue specific transcripts  and alternative splicing events. We also made available the Iso Seq data from embryos from different time points  hpf  0  6  12  and 24. This dataset enhances gene annotation  improves reference genome annotations  and provides insights into zebrafish organ specific gene expression.,,,,Iso Seq RNA from embryo zero hpf,C2 F2 12,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:time 12 hours|dev stage:Embyoys|collection date:2024 06|geo loc name:USA|sex:male|tissue:muscle|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from embyo 12 hpf,C2 F2 12,C2 F2 12,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m54313U_231111_191642.hifi_reads.flnc.fastq.gz,fastq,7627931284.0,3897936.0,m54313U 231111 191642.hifi reads.flnc.fastq.gz,0:1956.92,A:2146633241;C:1706673950;G:1799625470;T:1974998623;N:0,1956,,,,2146633241,1706673950,1799625470,1974998623,0,SRX27895217,SRS24266222,SRA2089085,National Human Genome Research Institute|Translational and Functional Genomics Branch,National Human Genome Research Institute National Human Genome Research Institute,,,,,,,,,,,,T,,long read,pacbio,pacbio_modern,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2025-03-06,Segmentation,Embryo,Muscle,Muscular System
75477,SRR24682231,SRX20461641,SRS17774512,SRP438861,PRJNA973729,Danio rerio strain:AB Raw sequence reads,PRJNA973729,Other,Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.,,,,,20 25 Somites,,strain:AB|dev stage:20 25 Somites|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,full length transcriptome of Danio rerio: 20 25 Somites,20 25 Somites,20 25 Somites,The RNA of each sample was reversely transcribed into cDNA using a SMARTer PCR cDNA Synthesis Kit. Prime STAR GXL DNA Polymerase Kit was used to PCR amplify the full length cDNA. The SMARTbell libraries were constructed with the SMARTbell template prep kit. Conduct damage repair and end repair. The stem loop sequencing adaptors were linked to both ends of the DNA fragment and used to remove the failed fragment using exonuclease.,,,FL-cDNA,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel,,SRP438861,,assembly:GRCz11,P02TYR22604108_1_r64399e_20220512_090859_1_A02.ccs.bam,bam,2078794793.0,725960.0,P02TYR22604108 1 r64399e 20220512 090859 1 A02.ccs.bam,0:2863.51,A:605292389;C:441948349;G:472618370;T:558935685;N:0,2863,,,,605292389,441948349,472618370,558935685,0,SRX20461641,SRS17774512,SRA1641718,"Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res","Institute of hydrobiology, chinese academy od sciences",1,0.55105,,0.00964,,0.80831,,0.45443,,1451,,T,,long read,pacbio,pacbio_modern,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,China,2023-05-21,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
75478,SRR24682233,SRX20461640,SRS17774511,SRP438861,PRJNA973729,Danio rerio strain:AB Raw sequence reads,PRJNA973729,Other,Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.,,,,,14 19 Somites,,strain:AB|dev stage:14 19 Somites|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,full length transcriptome of Danio rerio: 14 19 Somites,14 19 Somites,14 19 Somites,The RNA of each sample was reversely transcribed into cDNA using a SMARTer PCR cDNA Synthesis Kit. Prime STAR GXL DNA Polymerase Kit was used to PCR amplify the full length cDNA. The SMARTbell libraries were constructed with the SMARTbell template prep kit. Conduct damage repair and end repair. The stem loop sequencing adaptors were linked to both ends of the DNA fragment and used to remove the failed fragment using exonuclease.,,,FL-cDNA,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel,,SRP438861,,assembly:GRCz11,P02TYR22604106_1_r64399e_20220512_090859_1_A02.ccs.bam,bam,2511998751.0,864091.0,P02TYR22604106 1 r64399e 20220512 090859 1 A02.ccs.bam,0:2907.10,A:730743897;C:535154858;G:572074928;T:674025068;N:0,2907,,,,730743897,535154858,572074928,674025068,0,SRX20461640,SRS17774511,SRA1641718,"Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res","Institute of hydrobiology, chinese academy od sciences",1,0.54959,,0.01154,,0.816,,0.44689,,2262,,T,,long read,pacbio,pacbio_modern,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,China,2023-05-21,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
75479,SRR24682234,SRX20461639,SRS17774510,SRP438861,PRJNA973729,Danio rerio strain:AB Raw sequence reads,PRJNA973729,Other,Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.,,,,,1 4 Somites,,strain:AB|dev stage:1 4 Somites|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,full length transcriptome of Danio rerio: 1 4 Somites,1 4 Somites,1 4 Somites,The RNA of each sample was reversely transcribed into cDNA using a SMARTer PCR cDNA Synthesis Kit. Prime STAR GXL DNA Polymerase Kit was used to PCR amplify the full length cDNA. The SMARTbell libraries were constructed with the SMARTbell template prep kit. Conduct damage repair and end repair. The stem loop sequencing adaptors were linked to both ends of the DNA fragment and used to remove the failed fragment using exonuclease.,,,FL-cDNA,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel,,SRP438861,,assembly:GRCz11,P02TYR22604105_1_r64399e_20220512_090859_1_A02.ccs.bam,bam,2199775856.0,820475.0,P02TYR22604105 1 r64399e 20220512 090859 1 A02.ccs.bam,0:2681.10,A:637639661;C:475508465;G:505308978;T:581318752;N:0,2681,,,,637639661,475508465,505308978,581318752,0,SRX20461639,SRS17774510,SRA1641718,"Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res","Institute of hydrobiology, chinese academy od sciences",1,0.60261,,0.00759,,0.83583,,0.49086,,1389,,T,,long read,pacbio,pacbio_modern,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,China,2023-05-21,Segmentation,Embryo,Embryo Imprecise,All anatomical structures