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 34957,SRR32588714,SRX27895237,SRS24266239,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 Danio rerio,C2 F2 F MUS21,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:female|tissue:musle|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from muscle,C2 F2 F MUS21,C2 F2 F MUS21,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m84270_240911_190611_s3.skera.flnc.fastq.gz,fastq,86382018375.0,48203691.0,m84270 240911 190611 s3.skera.flnc.fastq.gz,0:1792.02,A:25051251986;C:19022185989;G:19130320983;T:23178259417;N:0,1792,,,,25051251986,19022185989,19130320983,23178259417,0,SRX27895237,SRS24266239,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,Adult,Adult,Muscle,Muscular System 34958,SRR32588715,SRX27895236,SRS24266238,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 Danio rerio,C2 F2 F L22,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:female|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from liver,C2 F2 F L22,C2 F2 F L22,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m64467e_240816_172726.hifi_reads.flnc.fastq.gz,fastq,15103018596.0,3471157.0,m64467e 240816 172726.hifi reads.flnc.fastq.gz,0:4351.00,A:4102928612;C:3526979790;G:3455927740;T:4017182454;N:0,4351,,,,4102928612,3526979790,3455927740,4017182454,0,SRX27895236,SRS24266238,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,Adult,Adult,Liver,Liver and Biliary System 34959,SRR32588716,SRX27895235,SRS24266237,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 Danio rerio,C2 F2 F L21,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:female|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from liver,C2 F2 F L21,C2 F2 F L21,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m84270_240913_130745_s1.skera.flnc.fastq.gz,fastq,91129501236.0,45094963.0,m84270 240913 130745 s1.skera.flnc.fastq.gz,0:2020.84,A:25808290124;C:20578070676;G:20740793271;T:24002347165;N:0,2020,,,,25808290124,20578070676,20740793271,24002347165,0,SRX27895235,SRS24266237,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,Adult,Adult,Liver,Liver and Biliary System 34960,SRR32588717,SRX27895234,SRS24266236,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 Danio rerio,C2 F2 F K,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:female|tissue:kidney|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from kidney,C2 F2 F K,C2 F2 F K,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m84270_240904_132604_s1.skera.flnc.fastq.gz,fastq,109258150145.0,61126158.0,m84270 240904 132604 s1.skera.flnc.fastq.gz,0:1787.42,A:32153042096;C:22604112467;G:23394852841;T:31106142741;N:0,1787,,,,32153042096,22604112467,23394852841,31106142741,0,SRX27895234,SRS24266236,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,Adult,Adult,Kidney,Renal System 34961,SRR32588718,SRX27895233,SRS24266235,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 Danio rerio,C2 F2 F IE,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:female|tissue:inner ear|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from inner ear,C2 F2 F IE,C2 F2 F IE,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m84270_240904_152521_s2.skera.flnc.fastq.gz,fastq,93609779073.0,46650644.0,m84270 240904 152521 s2.skera.flnc.fastq.gz,0:2006.61,A:27359819621;C:19471270902;G:20218480457;T:26560208093;N:0,2006,,,,27359819621,19471270902,20218480457,26560208093,0,SRX27895233,SRS24266235,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,Adult,Adult,Undetermined,Undetermined 34962,SRR32588719,SRX27895232,SRS24266231,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 Danio rerio,C2 F2 F EYE,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:female|tissue:eye|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from eye,C2 F2 F EYE,C2 F2 F EYE,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m64467e_240703_141215.skera.flnc.fastq.gz,fastq,36628626441.0,15348616.0,m64467e 240703 141215.skera.flnc.fastq.gz,0:2386.44,A:10655476547;C:7616418469;G:7889834035;T:10466897390;N:0,2386,,,,10655476547,7616418469,7889834035,10466897390,0,SRX27895232,SRS24266231,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,Adult,Adult,Eye,Sensory System 34963,SRR32588720,SRX27895231,SRS24266232,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 6,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:time 6 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 6 hpf,C2 F2 6,C2 F2 6,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m54313U_231108_155338.hifi_reads.flnc.fastq.gz,fastq,6758669497.0,3269612.0,m54313U 231108 155338.hifi reads.flnc.fastq.gz,0:2067.12,A:1903955333;C:1520080315;G:1594879456;T:1739754393;N:0,2067,,,,1903955333,1520080315,1594879456,1739754393,0,SRX27895231,SRS24266232,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,Gastrula,Embryo,Muscle,Muscular System 34964,SRR32588721,SRX27895230,SRS24266233,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 Danio rerio,C2 F2 F B,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:female|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from brain,C2 F2 F B,C2 F2 F B,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m64467e_240523_204656.skera.flnc.fastq.gz,fastq,11267908778.0,6337509.0,m64467e 240523 204656.skera.flnc.fastq.gz,0:1777.97,A:3374083285;C:2369790412;G:2399920883;T:3124114198;N:0,1777,,,,3374083285,2369790412,2399920883,3124114198,0,SRX27895230,SRS24266233,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,Adult,Adult,Brain,Nervous System 34965,SRR32588722,SRX27895229,SRS24266229,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 Danio rerio,C2 F2 M T,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:male|tissue:testis|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from testis,C2 F2 M T,C2 F2 M T,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m84270_240911_150713_s1.skera.flnc.fastq.gz,fastq,103111938047.0,50624762.0,m84270 240911 150713 s1.skera.flnc.fastq.gz,0:2036.79,A:30106378730;C:21760983790;G:23176083069;T:28068492458;N:0,2036,,,,30106378730,21760983790,23176083069,28068492458,0,SRX27895229,SRS24266229,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,Adult,Adult,Gonad,Reproductive System 34966,SRR32588723,SRX27895228,SRS24266230,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 24,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:time 24 hours|dev stage:Embyoys|collection date:2024 06|geo loc name:USA|sex:female|tissue:muscle|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from embyo 24 hpf,C2 F2 24,C2 F2 24,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m54313U_231109_165320.hifi_reads.flnc.fastq.gz,fastq,7642144881.0,3850910.0,m54313U 231109 165320.hifi reads.flnc.fastq.gz,0:1984.50,A:2137607023;C:1720821414;G:1812220379;T:1971496065;N:0,1984,,,,2137607023,1720821414,1812220379,1971496065,0,SRX27895228,SRS24266230,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,Pharyngula,Embryo,Muscle,Muscular System 34967,SRR32588724,SRX27895227,SRS24266228,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 Danio rerio,C2 F2 M MUS22,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:male|tissue:muscle|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from muscle,C2 F2 M MUS22,C2 F2 M MUS22,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m64467e_240817_183852.hifi_reads.flnc.fastq.gz,fastq,14631605009.0,3302436.0,m64467e 240817 183852.hifi reads.flnc.fastq.gz,0:4430.55,A:4285049339;C:3157147611;G:3606320925;T:3583087134;N:0,4430,,,,4285049339,3157147611,3606320925,3583087134,0,SRX27895227,SRS24266228,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,Adult,Adult,Muscle,Muscular System 34968,SRR32588725,SRX27895226,SRS24266227,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 Danio rerio,C2 F2 M mus2,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:male|tissue:Muscle|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from muscle,C2 F2 M mus2,C2 F2 M mus2,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m84270_240913_150707_s2.skera.flnc.fastq.gz,fastq,105235491521.0,56491114.0,m84270 240913 150707 s2.skera.flnc.fastq.gz,0:1862.87,A:30649812728;C:23382133477;G:23762971602;T:27440573714;N:0,1862,,,,30649812728,23382133477,23762971602,27440573714,0,SRX27895226,SRS24266227,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,Adult,Adult,Muscle,Muscular System 34969,SRR32588726,SRX27895225,SRS24266223,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 Danio rerio,C2 F2 M L,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:male|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from liver,C2 F2 M L,C2 F2 M L,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m84270_240911_170652_s2.skera.flnc.fastq.gz,fastq,103288926144.0,58528654.0,m84270 240911 170652 s2.skera.flnc.fastq.gz,0:1764.76,A:30548263427;C:22289732504;G:23327561779;T:27123368434;N:0,1764,,,,30548263427,22289732504,23327561779,27123368434,0,SRX27895225,SRS24266223,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,Adult,Adult,Liver,Liver and Biliary System 34970,SRR32588727,SRX27895224,SRS24266224,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 Danio rerio,C2 F2 M K22,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:male|tissue:kidney|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from kidney,C2 F2 M K22,C2 F2 M K22,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m64467e_240829_144745.hifi_reads.flnc.fastq.gz,fastq,14838539048.0,3383142.0,m64467e 240829 144745.hifi reads.flnc.fastq.gz,0:4386.02,A:4211191682;C:3185079857;G:3320422646;T:4121844863;N:0,4386,,,,4211191682,3185079857,3320422646,4121844863,0,SRX27895224,SRS24266224,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,Adult,Adult,Kidney,Renal System 34971,SRR32588728,SRX27895223,SRS24266234,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 Danio rerio,C2 F2 M K21,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:male|tissue:Kidney|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from kidney,C2 F2 M K21,C2 F2 M K21,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m84270_240913_170640_s3.skera.flnc.fastq.gz,fastq,100849133955.0,51593887.0,m84270 240913 170640 s3.skera.flnc.fastq.gz,0:1954.67,A:28887816631;C:21568633305;G:22323254809;T:28069429210;N:0,1954,,,,28887816631,21568633305,22323254809,28069429210,0,SRX27895223,SRS24266234,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,Adult,Adult,Kidney,Renal System 34972,SRR32588729,SRX27895222,SRS24266219,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 Danio rerio,C2 F2 M EYE,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:male|tissue:eye|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from eye,C2 F2 M EYE,C2 F2 M EYE,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m84270_240904_172441_s3.skera.flnc.fastq.gz,fastq,80921799737.0,39038804.0,m84270 240904 172441 s3.skera.flnc.fastq.gz,0:2072.86,A:23445079372;C:17292916271;G:17758249005;T:22425555089;N:0,2072,,,,23445079372,17292916271,17758249005,22425555089,0,SRX27895222,SRS24266219,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,Adult,Adult,Eye,Sensory System 34973,SRR32588730,SRX27895221,SRS24266225,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 Danio rerio,C2 F2 M B,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:male|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from brain,C2 F2 M B,C2 F2 M B,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m84270_240904_192359_s4.skera.flnc.fastq.gz,fastq,64391727308.0,29612753.0,m84270 240904 192359 s4.skera.flnc.fastq.gz,0:2174.46,A:18972670876;C:13388478305;G:13738034427;T:18292543700;N:0,2174,,,,18972670876,13388478305,13738034427,18292543700,0,SRX27895221,SRS24266225,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,Adult,Adult,Brain,Nervous System 34974,SRR32588731,SRX27895220,SRS24266226,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 Danio rerio,C2 F2 F O32,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:female|tissue:ovary|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from ovary,C2 F2 F O32,C2 F2 F O32,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m64467e_240815_161552.hifi_reads.flnc.fastq.gz,fastq,12555748052.0,3350326.0,m64467e 240815 161552.hifi reads.flnc.fastq.gz,0:3747.62,A:3457885256;C:2882310858;G:2971165409;T:3244386529;N:0,3747,,,,3457885256,2882310858,2971165409,3244386529,0,SRX27895220,SRS24266226,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,Adult,Adult,Gonad,Reproductive System 34975,SRR32588732,SRX27895219,SRS24266221,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 Danio rerio,C2 F2 F O31,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:female|tissue:Ovary|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from ovary,C2 F2 F O31,C2 F2 F O31,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m84270_240911_210533_s4.skera.flnc.fastq.gz,fastq,91708771607.0,33888263.0,m84270 240911 210533 s4.skera.flnc.fastq.gz,0:2706.21,A:25318206966;C:20635348405;G:21357313254;T:24397902982;N:0,2706,,,,25318206966,20635348405,21357313254,24397902982,0,SRX27895219,SRS24266221,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,Adult,Adult,Gonad,Reproductive System 34976,SRR32588733,SRX27895218,SRS24266220,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 Danio rerio,C2 F2 F MUS22,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:female|tissue:muscle|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from muscle,C2 F2 F MUS22,C2 F2 F MUS22,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m64467e_240814_151650.hifi_reads.flnc.fastq.gz,fastq,12063904861.0,3021713.0,m64467e 240814 151650.hifi reads.flnc.fastq.gz,0:3992.41,A:3499589691;C:2629790020;G:2965002855;T:2969522295;N:0,3992,,,,3499589691,2629790020,2965002855,2969522295,0,SRX27895218,SRS24266220,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,Adult,Adult,Muscle,Muscular System 34977,SRR32588734,SRX27895217,SRS24266222,SRP568323,PRJNA1232602,Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains,PRJNA1232602,Other,In this study Iso Seq was performed on different zebrafish body organs enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues including the brain testis liver eye muscle ovary inner ear and kidney to identify novel isoforms tissue specific transcripts and alternative splicing events. We also made available the Iso Seq data from embryos from different time points hpf 0 6 12 and 24. This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression.,,,,Iso Seq RNA from embryo zero hpf,C2 F2 12,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:time 12 hours|dev stage:Embyoys|collection date:2024 06|geo loc name:USA|sex:male|tissue:muscle|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from embyo 12 hpf,C2 F2 12,C2 F2 12,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m54313U_231111_191642.hifi_reads.flnc.fastq.gz,fastq,7627931284.0,3897936.0,m54313U 231111 191642.hifi reads.flnc.fastq.gz,0:1956.92,A:2146633241;C:1706673950;G:1799625470;T:1974998623;N:0,1956,,,,2146633241,1706673950,1799625470,1974998623,0,SRX27895217,SRS24266222,SRA2089085,National Human Genome Research Institute|Translational and Functional Genomics Branch,National Human Genome Research Institute National Human Genome Research Institute,,,,,,,,,,,,T,,long read,pacbio,pacbio_modern,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2025-03-06,Segmentation,Embryo,Muscle,Muscular System 34978,SRR32588735,SRX27895216,SRS24266218,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 0,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:time 0 hours|dev stage:Embyoys|collection date:2024 06|geo loc name:USA|sex:female|tissue:muscle|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from embyo 0 hpf,C2 F2 0,C2 F2 0,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m54313U_231110_180503.hifi_reads.flnc.fastq.gz,fastq,8144050440.0,3744842.0,m54313U 231110 180503.hifi reads.flnc.fastq.gz,0:2174.74,A:2267401658;C:1836982566;G:1935470734;T:2104195482;N:0,2174,,,,2267401658,1836982566,1935470734,2104195482,0,SRX27895216,SRS24266218,SRA2089085,National Human Genome Research Institute|Translational and Functional Genomics Branch,National Human Genome Research Institute National Human Genome Research Institute,1,0.76793,,0.00473,,0.80371,,0.50925,,1489,,T,,long read,pacbio,pacbio_modern,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2025-03-06,Zygote,Embryo,Muscle,Muscular System 42960,SRR5865382,SRX3033432,SRS2382228,SRP113522,PRJNA395690,High resolution annotation of Zebrafish transcriptome using long read sequencing,GSE101843,Transcriptome Analysis,With the emergence of zebrafish as an important model organism a concerted effort has been made to study its transcriptome. This effort is limited by gaps in zebrafish annotation which is especially pronounced concerning transcripts dynamically expressed during zygotic genome activation ZGA. To date short read sequencing has been the principal technology for zebrafish transcriptome annotation. In part because these sequence reads are too short for assembly methods to resolve the full complexity of the transcriptome the current annotation is rudimentary. By providing direct observation of full length transcripts recently refined long read sequencing platforms can dramatically improve annotation coverage and accuracy. Here we leveraged the SMRT platform to study the early ZGA stage zebrafish transcriptome. Our analysis revealed additional novelty and complexity in the zebrafish transcriptome identifying 2748 high confidence novel transcripts that originated from previously unannotated loci and 1835 new isoforms in previously annotated genes. Overall design: Pooled RNA of a amanitin / untreated embryos were collected and profiled with long read sequencing. Temporally corresponding pre/post ZGA pooled embryonic RNA samples were profiled with short read RNA seq. Long read raw data were assembled into transcripts using IsoSeq  PMID: 27407110 mapped to the reference GRCz10 genome using GMAP [PMID:15728110] and annotated against the reference transcriptome using Cuffcompare [PMC3334321]. Novel transcripts were compared to short read data and computationally validated in constructing a final long read augmented transcriptome.,,pubmed:30061115,,long reads postZGA,GSM2717136,,tissue:epiboly|treatment:untreated|developmental stage:6 hpf,long reads postZGA,Samples were run on the HiSeq2500 System and base calling and Q scoring was performed with Illumina’s Real Time Analysis RTA version 1.18.64. bcl2fastq 1.8.3 was used to demulitplex and convert files to the fastq format isoforms were quantified using kallisto Genome build: GRCz10,epiboly,The procedure for achieving suppression of ZGA is treatment of one to four cell embryos by injection of 0.2nmol of the RNA Polymerase inhibitor α amanitin. Pools of 15 embryos each for both untreated wild type embryos and embryos injected with 0.2nmol α amanitin to abolish zygotic transcription as described previously Zamir et al. 1997,RNA was isolated from zebrafish embryos via standard Trizol protocol as described Kent et al. 2016. Reverse transcription was accomplished using the Superscript III kit from Invitrogen with 2ug total RNA. RT PCR reactions were prepared with 50ng cDNA per reaction and RedTaq reverse transcriptase mix Sigma. Annealing temperature was 58° C and extension time was 3 minutes. RT qPCR reactions were prepared with 20ng cDNA per sample and set up according to the Promega GoTaq 2 Step SybrGreen™ kit using a fast 2 step protocol on the Agilent Mx3000P qPCR system and initial melting time of 3 minutes. For short read sequencing RNA was isolated from sample sets of approximately 20 embryos at 2.5 hpfand 5.25 hpf stages. RNA quality was assessed by Agilent Bioanalyzer. Samples with a RIN score of 9 or greater were used to generate cDNA libraries following treatment with the Ribo Zero rRNA removal kit Illumina,Zebrafish were maintained according to standard protocols and embryos were obtained during natural spawning of either AB TAB14 or TAB5 WT adults. The IACUC committee of the Icahn School of Medicine at Mount Sinai approved all protocols. Fertilized eggs were collected and staged based on morphological criteria to identify embryos at pre 256 cell stage and post ZGA,treatment:untreated|developmental stage:6 hpf,GSM2717136,GSM2717136: long reads postZGA; Danio rerio; RNA Seq,GSM2717136,,1,RNA was isolated from zebrafish embryos via standard Trizol protocol as described Kent et al. 2016. Reverse transcription was accomplished using the Superscript III kit from Invitrogen with 2ug total RNA. RT PCR reactions were prepared with 50ng cDNA per reaction and RedTaq reverse transcriptase mix Sigma. Annealing temperature was 58° C and extension time was 3 minutes. RT qPCR reactions were prepared with 20ng cDNA per sample and set up according to the Promega GoTaq 2 Step SybrGreen™ kit using a fast 2 step protocol on the Agilent Mx3000P qPCR system and initial melting time of 3 minutes. For short read sequencing RNA was isolated from sample sets of approximately 20 embryos at 2.5 hpfand 5.25 hpf stages. RNA quality was assessed by Agilent Bioanalyzer. Samples with a RIN score of 9 or greater were used to generate cDNA libraries following treatment with the Ribo Zero rRNA removal kit Illumina,GEO Accession:GSM2717136,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,PacBio RS,,SRP113522,,loader:fastq load.py,Zebrafish_ctrl.fastq,pacbio_native,84277710.0,71570.0,GSM2717136 r1,,A:23712654;C:18242312;G:19552931;T:22769813;N:0,,,,,23712654,18242312,19552931,22769813,0,SRX3033432,SRS2382228,SRA591628,GEO,"Sealfon, Department of Neurology, Icahn School of Medicine at Mount Sinai",2,0.65823,0.65823,0.01265,0.01265,0.99904,0.99904,0.40425,0.42553,895,895,B,B,biological fallback assumption,pacbio,pacbio_early,full_length,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2017-07-25,Gastrula,Embryo,Embryo Imprecise,All anatomical structures 42961,SRR5865381,SRX3033431,SRS2382227,SRP113522,PRJNA395690,High resolution annotation of Zebrafish transcriptome using long read sequencing,GSE101843,Transcriptome Analysis,With the emergence of zebrafish as an important model organism a concerted effort has been made to study its transcriptome. This effort is limited by gaps in zebrafish annotation which is especially pronounced concerning transcripts dynamically expressed during zygotic genome activation ZGA. To date short read sequencing has been the principal technology for zebrafish transcriptome annotation. In part because these sequence reads are too short for assembly methods to resolve the full complexity of the transcriptome the current annotation is rudimentary. By providing direct observation of full length transcripts recently refined long read sequencing platforms can dramatically improve annotation coverage and accuracy. Here we leveraged the SMRT platform to study the early ZGA stage zebrafish transcriptome. Our analysis revealed additional novelty and complexity in the zebrafish transcriptome identifying 2748 high confidence novel transcripts that originated from previously unannotated loci and 1835 new isoforms in previously annotated genes. Overall design: Pooled RNA of a amanitin / untreated embryos were collected and profiled with long read sequencing. Temporally corresponding pre/post ZGA pooled embryonic RNA samples were profiled with short read RNA seq. Long read raw data were assembled into transcripts using IsoSeq  PMID: 27407110 mapped to the reference GRCz10 genome using GMAP [PMID:15728110] and annotated against the reference transcriptome using Cuffcompare [PMC3334321]. Novel transcripts were compared to short read data and computationally validated in constructing a final long read augmented transcriptome.,,pubmed:30061115,,long reads preZGA,GSM2717135,,tissue:256 cell|treatment:a amanitin|developmental stage:6 hpf,long reads preZGA,Samples were run on the HiSeq2500 System and base calling and Q scoring was performed with Illumina’s Real Time Analysis RTA version 1.18.64. bcl2fastq 1.8.3 was used to demulitplex and convert files to the fastq format isoforms were quantified using kallisto Genome build: GRCz10,256 cell,The procedure for achieving suppression of ZGA is treatment of one to four cell embryos by injection of 0.2nmol of the RNA Polymerase inhibitor α amanitin. Pools of 15 embryos each for both untreated wild type embryos and embryos injected with 0.2nmol α amanitin to abolish zygotic transcription as described previously Zamir et al. 1997,RNA was isolated from zebrafish embryos via standard Trizol protocol as described Kent et al. 2016. Reverse transcription was accomplished using the Superscript III kit from Invitrogen with 2ug total RNA. RT PCR reactions were prepared with 50ng cDNA per reaction and RedTaq reverse transcriptase mix Sigma. Annealing temperature was 58° C and extension time was 3 minutes. RT qPCR reactions were prepared with 20ng cDNA per sample and set up according to the Promega GoTaq 2 Step SybrGreen™ kit using a fast 2 step protocol on the Agilent Mx3000P qPCR system and initial melting time of 3 minutes. For short read sequencing RNA was isolated from sample sets of approximately 20 embryos at 2.5 hpfand 5.25 hpf stages. RNA quality was assessed by Agilent Bioanalyzer. Samples with a RIN score of 9 or greater were used to generate cDNA libraries following treatment with the Ribo Zero rRNA removal kit Illumina,Zebrafish were maintained according to standard protocols and embryos were obtained during natural spawning of either AB TAB14 or TAB5 WT adults. The IACUC committee of the Icahn School of Medicine at Mount Sinai approved all protocols. Fertilized eggs were collected and staged based on morphological criteria to identify embryos at pre 256 cell stage and post ZGA,treatment:a amanitin|developmental stage:6 hpf,GSM2717135,GSM2717135: long reads preZGA; Danio rerio; RNA Seq,GSM2717135,,1,RNA was isolated from zebrafish embryos via standard Trizol protocol as described Kent et al. 2016. Reverse transcription was accomplished using the Superscript III kit from Invitrogen with 2ug total RNA. RT PCR reactions were prepared with 50ng cDNA per reaction and RedTaq reverse transcriptase mix Sigma. Annealing temperature was 58° C and extension time was 3 minutes. RT qPCR reactions were prepared with 20ng cDNA per sample and set up according to the Promega GoTaq 2 Step SybrGreen™ kit using a fast 2 step protocol on the Agilent Mx3000P qPCR system and initial melting time of 3 minutes. For short read sequencing RNA was isolated from sample sets of approximately 20 embryos at 2.5 hpfand 5.25 hpf stages. RNA quality was assessed by Agilent Bioanalyzer. Samples with a RIN score of 9 or greater were used to generate cDNA libraries following treatment with the Ribo Zero rRNA removal kit Illumina,GEO Accession:GSM2717135,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,PacBio RS,,SRP113522,,loader:fastq load.py,Zebrafish_a_aman.fastq,pacbio_native,90521885.0,73347.0,GSM2717135 r1,,A:25481448;C:19609613;G:20975956;T:24454868;N:0,,,,,25481448,19609613,20975956,24454868,0,SRX3033431,SRS2382227,SRA591628,GEO,"Sealfon, Department of Neurology, Icahn School of Medicine at Mount Sinai",2,0.61069,0.61069,0.0,0.0,0.99857,0.99857,0.43661,0.43661,1668,1668,B,B,biological fallback assumption,pacbio,pacbio_early,full_length,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2017-07-25,Gastrula,Embryo,Embryo Imprecise,All anatomical structures 75461,SRR24682216,SRX20461657,SRS17774528,SRP438861,PRJNA973729,Danio rerio strain:AB Raw sequence reads,PRJNA973729,Other,Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.,,,,,75% epiboly,,strain:AB|dev stage:75% epiboly|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,full length transcriptome of Danio rerio: 75% epiboly,75% epiboly,75% epiboly,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,P02TYR22604104_1_r64400e_20220511_065818_2_E02.ccs.bam,bam,2445533795.0,757816.0,P02TYR22604104 1 r64400e 20220511 065818 2 E02.ccs.bam,0:3227.08,A:707827290;C:530585152;G:559097725;T:648023628;N:0,3227,,,,707827290,530585152,559097725,648023628,0,SRX20461657,SRS17774528,SRA1641718,"Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res","Institute of hydrobiology, chinese academy od sciences",1,0.54087,,0.01072,,0.84772,,0.44148,,4236,,T,,long read,pacbio,pacbio_modern,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,China,2023-05-21,Gastrula,Embryo,Embryo Imprecise,All anatomical structures 75462,SRR24682217,SRX20461656,SRS17774527,SRP438861,PRJNA973729,Danio rerio strain:AB Raw sequence reads,PRJNA973729,Other,Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.,,,,,Shield,,strain:AB|dev stage:Shield|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,full length transcriptome of Danio rerio: Shield,Shield,Shield,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,P02TYR22604103_1_r64400e_20220511_065818_2_E02.ccs.bam,bam,2465358437.0,742181.0,P02TYR22604103 1 r64400e 20220511 065818 2 E02.ccs.bam,0:3321.78,A:703901230;C:545159399;G:572405158;T:643892650;N:0,3321,,,,703901230,545159399,572405158,643892650,0,SRX20461656,SRS17774527,SRA1641718,"Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res","Institute of hydrobiology, chinese academy od sciences",1,0.53343,,0.00627,,0.84307,,0.44973,,3519,,T,,long read,pacbio,pacbio_modern,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,China,2023-05-21,Gastrula,Embryo,Embryo Imprecise,All anatomical structures 75463,SRR24682218,SRX20461655,SRS17774526,SRP438861,PRJNA973729,Danio rerio strain:AB Raw sequence reads,PRJNA973729,Other,Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.,,,,,50% epiboly,,strain:AB|dev stage:50% epiboly|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,full length transcriptome of Danio rerio: 50% epiboly,50% epiboly,50% epiboly,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,P02TYR22604117_1_r64400e_20220511_065818_2_E02.ccs.bam,bam,2347198259.0,696031.0,P02TYR22604117 1 r64400e 20220511 065818 2 E02.ccs.bam,0:3372.26,A:663704982;C:525754765;G:550887011;T:606851501;N:0,3372,,,,663704982,525754765,550887011,606851501,0,SRX20461655,SRS17774526,SRA1641718,"Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res","Institute of hydrobiology, chinese academy od sciences",1,0.53029,,0.00409,,0.84798,,0.45394,,3517,,T,,long read,pacbio,pacbio_modern,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,China,2023-05-21,Gastrula,Embryo,Embryo Imprecise,All anatomical structures 75464,SRR24682219,SRX20461654,SRS17774525,SRP438861,PRJNA973729,Danio rerio strain:AB Raw sequence reads,PRJNA973729,Other,Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.,,,,,Dome,,strain:AB|dev stage:Dome|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,full length transcriptome of Danio rerio: Dome,Dome,Dome,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,P02TYR22604102_1_r64400e_20220511_065818_2_E02.ccs.bam,bam,3154546886.0,890787.0,P02TYR22604102 1 r64400e 20220511 065818 2 E02.ccs.bam,0:3541.30,A:897866757;C:700790757;G:734990612;T:820898760;N:0,3541,,,,897866757,700790757,734990612,820898760,0,SRX20461654,SRS17774525,SRA1641718,"Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res","Institute of hydrobiology, chinese academy od sciences",1,0.49522,,0.00439,,0.84411,,0.45054,,5785,,T,,long read,pacbio,pacbio_modern,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,China,2023-05-21,Blastula,Embryo,Embryo Imprecise,All anatomical structures 75465,SRR24682220,SRX20461653,SRS17774524,SRP438861,PRJNA973729,Danio rerio strain:AB Raw sequence reads,PRJNA973729,Other,Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.,,,,,Oblong,,strain:AB|dev stage:Oblong|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,full length transcriptome of Danio rerio: Oblong,Oblong,Oblong,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,P02TYR22604100_1_r64400e_20220511_065818_2_E02.ccs.bam,bam,3883927264.0,1087850.0,P02TYR22604100 1 r64400e 20220511 065818 2 E02.ccs.bam,0:3570.28,A:1097185313;C:871304396;G:915871000;T:999566555;N:0,3570,,,,1097185313,871304396,915871000,999566555,0,SRX20461653,SRS17774524,SRA1641718,"Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res","Institute of hydrobiology, chinese academy od sciences",1,0.50563,,0.00093,,0.84372,,0.45982,,4109,,T,,long read,pacbio,pacbio_modern,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,China,2023-05-21,Blastula,Embryo,Embryo Imprecise,All anatomical structures 75466,SRR24682221,SRX20461652,SRS17774523,SRP438861,PRJNA973729,Danio rerio strain:AB Raw sequence reads,PRJNA973729,Other,Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.,,,,,1k cell,,strain:AB|dev stage:1k cell|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,full length transcriptome of Danio rerio: 1k cell,1k cell,1k cell,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,P02TYR22604099_1_r64053_20220510_083113_3_G01.ccs.bam,bam,1879917938.0,693905.0,P02TYR22604099 1 r64053 20220510 083113 3 G01.ccs.bam,0:2709.19,A:532599205;C:423737589;G:447933988;T:475647156;N:0,2709,,,,532599205,423737589,447933988,475647156,0,SRX20461652,SRS17774523,SRA1641718,"Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res","Institute of hydrobiology, chinese academy od sciences",1,0.60112,,0.00068,,0.81998,,0.49181,,3694,,T,,long read,pacbio,pacbio_modern,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,China,2023-05-21,Blastula,Embryo,Embryo Imprecise,All anatomical structures 75467,SRR24682222,SRX20461651,SRS17774522,SRP438861,PRJNA973729,Danio rerio strain:AB Raw sequence reads,PRJNA973729,Other,Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.,,,,,128 cell,,strain:AB|dev stage:128 cell|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,full length transcriptome of Danio rerio: 128 cell,128 cell,128 cell,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,P02TYR22604098_1_r64053_20220510_083113_3_G01.ccs.bam,bam,2358442303.0,844527.0,P02TYR22604098 1 r64053 20220510 083113 3 G01.ccs.bam,0:2792.62,A:664024741;C:534780676;G:563369243;T:596267643;N:0,2792,,,,664024741,534780676,563369243,596267643,0,SRX20461651,SRS17774522,SRA1641718,"Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res","Institute of hydrobiology, chinese academy od sciences",1,0.58542,,0.00059,,0.82688,,0.49158,,2312,,T,,long read,pacbio,pacbio_modern,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,China,2023-05-21,Blastula,Embryo,Embryo Imprecise,All anatomical structures 75468,SRR24682223,SRX20461650,SRS17774521,SRP438861,PRJNA973729,Danio rerio strain:AB Raw sequence reads,PRJNA973729,Other,Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.,,,,,Day 6,,strain:AB|dev stage:Day 6|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,full length transcriptome of Danio rerio: Day 6,Day 6,Day 6,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,P02TYR22604121_1_r64053_20220510_083113_4_H01.ccs.bam,bam,3576691396.0,1042575.0,P02TYR22604121 1 r64053 20220510 083113 4 H01.ccs.bam,0:3430.63,A:1032009772;C:784907708;G:883573062;T:876200854;N:0,3430,,,,1032009772,784907708,883573062,876200854,0,SRX20461650,SRS17774521,SRA1641718,"Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res","Institute of hydrobiology, chinese academy od sciences",1,0.55138,,0.00608,,0.81343,,0.43998,,3611,,T,,long read,pacbio,pacbio_modern,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,China,2023-05-21,Larval,Larval,Embryo Imprecise,All anatomical structures 75469,SRR24682224,SRX20461649,SRS17774520,SRP438861,PRJNA973729,Danio rerio strain:AB Raw sequence reads,PRJNA973729,Other,Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.,,,,,2 cell,,strain:AB|dev stage:2 cell|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,full length transcriptome of Danio rerio: 2 cell,2 cell,2 cell,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,P02TYR22604097_1_r64053_20220510_083113_3_G01.ccs.bam,bam,2615775919.0,929356.0,P02TYR22604097 1 r64053 20220510 083113 3 G01.ccs.bam,0:2814.61,A:735214781;C:591950532;G:624727601;T:663883005;N:0,2814,,,,735214781,591950532,624727601,663883005,0,SRX20461649,SRS17774520,SRA1641718,"Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res","Institute of hydrobiology, chinese academy od sciences",1,0.58166,,0.00058,,0.82933,,0.48648,,1706,,T,,long read,pacbio,pacbio_modern,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,China,2023-05-21,Cleavage,Embryo,Embryo Imprecise,All anatomical structures 75470,SRR24682225,SRX20461648,SRS17774519,SRP438861,PRJNA973729,Danio rerio strain:AB Raw sequence reads,PRJNA973729,Other,Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.,,,,,Day 5,,strain:AB|dev stage:Day 5|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,full length transcriptome of Danio rerio: Day 5,Day 5,Day 5,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,P02TYR22614797_1_r64053_20220510_083113_4_H01.ccs.bam,bam,923406733.0,413841.0,P02TYR22614797 1 r64053 20220510 083113 4 H01.ccs.bam,0:2231.31,A:257122055;C:215009385;G:229534901;T:221740392;N:0,2231,,,,257122055,215009385,229534901,221740392,0,SRX20461648,SRS17774519,SRA1641718,"Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res","Institute of hydrobiology, chinese academy od sciences",1,0.70962,,0.00154,,0.83396,,0.39035,,1103,,T,,long read,pacbio,pacbio_modern,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,China,2023-05-21,Larval,Larval,Embryo Imprecise,All anatomical structures 75471,SRR24682232,SRX20461647,SRS17774518,SRP438861,PRJNA973729,Danio rerio strain:AB Raw sequence reads,PRJNA973729,Other,Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.,,,,,Day 4,,strain:AB|dev stage:Day 4|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,full length transcriptome of Danio rerio: Day 4,Day 4,Day 4,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,P02TYR22604118_1_r64053_20220510_083113_4_H01.ccs.bam,bam,2334261139.0,804621.0,P02TYR22604118 1 r64053 20220510 083113 4 H01.ccs.bam,0:2901.07,A:674950884;C:505309669;G:540040111;T:613960475;N:0,2901,,,,674950884,505309669,540040111,613960475,0,SRX20461647,SRS17774518,SRA1641718,"Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res","Institute of hydrobiology, chinese academy od sciences",1,0.55416,,0.00471,,0.7876,,0.47236,,1761,,T,,long read,pacbio,pacbio_modern,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,China,2023-05-21,Larval,Larval,Embryo Imprecise,All anatomical structures 75472,SRR24682226,SRX20461646,SRS17774517,SRP438861,PRJNA973729,Danio rerio strain:AB Raw sequence reads,PRJNA973729,Other,Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.,,,,,Protruding mouth,,strain:AB|dev stage:Protruding mouth|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,full length transcriptome of Danio rerio: Protruding mouth,Protruding mouth,Protruding mouth,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,P02TYR22604116_1_r64053_20220510_083113_4_H01.ccs.bam,bam,1077487821.0,468721.0,P02TYR22604116 1 r64053 20220510 083113 4 H01.ccs.bam,0:2298.78,A:311816839;C:236155861;G:251680246;T:277834875;N:0,2298,,,,311816839,236155861,251680246,277834875,0,SRX20461646,SRS17774517,SRA1641718,"Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res","Institute of hydrobiology, chinese academy od sciences",1,0.64634,,0.00375,,0.79699,,0.49179,,1337,,T,,long read,pacbio,pacbio_modern,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,China,2023-05-21,Larval,Larval,Embryo Imprecise,All anatomical structures 75473,SRR24682227,SRX20461645,SRS17774516,SRP438861,PRJNA973729,Danio rerio strain:AB Raw sequence reads,PRJNA973729,Other,Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.,,,,,Long pec,,strain:AB|dev stage:Long pec|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,full length transcriptome of Danio rerio: Long pec,Long pec,Long pec,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,P02TYR22604115_1_r64053_20220510_083113_4_H01.ccs.bam,bam,1178984706.0,503711.0,P02TYR22604115 1 r64053 20220510 083113 4 H01.ccs.bam,0:2340.60,A:339563380;C:259007450;G:276316201;T:304097675;N:0,2340,,,,339563380,259007450,276316201,304097675,0,SRX20461645,SRS17774516,SRA1641718,"Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res","Institute of hydrobiology, chinese academy od sciences",1,0.62569,,0.00525,,0.80267,,0.47146,,1199,,T,,long read,pacbio,pacbio_modern,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,China,2023-05-21,Hatching,Embryo,Embryo Imprecise,All anatomical structures 75474,SRR24682228,SRX20461644,SRS17774515,SRP438861,PRJNA973729,Danio rerio strain:AB Raw sequence reads,PRJNA973729,Other,Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.,,,,,Prim 25,,strain:AB|dev stage:Prim 25|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,full length transcriptome of Danio rerio: Prim 25,Prim 25,Prim 25,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,P02TYR22604113_1_r64053_20220510_083113_4_H01.ccs.bam,bam,1418704698.0,658058.0,P02TYR22604113 1 r64053 20220510 083113 4 H01.ccs.bam,0:2155.90,A:417372714;C:300192249;G:323204197;T:377935538;N:0,2155,,,,417372714,300192249,323204197,377935538,0,SRX20461644,SRS17774515,SRA1641718,"Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res","Institute of hydrobiology, chinese academy od sciences",1,0.62867,,0.0097,,0.79415,,0.47483,,3839,,T,,long read,pacbio,pacbio_modern,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,China,2023-05-21,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures 75475,SRR24682229,SRX20461643,SRS17774514,SRP438861,PRJNA973729,Danio rerio strain:AB Raw sequence reads,PRJNA973729,Other,Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.,,,,,Prim 15,,strain:AB|dev stage:Prim 15|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,full length transcriptome of Danio rerio: Prim 15,Prim 15,Prim 15,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,P02TYR22604112_1_r64399e_20220512_090859_1_A02.ccs.bam,bam,1383213564.0,564062.0,P02TYR22604112 1 r64399e 20220512 090859 1 A02.ccs.bam,0:2452.24,A:403982699;C:294632569;G:316412345;T:368185951;N:0,2452,,,,403982699,294632569,316412345,368185951,0,SRX20461643,SRS17774514,SRA1641718,"Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res","Institute of hydrobiology, chinese academy od sciences",1,0.5998,,0.0069,,0.79636,,0.46586,,2601,,T,,long read,pacbio,pacbio_modern,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,China,2023-05-21,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures 75476,SRR24682230,SRX20461642,SRS17774513,SRP438861,PRJNA973729,Danio rerio strain:AB Raw sequence reads,PRJNA973729,Other,Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.,,,,,Prim 5,,strain:AB|dev stage:Prim 5|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,full length transcriptome of Danio rerio: Prim 5,Prim 5,Prim 5,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,P02TYR22604110_1_r64399e_20220512_090859_1_A02.ccs.bam,bam,1245119132.0,541632.0,P02TYR22604110 1 r64399e 20220512 090859 1 A02.ccs.bam,0:2298.83,A:367833391;C:262003404;G:283350026;T:331932311;N:0,2298,,,,367833391,262003404,283350026,331932311,0,SRX20461642,SRS17774513,SRA1641718,"Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res","Institute of hydrobiology, chinese academy od sciences",1,0.62578,,0.00824,,0.79669,,0.47095,,636,,T,,long read,pacbio,pacbio_modern,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,China,2023-05-21,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures 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 75480,SRR24682235,SRX20461638,SRS17774509,SRP438861,PRJNA973729,Danio rerio strain:AB Raw sequence reads,PRJNA973729,Other,Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.,,,,,1 cell,,strain:AB|dev stage:1cell|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,full length transcriptome of Danio rerio: 1 cell,1 cell,1 cell,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,P02TYR22604096_1_r64053_20220510_083113_3_G01.ccs.bam,bam,2275468478.0,775186.0,P02TYR22604096 1 r64053 20220510 083113 3 G01.ccs.bam,0:2935.38,A:638155276;C:516035520;G:543447739;T:577829943;N:0,2935,,,,638155276,516035520,543447739,577829943,0,SRX20461638,SRS17774509,SRA1641718,"Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res","Institute of hydrobiology, chinese academy od sciences",1,0.56682,,0.00066,,0.82994,,0.48167,,1465,,T,,long read,pacbio,pacbio_modern,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,China,2023-05-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 75481,SRR24682236,SRX20461637,SRS17774508,SRP438861,PRJNA973729,Danio rerio strain:AB Raw sequence reads,PRJNA973729,Other,Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.,,,,,unfertilized,,strain:AB|dev stage:unfertilized|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,full length transcriptome of Danio rerio: unfertilized,unfertilized,unfertilized,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,P02TYR22614794_1_r64053_20220510_083113_3_G01.ccs.bam,bam,2243456468.0,884312.0,P02TYR22614794 1 r64053 20220510 083113 3 G01.ccs.bam,0:2536.95,A:619660008;C:518127052;G:544711614;T:560957794;N:0,2536,,,,619660008,518127052,544711614,560957794,0,SRX20461637,SRS17774508,SRA1641718,"Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res","Institute of hydrobiology, chinese academy od sciences",1,0.61172,,0.00053,,0.84859,,0.47684,,2357,,T,,long read,pacbio,pacbio_modern,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,China,2023-05-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures