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18 rows where devstage_curation_coarse = "Adult" and experiment.platform = "PACBIO_SMRT"

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tissue_curation 7

technology 1

experiment.platform 1

  • PACBIO_SMRT · 18 ✖

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

experiment.library_layout 1

devstage_curation_coarse 1

  • Adult · 18 ✖

devstage_curation 1

Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
34957 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 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 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 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 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 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
34964 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 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
34967 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 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 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 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 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 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 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 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 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 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

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