run_metadata
3 rows where experiment.library_strategy = "RNA-Seq", experiment.platform = "PACBIO_SMRT" and tissue_curation_coarse = "Renal System"
This data as json, CSV (advanced)
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | |||||||||||||||||||||||||||||||||
| 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 |
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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");;