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run_metadata

9 rows where experiment.library_selection = "PolyA" and tissue_curation = "Muscle"

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tissue_curation_coarse 1

tissue_curation 1

  • Muscle · 9 ✖

technology 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • PolyA · 9 ✖

experiment.library_layout 1

devstage_curation_coarse 1

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
70105 70105 SRR19561925 SRX15614025 SRS13314708 SRP378802 PRJNA846110 Danio rerio Raw sequence reads PRJNA846110 Other Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio       Dr27 2 Dr27 2   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:adult|sex:female|tissue:multi tissue|aliquot:27 replicate 2|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: adult female 9 27 2 muscle 9 27 2 muscle 9 27 2 muscle All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2 Vazyme Biotech Co. Ltd NR612 02 and subjected to 150bp paired end sequencing on a Novaseq 6009 illumina platform.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP378802     9-27-2-muscle-RNA_R1.fq.gz 9-27-2-muscle-RNA_R2.fq.gz fastq fastq 7055979300.0 23519931.0 9 27 2 muscle RNA R1.fq.gz 0:150 1:150 A:1788950689;C:1717189434;G:1744914054;T:1804787090;N:138033 150 150     1788950689 1717189434 1744914054 1804787090 138033 SRX15614025 SRS13314708 SRA1432943 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university 2 0.97194 0.97273 0.02502 0.02486 0.80458 0.80957 0.57852 0.57826 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-06-07 Adult Adult Muscle Muscular System
70111 70111 SRR19561931 SRX15614019 SRS13314715 SRP378802 PRJNA846110 Danio rerio Raw sequence reads PRJNA846110 Other Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio       Dr13 3 Dr13 3   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:adult|sex:female|tissue:multi tissue|aliquot:13 replicate 3|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: adult female 44 13 3 muscle 44 13 3 muscle 44 13 3 muscle All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2 Vazyme Biotech Co. Ltd NR612 02 and subjected to 150bp paired end sequencing on a Novaseq 6051 illumina platform.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP378802     44-13-3-muscle-RNA_R1.fq.gz 44-13-3-muscle-RNA_R2.fq.gz fastq fastq 10119909900.0 33733033.0 44 13 3 muscle RNA R1.fq.gz 0:150 1:150 A:2638310381;C:2403694806;G:2414321869;T:2663399674;N:183170 150 150     2638310381 2403694806 2414321869 2663399674 183170 SRX15614019 SRS13314715 SRA1432943 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university 2 0.95716 0.96127 0.0422 0.04147 0.77603 0.78346 0.52389 0.52671 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-06-07 Adult Adult Muscle Muscular System
70118 70118 SRR19561938 SRX15614012 SRS13314714 SRP378802 PRJNA846110 Danio rerio Raw sequence reads PRJNA846110 Other Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio       Dr13 2 Dr13 2   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:adult|sex:female|tissue:multi tissue|aliquot:13 replicate 2|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: adult female 39 13 2 muscle 39 13 2 muscle 39 13 2 muscle All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2 Vazyme Biotech Co. Ltd NR612 02 and subjected to 150bp paired end sequencing on a Novaseq 6045 illumina platform.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP378802     39-13-2-muscle-RNA_R1.fq.gz 39-13-2-muscle-RNA_R2.fq.gz fastq fastq 7640202600.0 25467342.0 39 13 2 muscle RNA R1.fq.gz 0:150 1:150 A:2016538268;C:1785512036;G:1809389762;T:2028627340;N:135194 150 150     2016538268 1785512036 1809389762 2028627340 135194 SRX15614012 SRS13314714 SRA1432943 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university 2 0.95971 0.96138 0.04474 0.04437 0.77849 0.78644 0.59289 0.58077 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-06-07 Adult Adult Muscle Muscular System
70125 70125 SRR19561945 SRX15614005 SRS13314713 SRP378802 PRJNA846110 Danio rerio Raw sequence reads PRJNA846110 Other Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio       Dr13 1 Dr13 1   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:adult|sex:female|tissue:multi tissue|aliquot:13 replicate 1|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: adult female 34 13 1 muscle 34 13 1 muscle 34 13 1 muscle All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2 Vazyme Biotech Co. Ltd NR612 02 and subjected to 150bp paired end sequencing on a Novaseq 6039 illumina platform.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP378802     34-13-1-muscle-RNA_R1.fq.gz 34-13-1-muscle-RNA_R2.fq.gz fastq fastq 7627032900.0 25423443.0 34 13 1 muscle RNA R1.fq.gz 0:150 1:150 A:2000446409;C:1801060748;G:1805476033;T:2019901377;N:148333 150 150     2000446409 1801060748 1805476033 2019901377 148333 SRX15614005 SRS13314713 SRA1432943 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university 2 0.95835 0.96224 0.04308 0.04317 0.7865 0.79024 0.60297 0.57962 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-06-07 Adult Adult Muscle Muscular System
70131 70131 SRR19561951 SRX15613999 SRS13314712 SRP378802 PRJNA846110 Danio rerio Raw sequence reads PRJNA846110 Other Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio       Dr18 3 Dr18 3   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:adult|sex:female|tissue:multi tissue|aliquot:18 replicate 3|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: adult female 29 18 3 muscle 29 18 3 muscle 29 18 3 muscle All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2 Vazyme Biotech Co. Ltd NR612 02 and subjected to 150bp paired end sequencing on a Novaseq 6033 illumina platform.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP378802     29-18-3-muscle-RNA_R1.fq.gz 29-18-3-muscle-RNA_R2.fq.gz fastq fastq 6839215800.0 22797386.0 29 18 3 muscle RNA R1.fq.gz 0:150 1:150 A:1771968648;C:1634874135;G:1637503861;T:1794736189;N:132967 150 150     1771968648 1634874135 1637503861 1794736189 132967 SRX15613999 SRS13314712 SRA1432943 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university 2 0.96541 0.96842 0.03381 0.03391 0.80592 0.80919 0.61578 0.61584 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-06-07 Adult Adult Muscle Muscular System
70135 70135 SRR19561955 SRX15613995 SRS13314707 SRP378802 PRJNA846110 Danio rerio Raw sequence reads PRJNA846110 Other Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio       Dr27 1 Dr27 1   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:adult|sex:female|tissue:multi tissue|aliquot:27 replicate 1|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: adult female 4 27 1 muscle 4 27 1 muscle 4 27 1 muscle All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2 Vazyme Biotech Co. Ltd NR612 02 and subjected to 150bp paired end sequencing on a Novaseq 6003 illumina platform.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP378802     4-27-1-muscle-RNA_R1.fq.gz 4-27-1-muscle-RNA_R2.fq.gz fastq fastq 6823613400.0 22745378.0 4 27 1 muscle RNA R1.fq.gz 0:150 1:150 A:1741210745;C:1651572336;G:1669865495;T:1760830291;N:134533 150 150     1741210745 1651572336 1669865495 1760830291 134533 SRX15613995 SRS13314707 SRA1432943 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university 2 0.97012 0.9708 0.02719 0.0271 0.80852 0.81393 0.5763 0.57466 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-06-07 Adult Adult Muscle Muscular System
70138 70138 SRR19561958 SRX15613992 SRS13314711 SRP378802 PRJNA846110 Danio rerio Raw sequence reads PRJNA846110 Other Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio       Dr18 2 Dr18 2   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:adult|sex:female|tissue:multi tissue|aliquot:18 replicate 2|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: adult female 24 18 2 muscle 24 18 2 muscle 24 18 2 muscle All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2 Vazyme Biotech Co. Ltd NR612 02 and subjected to 150bp paired end sequencing on a Novaseq 6027 illumina platform.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP378802     24-18-2-muscle-RNA_R1.fq.gz 24-18-2-muscle-RNA_R2.fq.gz fastq fastq 7665641700.0 25552139.0 24 18 2 muscle RNA R1.fq.gz 0:150 1:150 A:1987229999;C:1827872419;G:1838358203;T:2012034222;N:146857 150 150     1987229999 1827872419 1838358203 2012034222 146857 SRX15613992 SRS13314711 SRA1432943 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university 2 0.96136 0.96358 0.04456 0.04444 0.74805 0.75097 0.56743 0.56986 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-06-07 Adult Adult Muscle Muscular System
70144 70144 SRR19561964 SRX15613986 SRS13314710 SRP378802 PRJNA846110 Danio rerio Raw sequence reads PRJNA846110 Other Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio       Dr18 1 Dr18 1   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:adult|sex:female|tissue:multi tissue|aliquot:18 replicate 1|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: adult female 19 18 1 muscle 19 18 1 muscle 19 18 1 muscle All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2 Vazyme Biotech Co. Ltd NR612 02 and subjected to 150bp paired end sequencing on a Novaseq 6021 illumina platform.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP378802     19-18-1-muscle-RNA_R1.fq.gz 19-18-1-muscle-RNA_R2.fq.gz fastq fastq 7218908100.0 24063027.0 19 18 1 muscle RNA R1.fq.gz 0:150 1:150 A:1857995996;C:1730711520;G:1753322708;T:1876737616;N:140260 150 150     1857995996 1730711520 1753322708 1876737616 140260 SRX15613986 SRS13314710 SRA1432943 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university 2 0.95993 0.96231 0.04063 0.04055 0.75534 0.76053 0.52939 0.53582 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-06-07 Adult Adult Muscle Muscular System
70151 70151 SRR19561971 SRX15613979 SRS13314709 SRP378802 PRJNA846110 Danio rerio Raw sequence reads PRJNA846110 Other Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio       Dr27 3 Dr27 3   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:adult|sex:female|tissue:multi tissue|aliquot:27 replicate 3|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: adult female 14 27 3 muscle 14 27 3 muscle 14 27 3 muscle All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2 Vazyme Biotech Co. Ltd NR612 02 and subjected to 150bp paired end sequencing on a Novaseq 6015 illumina platform.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP378802     14-27-3-muscle-RNA_R1.fq.gz 14-27-3-muscle-RNA_R2.fq.gz fastq fastq 6507643200.0 21692144.0 14 27 3 muscle RNA R1.fq.gz 0:150 1:150 A:1616055538;C:1616019040;G:1644899613;T:1630543342;N:125667 150 150     1616055538 1616019040 1644899613 1630543342 125667 SRX15613979 SRS13314709 SRA1432943 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university 2 0.97374 0.97402 0.01996 0.0199 0.82749 0.8323 0.55815 0.54732 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-06-07 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");;