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run_metadata

4 rows where devstage_curation = "Juvenile" and tissue_curation = "Tail"

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tissue_curation_coarse 1

tissue_curation 1

  • Tail · 4 ✖

technology 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

experiment.library_layout 1

devstage_curation_coarse 1

devstage_curation 1

  • Juvenile · 4 ✖
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
72464 72464 SRR22574253 SRX18537350 SRS16001767 SRP411954 PRJNA909445 Danio rerio Raw sequence reads PRJNA909445 Other Whole transcriptome analysis       Model organism or animal sample from zebrafish zebrafish strains with IBs wild type fish and without xxx runx2b gene editing fish   strain:zebrafish strains with IBs wild type fish and without xxx runx2b gene editing fish|age:60dpf|sex:pooled male and female|tissue:tail|BioSampleModel:Model organism or animal                 wt 2 R1.fastq wt 2 R1.fastq wt 2 R1.fastq tail muscule     RNA-Seq TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP411954     wt_2_R1.fastq.gz wt_2_R2.fastq.gz fastq fastq 20138999100.0 67129997.0 wt 2 R1.fastq.gz 0:150 1:150 A:5269495885;C:4709732469;G:4941455861;T:5217751419;N:563466 150 150     5269495885 4709732469 4941455861 5217751419 563466 SRX18537350 SRS16001767 SRA1555446 Fisheries College of Huazhong Agricultural University|Fisheries College of Huazhong Agricultural Univers Fisheries College of Huazhong Agricultural University 2 0.95899 0.96368 0.14222 0.14005 0.82102 0.81862 0.43313 0.43965 150 150 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown bulk unknown unknown   China 2022-12-08 Juvenile Juvenile Tail Multi-system
72465 72465 SRR22574254 SRX18537349 SRS16001767 SRP411954 PRJNA909445 Danio rerio Raw sequence reads PRJNA909445 Other Whole transcriptome analysis       Model organism or animal sample from zebrafish zebrafish strains with IBs wild type fish and without xxx runx2b gene editing fish   strain:zebrafish strains with IBs wild type fish and without xxx runx2b gene editing fish|age:60dpf|sex:pooled male and female|tissue:tail|BioSampleModel:Model organism or animal                 wt 1 R1.fastq wt 1 R1.fastq wt 1 R1.fastq tail muscule     RNA-Seq TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP411954     wt_1_R1.fastq.gz wt_1_R2.fastq.gz fastq fastq 23358126000.0 77860420.0 wt 1 R1.fastq.gz 0:150 1:150 A:6038817592;C:5541964880;G:5789495907;T:5987202665;N:644956 150 150     6038817592 5541964880 5789495907 5987202665 644956 SRX18537349 SRS16001767 SRA1555446 Fisheries College of Huazhong Agricultural University|Fisheries College of Huazhong Agricultural Univers Fisheries College of Huazhong Agricultural University 2 0.95378 0.95798 0.14042 0.13872 0.82065 0.81809 0.45238 0.37872 150 150 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown bulk unknown unknown   China 2022-12-08 Juvenile Juvenile Tail Multi-system
72466 72466 SRR22574255 SRX18537348 SRS16001767 SRP411954 PRJNA909445 Danio rerio Raw sequence reads PRJNA909445 Other Whole transcriptome analysis       Model organism or animal sample from zebrafish zebrafish strains with IBs wild type fish and without xxx runx2b gene editing fish   strain:zebrafish strains with IBs wild type fish and without xxx runx2b gene editing fish|age:60dpf|sex:pooled male and female|tissue:tail|BioSampleModel:Model organism or animal                 mut 2 R1.fastq mut 2 R1.fastq mut 2 R1.fastq tail muscule     RNA-Seq TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP411954     mut_2_R1.fastq.gz mut_2_R2.fastq.gz fastq fastq 19326017700.0 64420059.0 mut 2 R1.fastq.gz 0:150 1:150 A:5060790268;C:4512966975;G:4744771851;T:5006953597;N:535009 150 150     5060790268 4512966975 4744771851 5006953597 535009 SRX18537348 SRS16001767 SRA1555446 Fisheries College of Huazhong Agricultural University|Fisheries College of Huazhong Agricultural Univers Fisheries College of Huazhong Agricultural University 2 0.95472 0.95941 0.14789 0.14566 0.81746 0.81509 0.46875 0.39789 150 150 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown bulk unknown unknown   China 2022-12-08 Juvenile Juvenile Tail Multi-system
72467 72467 SRR22574256 SRX18537347 SRS16001767 SRP411954 PRJNA909445 Danio rerio Raw sequence reads PRJNA909445 Other Whole transcriptome analysis       Model organism or animal sample from zebrafish zebrafish strains with IBs wild type fish and without xxx runx2b gene editing fish   strain:zebrafish strains with IBs wild type fish and without xxx runx2b gene editing fish|age:60dpf|sex:pooled male and female|tissue:tail|BioSampleModel:Model organism or animal                 mut 1 R1.fastq mut 1 R1.fastq mut 1 R1.fastq tail muscule     RNA-Seq TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP411954     mut_1_R1.fastq.gz mut_1_R2.fastq.gz fastq fastq 22794782400.0 75982608.0 mut 1 R1.fastq.gz 0:150 1:150 A:5961354939;C:5333450654;G:5606279874;T:5893060023;N:636910 150 150     5961354939 5333450654 5606279874 5893060023 636910 SRX18537347 SRS16001767 SRA1555446 Fisheries College of Huazhong Agricultural University|Fisheries College of Huazhong Agricultural Univers Fisheries College of Huazhong Agricultural University 2 0.9557 0.95853 0.14259 0.13878 0.81771 0.81533 0.45125 0.3948 150 150 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown bulk unknown unknown   China 2022-12-08 Juvenile Juvenile Tail Multi-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");;