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run_metadata

6 rows where experiment.library_selection = "PCR", experiment.library_strategy = "RNA-Seq" and tissue_curation_coarse = "Digestive System"

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tissue_curation_coarse 1

  • Digestive System · 6 ✖

tissue_curation 1

technology 1

experiment.platform 1

experiment.library_strategy 1

  • RNA-Seq · 6 ✖

experiment.library_source 1

experiment.library_selection 1

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
52338 52338 SRR9141302 SRX5914456 SRS4832644 SRP199735 PRJNA545244 Zebrafish transcriptome data PRJNA545244 Other Heavy metals stimulate zebrafish         Drt1 2 aliquot   isolate:missing|age:missing|sex:male|tissue:intestinal|tmp:Drt1 2|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: adult female gut Drt1 2 Drt1 2 Gene expression in zebrafish stimulated by heavy metals     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq X Ten   SRP199735     Drt1-2 (pooling35-GCCAAT_HY2FYCCXY_L8_1.fq and pooling35-GCCAAT_HY2FYCCXY_L8_2.fq).gz fastq 4010314800.0 26735432.0 Drt1 2 pooling35 GCCAAT HY2FYCCXY L8 1.fq and pooling35 GCCAAT HY2FYCCXY L8 2.fq.gz 0:0 1:150 A:1109402697;C:898932519;G:975504514;T:1026302103;N:172967 0 150     1109402697 898932519 975504514 1026302103 172967 SRX5914456 SRS4832644 SRA891446 Kunming University of Science and Technology|College of Life Science Kunming University of Science and Technology 1 0.92372   0.03616   0.74588   0.49008   150   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2019-05-29 Adult Adult Gut Digestive System
52339 52339 SRR9141303 SRX5914455 SRS4832643 SRP199735 PRJNA545244 Zebrafish transcriptome data PRJNA545244 Other Heavy metals stimulate zebrafish         Drt1 3 aliquot   isolate:missing|age:missing|sex:male|tissue:intestinal|tmp:Drt1 3|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: adult female gut Drt1 3 Drt1 3 Gene expression in zebrafish stimulated by heavy metals     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq X Ten   SRP199735     Drt1-3 (pooling35-CAGATC_HY2FYCCXY_L8_1.fq and pooling35-CAGATC_HY2FYCCXY_L8_2.fq).gz fastq 3497539200.0 23316928.0 Drt1 3 pooling35 CAGATC HY2FYCCXY L8 1.fq and pooling35 CAGATC HY2FYCCXY L8 2.fq.gz 0:0 1:150 A:965958483;C:783630086;G:850473225;T:897324973;N:152433 0 150     965958483 783630086 850473225 897324973 152433 SRX5914455 SRS4832643 SRA891446 Kunming University of Science and Technology|College of Life Science Kunming University of Science and Technology 1 0.92356   0.03568   0.7417   0.48985   150   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2019-05-29 Adult Adult Gut Digestive System
52340 52340 SRR9141304 SRX5914454 SRS4832642 SRP199735 PRJNA545244 Zebrafish transcriptome data PRJNA545244 Other Heavy metals stimulate zebrafish         Drck3 aliquot   isolate:missing|age:missing|sex:male|tissue:intestinal|tmp:Drck3|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: adult female gut Drck3 Drck3 Gene expression in zebrafish stimulated by heavy metals     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq X Ten   SRP199735     Drck3 (pooling35-TAGCTT_HY2FYCCXY_L8_1.fq and pooling35-TAGCTT_HY2FYCCXY_L8_2.fq).gz fastq 4199739150.0 27998261.0 Drck3 pooling35 TAGCTT HY2FYCCXY L8 1.fq and pooling35 TAGCTT HY2FYCCXY L8 2.fq.gz 0:0 1:150 A:1173351504;C:941132248;G:1019438569;T:1065634216;N:182613 0 150     1173351504 941132248 1019438569 1065634216 182613 SRX5914454 SRS4832642 SRA891446 Kunming University of Science and Technology|College of Life Science Kunming University of Science and Technology 1 0.92976   0.0377   0.71709   0.48608   150   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2019-05-29 Adult Adult Gut Digestive System
52341 52341 SRR9141305 SRX5914453 SRS4832641 SRP199735 PRJNA545244 Zebrafish transcriptome data PRJNA545244 Other Heavy metals stimulate zebrafish         Drt1 1 aliquot   isolate:missing|age:missing|sex:male|tissue:intestinal|tmp:Drt1 1|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: adult female gut Drt1 1 Drt1 1 Gene expression in zebrafish stimulated by heavy metals     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq X Ten   SRP199735     Drt1-1 (pooling35-ACAGTG_HY2FYCCXY_L8_1.fq and pooling35-ACAGTG_HY2FYCCXY_L8_2.fq).gz fastq 3657007500.0 24380050.0 Drt1 1 pooling35 ACAGTG HY2FYCCXY L8 1.fq and pooling35 ACAGTG HY2FYCCXY L8 2.fq.gz 0:150 1:0 A:963212012;C:848159609;G:822435259;T:1023096853;N:103767 150 0     963212012 848159609 822435259 1023096853 103767 SRX5914453 SRS4832641 SRA891446 Kunming University of Science and Technology|College of Life Science Kunming University of Science and Technology 1 0.92318   0.03725   0.72997   0.48413   150   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2019-05-29 Adult Adult Gut Digestive System
52342 52342 SRR9141306 SRX5914452 SRS4832640 SRP199735 PRJNA545244 Zebrafish transcriptome data PRJNA545244 Other Heavy metals stimulate zebrafish         Drck1 aliquot   isolate:missing|age:missing|sex:male|tissue:intestinal|tmp:Drck1|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: adult female gut Drck1 Drck1 Gene expression in zebrafish stimulated by heavy metals     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq X Ten   SRP199735     Drck1 (pooling35-ACTTGA_HY2FYCCXY_L8_1.fq and pooling35-ACTTGA_HY2FYCCXY_L8_2.fq).gz fastq 3523656300.0 23491042.0 Drck1 pooling35 ACTTGA HY2FYCCXY L8 1.fq and pooling35 ACTTGA HY2FYCCXY L8 2.fq.gz 0:0 1:150 A:973145926;C:804077269;G:862830763;T:883447878;N:154464 0 150     973145926 804077269 862830763 883447878 154464 SRX5914452 SRS4832640 SRA891446 Kunming University of Science and Technology|College of Life Science Kunming University of Science and Technology 1 0.93236   0.03761   0.7134   0.49667   150   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2019-05-29 Adult Adult Gut Digestive System
52343 52343 SRR9141307 SRX5914451 SRS4832639 SRP199735 PRJNA545244 Zebrafish transcriptome data PRJNA545244 Other Heavy metals stimulate zebrafish         Drck2 aliquot   isolate:missing|age:missing|sex:male|tissue:intestinal|tmp:Drck2|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: adult female gut Drck2 Drck2 Gene expression in zebrafish stimulated by heavy metals     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq X Ten   SRP199735     Drck2 (pooling35-GATCAG_HY2FYCCXY_L8_1.fq and pooling35-GATCAG_HY2FYCCXY_L8_2.fq).gz fastq 3720733950.0 24804893.0 Drck2 pooling35 GATCAG HY2FYCCXY L8 1.fq and pooling35 GATCAG HY2FYCCXY L8 2.fq.gz 0:0 1:150 A:1041160797;C:830715515;G:904059203;T:944636106;N:162329 0 150     1041160797 830715515 904059203 944636106 162329 SRX5914451 SRS4832639 SRA891446 Kunming University of Science and Technology|College of Life Science Kunming University of Science and Technology 1 0.91965   0.0417   0.70483   0.48829   150   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2019-05-29 Adult Adult Gut Digestive 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");;