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run_metadata

4 rows where experiment.library_selection = "PolyA", experiment.library_strategy = "RNA-Seq" and tissue_curation = "Scale"

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tissue_curation_coarse 1

tissue_curation 1

  • Scale · 4 ✖

technology 1

experiment.platform 1

experiment.library_strategy 1

  • RNA-Seq · 4 ✖

experiment.library_source 1

experiment.library_selection 1

  • PolyA · 4 ✖

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
47613 47613 SRR6760977 SRX3733411 SRS2990508 SRP133266 PRJNA434353 Transcriptome assemblies 10 vertebrate species PRJNA434353 Other 2 types of content: a Raw RNA seq files from cell lines of 10 vertebrate species human mouse cow tasmanian devil chicken duck zebra finch xenopus medaka and zebrafish 4 replicates per species. b Refined transcriptomes post combining with paired proteomics data and data curation.     4 replicates   Zebrafish   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:missing|tissue:scale|cell line:BRF41|cell type:fibroblast|BioSampleModel:Model organism or animal                 Transcriptome assemblies 10 vertebrate species zebrafish replicate2 zebrafish replicate2 Zebrafish sample replicate 2     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP133266     Sample_imb_butter_2014_04_30_zebrafish_B_R2.fastq.gz Sample_imb_butter_2014_04_30_zebrafish_B_R1.fastq.gz fastq fastq 8021078014.0 39708307.0 Sample imb butter 2014 04 30 zebrafish B R2.fastq.gz 0:101 1:101 A:2198831905;C:1810184353;G:1779924959;T:2210094554;N:22042243 101 101     2198831905 1810184353 1779924959 2210094554 22042243 SRX3733411 SRS2990508 SRA660975 Institute of Molecular Biology|Quantitative Proteomics Institute of Molecular Biology 2 0.94194 0.93911 0.07724 0.08406 0.75724 0.75558 0.47712 0.49049 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Unknown 2019-02-15 Undetermined Undetermined Scale Surface Structure
47614 47614 SRR6760978 SRX3733410 SRS2990508 SRP133266 PRJNA434353 Transcriptome assemblies 10 vertebrate species PRJNA434353 Other 2 types of content: a Raw RNA seq files from cell lines of 10 vertebrate species human mouse cow tasmanian devil chicken duck zebra finch xenopus medaka and zebrafish 4 replicates per species. b Refined transcriptomes post combining with paired proteomics data and data curation.     4 replicates   Zebrafish   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:missing|tissue:scale|cell line:BRF41|cell type:fibroblast|BioSampleModel:Model organism or animal                 Transcriptome assemblies 10 vertebrate species zebrafish replicate1 zebrafish replicate1 Zebrafish sample replicate 1     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP133266     Sample_imb_butter_2014_04_29_zebrafish_A_R1.fastq.gz Sample_imb_butter_2014_04_29_zebrafish_A_R2.fastq.gz fastq fastq 7117920864.0 35237232.0 Sample imb butter 2014 04 29 zebrafish A R2.fastq.gz 0:101 1:101 A:1980152632;C:1580333689;G:1558362064;T:1979596193;N:19476286 101 101     1980152632 1580333689 1558362064 1979596193 19476286 SRX3733410 SRS2990508 SRA660975 Institute of Molecular Biology|Quantitative Proteomics Institute of Molecular Biology 2 0.9342 0.93044 0.08741 0.09642 0.75674 0.75497 0.49192 0.46492 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Unknown 2018-02-22 Undetermined Undetermined Scale Surface Structure
47615 47615 SRR6760981 SRX3733407 SRS2990508 SRP133266 PRJNA434353 Transcriptome assemblies 10 vertebrate species PRJNA434353 Other 2 types of content: a Raw RNA seq files from cell lines of 10 vertebrate species human mouse cow tasmanian devil chicken duck zebra finch xenopus medaka and zebrafish 4 replicates per species. b Refined transcriptomes post combining with paired proteomics data and data curation.     4 replicates   Zebrafish   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:missing|tissue:scale|cell line:BRF41|cell type:fibroblast|BioSampleModel:Model organism or animal                 Transcriptome assemblies 10 vertebrate species zebrafish replicate4 zebrafish replicate4 Zebrafish sample replicate 4     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP133266     Sample_imb_butter_2014_04_32_zebrafish_D_R1.fastq.gz Sample_imb_butter_2014_04_32_zebrafish_D_R2.fastq.gz fastq fastq 8570683654.0 42429127.0 Sample imb butter 2014 04 32 zebrafish D R1.fastq.gz 0:101 1:101 A:2343151377;C:1943560489;G:1909682494;T:2350658549;N:23630745 101 101     2343151377 1943560489 1909682494 2350658549 23630745 SRX3733407 SRS2990508 SRA660975 Institute of Molecular Biology|Quantitative Proteomics Institute of Molecular Biology 2 0.94036 0.94349 0.0838 0.0779 0.75538 0.75737 0.4881 0.48296 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Unknown 2019-02-15 Undetermined Undetermined Scale Surface Structure
47616 47616 SRR6760982 SRX3733406 SRS2990508 SRP133266 PRJNA434353 Transcriptome assemblies 10 vertebrate species PRJNA434353 Other 2 types of content: a Raw RNA seq files from cell lines of 10 vertebrate species human mouse cow tasmanian devil chicken duck zebra finch xenopus medaka and zebrafish 4 replicates per species. b Refined transcriptomes post combining with paired proteomics data and data curation.     4 replicates   Zebrafish   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:missing|tissue:scale|cell line:BRF41|cell type:fibroblast|BioSampleModel:Model organism or animal                 Transcriptome assemblies 10 vertebrate species zebrafish replicate3 zebrafish replicate3 Zebrafish sample replicate 3     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP133266     Sample_imb_butter_2014_04_31_zebrafish_C_R1.fastq.gz Sample_imb_butter_2014_04_31_zebrafish_C_R2.fastq.gz fastq fastq 5889796416.0 29157408.0 Sample imb butter 2014 04 31 zebrafish C R1.fastq.gz 0:101 1:101 A:1629550499;C:1313886355;G:1293890602;T:1636478119;N:15990841 101 101     1629550499 1313886355 1293890602 1636478119 15990841 SRX3733406 SRS2990508 SRA660975 Institute of Molecular Biology|Quantitative Proteomics Institute of Molecular Biology 2 0.93285 0.93628 0.09745 0.0871 0.7586 0.7611 0.47374 0.47763 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Unknown 2018-02-22 Undetermined Undetermined Scale Surface Structure

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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");;