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run_metadata

3 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "RANDOM" and tissue_curation = "Multi-tissue"

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tissue_curation_coarse 1

tissue_curation 1

  • Multi-tissue · 3 ✖

technology 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • RANDOM · 3 ✖

experiment.library_layout 1

  • SINGLE · 3 ✖

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
41035 41035 SRR3581677 SRX1797273 SRS1465195 SRP075626 PRJNA322629 Mycobacterial infection of adult zebrafish PRJNA322629 Other RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.       Fluorescence activated cell sorted macrophages4 iRed4   breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Fluorescence activated cell sorted macrophages from kidney|BioSampleModel:Model organism or animal                 iRed4 iRed4 iRed4 1     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP075626     iRed4.fastq.gz fastq 2577391029.0 50537079.0 iRed4.fastq.gz 0:51 A:740368299;C:555561208;G:558570747;T:722870515;N:20260 51       740368299 555561208 558570747 722870515 20260 SRX1797273 SRS1465195 SRA429040 Duke University|Molecular Genetics & Microbiology Duke University 1 0.87886   0.09748   0.75676   0.49364   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2016-05-25 Adult Adult Multi-tissue Multi-system
41036 41036 SRR3581675 SRX1797272 SRS1465194 SRP075626 PRJNA322629 Mycobacterial infection of adult zebrafish PRJNA322629 Other RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.       Fluorescence activated cell sorted macrophages3 iRed3   breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Fluorescence activated cell sorted macrophages from kidney|BioSampleModel:Model organism or animal                 iRed3 iRed3 iRed3 1     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP075626     iRed3.fastq.gz fastq 2300094339.0 45099889.0 iRed3.fastq.gz 0:51 A:664396273;C:491535578;G:495836023;T:648307877;N:18588 51       664396273 491535578 495836023 648307877 18588 SRX1797272 SRS1465194 SRA429039 Duke University|Molecular Genetics & Microbiology Duke University 1 0.88281   0.15449   0.75507   0.47198   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2017-06-24 Adult Adult Multi-tissue Multi-system
41037 41037 SRR3581674 SRX1797271 SRS1465193 SRP075626 PRJNA322629 Mycobacterial infection of adult zebrafish PRJNA322629 Other RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.       Fluorescence activated cell sorted macrophages2 iRed2   breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Fluorescence activated cell sorted macrophages from kidney|BioSampleModel:Model organism or animal                 iRed2 iRed2 iRed2 1     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP075626     iRed2.fastq.gz fastq 1652550807.0 32402957.0 iRed2.fastq.gz 0:51 A:528348867;C:306088006;G:305625547;T:512475625;N:12762 51       528348867 306088006 305625547 512475625 12762 SRX1797271 SRS1465193 SRA429038 Duke University|Molecular Genetics & Microbiology Duke University 1 0.83699   0.16858   0.76688   0.49036   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2016-05-25 Adult Adult Multi-tissue 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");;