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run_metadata

10 rows where experiment.library_selection = "RANDOM", technology = "unknown" and tissue_curation = "Blood"

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experiment.library_layout 2

devstage_curation_coarse 2

devstage_curation 2

tissue_curation_coarse 1

tissue_curation 1

  • Blood · 10 ✖

technology 1

  • unknown · 10 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • RANDOM · 10 ✖
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
37103 37103 SRR891512 SRX298192 SRS673882 SRP024369 PRJNA207719 Tissue specific transcriptome profiling of zebrafish PRJNA207719 Other Tissue specific transcriptome profiling of zebrafish.         Danio rerio blood   sex:missing|strain:wild type|tissue:blood|health state:normal|collection date:2013|geo loc name:India|biomaterial provider:CSIR Institute of Genomics and Integrative Biology|age:adult|BioSampleModel:Model organism or animal                 Tissue specific transcriptome of zebrafish Transcriptome of zebrafish Danio rerio blood zebrafish blood 1     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP024369     lane6_NoIndex_L006_R2_cat.fastq lane6_NoIndex_L006_R1_cat.fastq fastq fastq 2122070832.0 20804616.0 Transcriptome of zebrafish Danio rerio blood 0:51 1:51 A:508869849;C:550502747;G:580539251;T:481927903;N:231082 51 51     508869849 550502747 580539251 481927903 231082 SRX298192 SRS673882 SRA089174 CSIR-IGIB CSIR-Institute of Genomics and Integrative Biology CSIR-Institute of Genomics and Integrative Biology 2 0.78255 0.77496 0.03257 0.03239 0.75672 0.75542 0.44135 0.44382 51 51 B B biological fallback assumption illumina early_illumina unknown random_priming unknown bulk unknown unknown   India 2013-06-10 Adult Adult Blood Hematopoietic System
41032 41032 SRR3581739 SRX1797279 SRS1465200 SRP075626 PRJNA322629 Mycobacterial infection of adult zebrafish PRJNA322629 Other RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.       Larval non fluorescent cells post macrophage sorting3 C NF3   breed:*AB|age:4dpf|dev stage:Larval|sex:not determined|tissue:Whole animal following macrophage depletion via FACS|BioSampleModel:Model organism or animal                 C NF3 C NF3 C NF3 1     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP075626     C_NF3.fastq.gz fastq 1745512893.0 34225743.0 C NF3.fastq.gz 0:51 A:470456301;C:396221813;G:401458508;T:477287506;N:88765 51       470456301 396221813 401458508 477287506 88765 SRX1797279 SRS1465200 SRA429046 Duke University|Molecular Genetics &amp; Microbiology Duke University 1 0.92839   0.06821   0.73099   0.44395   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2016-05-25 Larval Larval Blood Hematopoietic System
41033 41033 SRR3581729 SRX1797278 SRS1465199 SRP075626 PRJNA322629 Mycobacterial infection of adult zebrafish PRJNA322629 Other RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.       Larval non fluorescent cells post macrophage sorting2 C NF2   breed:*AB|age:4dpf|dev stage:Larval|sex:not determined|tissue:Whole animal following macrophage depletion via FACS|BioSampleModel:Model organism or animal                 C NF2 C NF2 C NF2 1     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP075626     C_NF2.fastq.gz fastq 2116510506.0 41500206.0 C NF2.fastq.gz 0:51 A:580244434;C:475940957;G:474848964;T:585459729;N:16422 51       580244434 475940957 474848964 585459729 16422 SRX1797278 SRS1465199 SRA429045 Duke University|Molecular Genetics &amp; Microbiology Duke University 1 0.90388   0.06926   0.78963   0.49501   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2017-06-24 Larval Larval Blood Hematopoietic System
41034 41034 SRR3581718 SRX1797274 SRS1465196 SRP075626 PRJNA322629 Mycobacterial infection of adult zebrafish PRJNA322629 Other RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.       Larval non fluorescent cells post macrophage sorting1 C NF1   breed:*AB|age:4dpf|dev stage:Larval|sex:not determined|tissue:Whole animal following macrophage depletion via FACS|BioSampleModel:Model organism or animal                 C NF1 C NF1 C NF1 1     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP075626     C_NF1.fastq.gz fastq 1492422690.0 29263190.0 C NF1.fastq.gz 0:51 A:421145406;C:327412398;G:328273236;T:415327504;N:264146 51       421145406 327412398 328273236 415327504 264146 SRX1797274 SRS1465196 SRA429041 Duke University|Molecular Genetics &amp; Microbiology Duke University 1 0.82347   0.08561   0.75207   0.45637   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2017-06-24 Larval Larval Blood Hematopoietic System
41038 41038 SRR3581671 SRX1797269 SRS1465191 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 macrophages1 iRed1   breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Fluorescence activated cell sorted macrophages|BioSampleModel:Model organism or animal                 iRed1 iRed1 iRed1 1     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP075626     iRed1.fastq.gz fastq 2227229772.0 43671172.0 iRed1.fastq.gz 0:51 A:643185725;C:477251583;G:480258902;T:626515881;N:17681 51       643185725 477251583 480258902 626515881 17681 SRX1797269 SRS1465191 SRA429036 Duke University|Molecular Genetics &amp; Microbiology Duke University 1 0.88005   0.11318   0.76197   0.49474   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2017-06-24 Adult Adult Blood Hematopoietic System
41039 41039 SRR3581670 SRX1797268 SRS1465190 SRP075626 PRJNA322629 Mycobacterial infection of adult zebrafish PRJNA322629 Other RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.       D rerio dissected M marinum granuloma5 disGran5   breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Dissected granuloma|BioSampleModel:Model organism or animal                 disGran5 disGran5 disGran5 1     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP075626     disGran5.fastq.gz fastq 2097698850.0 41131350.0 disGran5.fastq.gz 0:51 A:606466942;C:449212134;G:448063993;T:593938942;N:16839 51       606466942 449212134 448063993 593938942 16839 SRX1797268 SRS1465190 SRA429035 Duke University|Molecular Genetics &amp; Microbiology Duke University 1 0.89212   0.09154   0.76788   0.51096   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2017-06-24 Adult Adult Blood Hematopoietic System
41040 41040 SRR3581669 SRX1797267 SRS1465187 SRP075626 PRJNA322629 Mycobacterial infection of adult zebrafish PRJNA322629 Other RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.       D rerio dissected M marinum granuloma4 disGran4   breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Dissected granuloma|BioSampleModel:Model organism or animal                 disGran4 disGran4 disGran4 1     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP075626     disGran4.fastq.gz fastq 2969920485.0 58233735.0 disGran4.fastq.gz 0:51 A:861895830;C:635643178;G:635675729;T:836681349;N:24399 51       861895830 635643178 635675729 836681349 24399 SRX1797267 SRS1465187 SRA429034 Duke University|Molecular Genetics &amp; Microbiology Duke University 1 0.87215   0.09876   0.7498   0.55116   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2017-06-24 Adult Adult Blood Hematopoietic System
41041 41041 SRR3581668 SRX1797266 SRS1465186 SRP075626 PRJNA322629 Mycobacterial infection of adult zebrafish PRJNA322629 Other RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.       D rerio dissected M marinum granuloma3 disGran3   breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Dissected granuloma|BioSampleModel:Model organism or animal                 disGran3 disGran3 disGran3 1     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP075626     disGran3.fastq.gz fastq 2398905207.0 47037357.0 disGran3.fastq.gz 0:51 A:693817641;C:513302774;G:516121702;T:675643798;N:19292 51       693817641 513302774 516121702 675643798 19292 SRX1797266 SRS1465186 SRA429033 Duke University|Molecular Genetics &amp; Microbiology Duke University 1 0.88631   0.10719   0.75465   0.51255   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2017-06-24 Adult Adult Blood Hematopoietic System
41042 41042 SRR3581667 SRX1797265 SRS1465185 SRP075626 PRJNA322629 Mycobacterial infection of adult zebrafish PRJNA322629 Other RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.       D rerio dissected M marinum granuloma2 disGran2   breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Dissected granuloma|BioSampleModel:Model organism or animal                 disGran2 disGran2 disGran2 1     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP075626     disGran2.fastq.gz fastq 2108649213.0 41346063.0 disGran2.fastq.gz 0:51 A:606624392;C:457029369;G:459017347;T:585961261;N:16844 51       606624392 457029369 459017347 585961261 16844 SRX1797265 SRS1465185 SRA429032 Duke University|Molecular Genetics &amp; Microbiology Duke University 1 0.88259   0.10405   0.74282   0.536   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2017-06-24 Adult Adult Blood Hematopoietic System
41043 41043 SRR3581315 SRX1797076 SRS1465045 SRP075626 PRJNA322629 Mycobacterial infection of adult zebrafish PRJNA322629 Other RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.       D rerio dissected M marinum granuloma1 disGran1   breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Dissected granuloma|BioSampleModel:Model organism or animal                 disGran1 disGran1 disGran1 1     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP075626     disGran1.fastq.gz fastq 2529627234.0 49600534.0 disGran1.fastq.gz 0:51 A:738849065;C:530442613;G:521673896;T:738641232;N:20428 51       738849065 530442613 521673896 738641232 20428 SRX1797076 SRS1465045 SRA428910 Duke University|Molecular Genetics &amp; Microbiology Duke University 1 0.81713   0.09754   0.75213   0.51283   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2017-07-24 Adult Adult Blood Hematopoietic 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");;