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run_metadata

12 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "other" and tissue_curation = "Gut"

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tissue_curation_coarse 1

tissue_curation 1

  • Gut · 12 ✖

technology 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • other · 12 ✖

experiment.library_layout 1

  • SINGLE · 12 ✖

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
62981 62981 SRR13559185 SRX9957470 SRS8131854 SRP303451 PRJNA695140 Zebrafish caloric restriction PRJNA695140 Other Using Zebrafish Danio rerio as a model organism for aquaculture we investigated the impact of caloric restriction CR on growth gut morphology and gene expression.       100% feeding group replicate 2 CR 100perc 2   strain:AB Strain|dev stage:3 mpf|sex:pooled male and female|tissue:Intestine|treatment:100% feeding|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 100% feeding CR 100perc 2 CR 100perc 2 Stranded Total RNA Sample Preparation kit using Low Sample LS Protocol. Ribosomal RNA was depleted using Ribo Zero Gold kit.     RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   SRP303451     CR_100perc_2_S10_R1_001.fastq.gz fastq 1797322363.0 23790604.0 CR 100perc 2 S10 R1 001.fastq.gz 0:75.55 1:0 A:430558741;C:468161000;G:471226375;T:427297574;N:78673 75 0     430558741 468161000 471226375 427297574 78673 SRX9957470 SRS8131854 SRA1188331 Temasek Life Sciences Laboratory|Reproductive Genomics Group Temasek Life Sciences Laboratory 1 0.65722   0.19871   0.82339   0.66254   76   B   usable mapping rate illumina nextseq unknown rrna_depletion ribozero bulk unknown unknown   Singapore 2021-01-27 Adult Adult Gut Digestive System
62982 62982 SRR13559186 SRX9957469 SRS8131853 SRP303451 PRJNA695140 Zebrafish caloric restriction PRJNA695140 Other Using Zebrafish Danio rerio as a model organism for aquaculture we investigated the impact of caloric restriction CR on growth gut morphology and gene expression.       100% feeding group replicate 1 CR 100perc 1   strain:AB Strain|dev stage:3 mpf|sex:pooled male and female|tissue:Intestine|treatment:100% feeding|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 100% feeding CR 100perc 1 CR 100perc 1 Stranded Total RNA Sample Preparation kit using Low Sample LS Protocol. Ribosomal RNA was depleted using Ribo Zero Gold kit.     RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   SRP303451     CR_100perc_1_S9_R1_001.fastq.gz fastq 1534720214.0 20317497.0 CR 100perc 1 S9 R1 001.fastq.gz 0:75.54 1:0 A:375776426;C:394418295;G:367506580;T:396953400;N:65513 75 0     375776426 394418295 367506580 396953400 65513 SRX9957469 SRS8131853 SRA1188331 Temasek Life Sciences Laboratory|Reproductive Genomics Group Temasek Life Sciences Laboratory 1 0.84461   0.26652   0.76717   0.62282   76   B   usable mapping rate illumina nextseq unknown rrna_depletion ribozero bulk unknown unknown   Singapore 2021-01-27 Adult Adult Gut Digestive System
62983 62983 SRR13559187 SRX9957468 SRS8131852 SRP303451 PRJNA695140 Zebrafish caloric restriction PRJNA695140 Other Using Zebrafish Danio rerio as a model organism for aquaculture we investigated the impact of caloric restriction CR on growth gut morphology and gene expression.       85% feeding group replicate 4 CR 85perc 4   strain:AB Strain|dev stage:3 mpf|sex:pooled male and female|tissue:Intestine|treatment:85% feeding|replicate:biological replicate 4|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 85% feeding CR 85perc 4 CR 85perc 4 Stranded Total RNA Sample Preparation kit using Low Sample LS Protocol. Ribosomal RNA was depleted using Ribo Zero Gold kit.     RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   SRP303451     CR_85perc_4_S8_R1_001.fastq.gz fastq 1916818437.0 25373905.0 CR 85perc 4 S8 R1 001.fastq.gz 0:75.54 1:0 A:488054788;C:475184415;G:443451608;T:510046224;N:81402 75 0     488054788 475184415 443451608 510046224 81402 SRX9957468 SRS8131852 SRA1188331 Temasek Life Sciences Laboratory|Reproductive Genomics Group Temasek Life Sciences Laboratory 1 0.92737   0.2783   0.75909   0.57435   75   B   usable mapping rate illumina nextseq unknown rrna_depletion ribozero bulk unknown unknown   Singapore 2021-01-27 Adult Adult Gut Digestive System
62984 62984 SRR13559188 SRX9957467 SRS8131851 SRP303451 PRJNA695140 Zebrafish caloric restriction PRJNA695140 Other Using Zebrafish Danio rerio as a model organism for aquaculture we investigated the impact of caloric restriction CR on growth gut morphology and gene expression.       85% feeding group replicate 3 CR 85perc 3   strain:AB Strain|dev stage:3 mpf|sex:pooled male and female|tissue:Intestine|treatment:85% feeding|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 85% feeding CR 85perc 3 CR 85perc 3 Stranded Total RNA Sample Preparation kit using Low Sample LS Protocol. Ribosomal RNA was depleted using Ribo Zero Gold kit.     RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   SRP303451     CR_85perc_3_S7_R1_001.fastq.gz fastq 1843871333.0 24411281.0 CR 85perc 3 S7 R1 001.fastq.gz 0:75.53 1:0 A:441643488;C:487987766;G:446957305;T:467206076;N:76698 75 0     441643488 487987766 446957305 467206076 76698 SRX9957467 SRS8131851 SRA1188331 Temasek Life Sciences Laboratory|Reproductive Genomics Group Temasek Life Sciences Laboratory 1 0.91984   0.25275   0.77565   0.65163   74   B   usable mapping rate illumina nextseq unknown rrna_depletion ribozero bulk unknown unknown   Singapore 2021-01-27 Adult Adult Gut Digestive System
62985 62985 SRR13559189 SRX9957466 SRS8131850 SRP303451 PRJNA695140 Zebrafish caloric restriction PRJNA695140 Other Using Zebrafish Danio rerio as a model organism for aquaculture we investigated the impact of caloric restriction CR on growth gut morphology and gene expression.       85% feeding group replicate 2 CR 85perc 2   strain:AB Strain|dev stage:3 mpf|sex:pooled male and female|tissue:Intestine|treatment:85% feeding|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 85% feeding CR 85perc 2 CR 85perc 2 Stranded Total RNA Sample Preparation kit using Low Sample LS Protocol. Ribosomal RNA was depleted using Ribo Zero Gold kit.     RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   SRP303451     CR_85perc_2_S6_R1_001.fastq.gz fastq 2063663358.0 27321356.0 CR 85perc 2 S6 R1 001.fastq.gz 0:75.53 1:0 A:495156958;C:545615457;G:490454848;T:532349272;N:86823 75 0     495156958 545615457 490454848 532349272 86823 SRX9957466 SRS8131850 SRA1188331 Temasek Life Sciences Laboratory|Reproductive Genomics Group Temasek Life Sciences Laboratory 1 0.92542   0.29093   0.77743   0.62803   76   B   usable mapping rate illumina nextseq unknown rrna_depletion ribozero bulk unknown unknown   Singapore 2021-01-27 Adult Adult Gut Digestive System
62986 62986 SRR13559190 SRX9957465 SRS8131849 SRP303451 PRJNA695140 Zebrafish caloric restriction PRJNA695140 Other Using Zebrafish Danio rerio as a model organism for aquaculture we investigated the impact of caloric restriction CR on growth gut morphology and gene expression.       85% feeding group replicate 1 CR 85perc 1   strain:AB Strain|dev stage:3 mpf|sex:pooled male and female|tissue:Intestine|treatment:85% feeding|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 85% feeding CR 85perc 1 CR 85perc 1 Stranded Total RNA Sample Preparation kit using Low Sample LS Protocol. Ribosomal RNA was depleted using Ribo Zero Gold kit.     RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   SRP303451     CR_85perc_1_S5_R1_001.fastq.gz fastq 1987823280.0 26313964.0 CR 85perc 1 S5 R1 001.fastq.gz 0:75.54 1:0 A:489253658;C:511031006;G:469881720;T:517571925;N:84971 75 0     489253658 511031006 469881720 517571925 84971 SRX9957465 SRS8131849 SRA1188331 Temasek Life Sciences Laboratory|Reproductive Genomics Group Temasek Life Sciences Laboratory 1 0.91539   0.26469   0.75154   0.62387   73   B   usable mapping rate illumina nextseq unknown rrna_depletion ribozero bulk unknown unknown   Singapore 2021-01-27 Adult Adult Gut Digestive System
62987 62987 SRR13559191 SRX9957464 SRS8131848 SRP303451 PRJNA695140 Zebrafish caloric restriction PRJNA695140 Other Using Zebrafish Danio rerio as a model organism for aquaculture we investigated the impact of caloric restriction CR on growth gut morphology and gene expression.       70% feeding group replicate 4 CR 70perc 4   strain:AB Strain|dev stage:3 mpf|sex:pooled male and female|tissue:Intestine|treatment:70% feeding|replicate:biological replicate 4|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 70% feeding CR 70perc 4 CR 70perc 4 Stranded Total RNA Sample Preparation kit using Low Sample LS Protocol. Ribosomal RNA was depleted using Ribo Zero Gold kit.     RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   SRP303451     CR_70perc_4_S4_R1_001.fastq.gz fastq 1692306421.0 22402714.0 CR 70perc 4 S4 R1 001.fastq.gz 0:75.54 1:0 A:416831282;C:431623148;G:400872189;T:442907940;N:71862 75 0     416831282 431623148 400872189 442907940 71862 SRX9957464 SRS8131848 SRA1188331 Temasek Life Sciences Laboratory|Reproductive Genomics Group Temasek Life Sciences Laboratory 1 0.91284   0.27717   0.75702   0.58936   76   B   usable mapping rate illumina nextseq unknown rrna_depletion ribozero bulk unknown unknown   Singapore 2021-01-27 Adult Adult Gut Digestive System
62988 62988 SRR13559192 SRX9957463 SRS8131847 SRP303451 PRJNA695140 Zebrafish caloric restriction PRJNA695140 Other Using Zebrafish Danio rerio as a model organism for aquaculture we investigated the impact of caloric restriction CR on growth gut morphology and gene expression.       70% feeding group replicate 3 CR 70perc 3   strain:AB Strain|dev stage:3 mpf|sex:pooled male and female|tissue:Intestine|treatment:70% feeding|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 70% feeding CR 70perc 3 CR 70perc 3 Stranded Total RNA Sample Preparation kit using Low Sample LS Protocol. Ribosomal RNA was depleted using Ribo Zero Gold kit.     RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   SRP303451     CR_70perc_3_S3_R1_001.fastq.gz fastq 1743481023.0 23079781.0 CR 70perc 3 S3 R1 001.fastq.gz 0:75.54 1:0 A:440529322;C:430386534;G:405191664;T:467297560;N:75943 75 0     440529322 430386534 405191664 467297560 75943 SRX9957463 SRS8131847 SRA1188331 Temasek Life Sciences Laboratory|Reproductive Genomics Group Temasek Life Sciences Laboratory 1 0.92679   0.30032   0.7446   0.60383   76   B   usable mapping rate illumina nextseq unknown rrna_depletion ribozero bulk unknown unknown   Singapore 2021-01-27 Adult Adult Gut Digestive System
62989 62989 SRR13559193 SRX9957462 SRS8131846 SRP303451 PRJNA695140 Zebrafish caloric restriction PRJNA695140 Other Using Zebrafish Danio rerio as a model organism for aquaculture we investigated the impact of caloric restriction CR on growth gut morphology and gene expression.       100% feeding group replicate 4 CR 100perc 4   strain:AB Strain|dev stage:3 mpf|sex:pooled male and female|tissue:Intestine|treatment:100% feeding|replicate:biological replicate 4|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 100% feeding CR 100perc 4 CR 100perc 4 Stranded Total RNA Sample Preparation kit using Low Sample LS Protocol. Ribosomal RNA was depleted using Ribo Zero Gold kit.     RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   SRP303451     CR_100perc_4_S12_R1_001.fastq.gz fastq 2065187112.0 27339493.0 CR 100perc 4 S12 R1 001.fastq.gz 0:75.54 1:0 A:518989032;C:519066920;G:484077687;T:542966004;N:87469 75 0     518989032 519066920 484077687 542966004 87469 SRX9957462 SRS8131846 SRA1188331 Temasek Life Sciences Laboratory|Reproductive Genomics Group Temasek Life Sciences Laboratory 1 0.92848   0.28327   0.75371   0.58973   76   B   usable mapping rate illumina nextseq unknown rrna_depletion ribozero bulk unknown unknown   Singapore 2021-01-27 Adult Adult Gut Digestive System
62990 62990 SRR13559194 SRX9957461 SRS8131845 SRP303451 PRJNA695140 Zebrafish caloric restriction PRJNA695140 Other Using Zebrafish Danio rerio as a model organism for aquaculture we investigated the impact of caloric restriction CR on growth gut morphology and gene expression.       100% feeding group replicate 3 CR 100perc 3   strain:AB Strain|dev stage:3 mpf|sex:pooled male and female|tissue:Intestine|treatment:100% feeding|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 100% feeding CR 100perc 3 CR 100perc 3 Stranded Total RNA Sample Preparation kit using Low Sample LS Protocol. Ribosomal RNA was depleted using Ribo Zero Gold kit.     RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   SRP303451     CR_100perc_3_S11_R1_001.fastq.gz fastq 2335163022.0 30913920.0 CR 100perc 3 S11 R1 001.fastq.gz 0:75.54 1:0 A:569133042;C:607012551;G:552359956;T:606558343;N:99130 75 0     569133042 607012551 552359956 606558343 99130 SRX9957461 SRS8131845 SRA1188331 Temasek Life Sciences Laboratory|Reproductive Genomics Group Temasek Life Sciences Laboratory 1 0.92688   0.27391   0.75732   0.64476   76   B   usable mapping rate illumina nextseq unknown rrna_depletion ribozero bulk unknown unknown   Singapore 2021-01-27 Adult Adult Gut Digestive System
62991 62991 SRR13559195 SRX9957460 SRS8131844 SRP303451 PRJNA695140 Zebrafish caloric restriction PRJNA695140 Other Using Zebrafish Danio rerio as a model organism for aquaculture we investigated the impact of caloric restriction CR on growth gut morphology and gene expression.       70% feeding group replicate 2 CR 70perc 2   strain:AB Strain|dev stage:3 mpf|sex:pooled male and female|tissue:Intestine|treatment:70% feeding|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 70% feeding CR 70perc 2 CR 70perc 2 Stranded Total RNA Sample Preparation kit using Low Sample LS Protocol. Ribosomal RNA was depleted using Ribo Zero Gold kit.     RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   SRP303451     CR_70perc_2_S2_R1_001.fastq.gz fastq 1994514321.0 26408108.0 CR 70perc 2 S2 R1 001.fastq.gz 0:75.53 1:0 A:466027349;C:539707204;G:492197318;T:496496054;N:86396 75 0     466027349 539707204 492197318 496496054 86396 SRX9957460 SRS8131844 SRA1188331 Temasek Life Sciences Laboratory|Reproductive Genomics Group Temasek Life Sciences Laboratory 1 0.94608   0.26334   0.78084   0.65761   76   B   usable mapping rate illumina nextseq unknown rrna_depletion ribozero bulk unknown unknown   Singapore 2021-01-27 Adult Adult Gut Digestive System
62992 62992 SRR13559196 SRX9957459 SRS8131843 SRP303451 PRJNA695140 Zebrafish caloric restriction PRJNA695140 Other Using Zebrafish Danio rerio as a model organism for aquaculture we investigated the impact of caloric restriction CR on growth gut morphology and gene expression.       70% feeding group replicate 1 CR 70perc 1   strain:AB Strain|dev stage:3 mpf|sex:pooled male and female|tissue:Intestine|treatment:70% feeding|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: 70% feeding CR 70perc 1 CR 70perc 1 Stranded Total RNA Sample Preparation kit using Low Sample LS Protocol. Ribosomal RNA was depleted using Ribo Zero Gold kit.     RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   SRP303451     CR_70perc_1_S1_R1_001.fastq.gz fastq 1514616148.0 20051359.0 CR 70perc 1 S1 R1 001.fastq.gz 0:75.54 1:0 A:361412841;C:396741800;G:366909734;T:389486382;N:65391 75 0     361412841 396741800 366909734 389486382 65391 SRX9957459 SRS8131843 SRA1188331 Temasek Life Sciences Laboratory|Reproductive Genomics Group Temasek Life Sciences Laboratory 1 0.91894   0.27365   0.75941   0.62958   76   B   usable mapping rate illumina nextseq unknown rrna_depletion ribozero bulk unknown unknown   Singapore 2021-01-27 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");;