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run_metadata

4 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "RT-PCR" and tissue_curation_coarse = "Cardiovascular System"

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tissue_curation_coarse 1

  • Cardiovascular System · 4 ✖

tissue_curation 1

technology 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • RT-PCR · 4 ✖

experiment.library_layout 1

  • SINGLE · 4 ✖

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
52238 52238 SRR9044114 SRX5820656 SRS4749302 SRP197695 PRJNA542436 Regulation of hematopoiesis and endothelium function by endocytic trafficking PRJNA542436 Other Endocytic trafficking in endothelium         CT1   strain:AB|isolate:ctrl MO fluorescence activated cell sorting 1|cultivar:not applicable|ecotype:not applicable|age:1 year|sex:male and female|tissue:fli1a+ endothelium|BioSampleModel:Model organism or animal                 RNA seq of endothelial cells1 ct1 20191 ct1 20191 ctrl MO 1     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP197695     CT1.gz fastq 3222866250.0 21485775.0 CT1.gz 0:150 1:0 A:845914701;C:771891741;G:774348916;T:830705072;N:5820 150 0     845914701 771891741 774348916 830705072 5820 SRX5820656 SRS4749302 SRA885405 Chinese academy of sciences|institute of zoology Chinese academy of sciences 1 0.95232   0.09195   0.7837   0.45885   150   B   usable mapping rate illumina novaseq_era unknown other unknown bulk unknown unknown   China 2020-01-17 Adult Adult Endothelium Cardiovascular System
52239 52239 SRR9044115 SRX5820655 SRS4749299 SRP197695 PRJNA542436 Regulation of hematopoiesis and endothelium function by endocytic trafficking PRJNA542436 Other Endocytic trafficking in endothelium         CT2   strain:AB|isolate:ctrl MO fluorescence activated cell sorting 2|cultivar:not applicable|ecotype:not applicable|age:1 year|sex:male and female|tissue:fli1a+ endothelium|BioSampleModel:Model organism or animal                 RNA seq of endothelial cells2 ct1 20192 ct1 20192 ctrl MO 2     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP197695     CT2.gz fastq 3992117700.0 26614118.0 CT2.gz 0:150 1:0 A:1040923084;C:961956867;G:964333886;T:1024896832;N:7031 150 0     1040923084 961956867 964333886 1024896832 7031 SRX5820655 SRS4749299 SRA885405 Chinese academy of sciences|institute of zoology Chinese academy of sciences 1 0.95545   0.087   0.78488   0.46466   150   B   usable mapping rate illumina novaseq_era unknown other unknown bulk unknown unknown   China 2019-05-11 Adult Adult Endothelium Cardiovascular System
52240 52240 SRR9044116 SRX5820654 SRS4749301 SRP197695 PRJNA542436 Regulation of hematopoiesis and endothelium function by endocytic trafficking PRJNA542436 Other Endocytic trafficking in endothelium         SCMO1   strain:AB|isolate:5c MO fluorescence activated cell sorting 3|cultivar:not applicable|ecotype:not applicable|age:1 year|sex:male and female|tissue:fli1a+ endothelium|BioSampleModel:Model organism or animal                 RNA seq of endothelial cells3 5c 20191 5c 20191 5c MO 1     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP197695     SCMO1.gz fastq 2137379550.0 14249197.0 SCMO1.gz 0:150 1:0 A:558129907;C:517045618;G:515434728;T:546767387;N:1910 150 0     558129907 517045618 515434728 546767387 1910 SRX5820654 SRS4749301 SRA885405 Chinese academy of sciences|institute of zoology Chinese academy of sciences 1 0.94546   0.08686   0.78709   0.56163   150   B   usable mapping rate illumina novaseq_era unknown other unknown bulk unknown unknown   China 2020-01-17 Adult Adult Endothelium Cardiovascular System
52241 52241 SRR9044117 SRX5820653 SRS4749300 SRP197695 PRJNA542436 Regulation of hematopoiesis and endothelium function by endocytic trafficking PRJNA542436 Other Endocytic trafficking in endothelium         SCMO2   strain:AB|isolate:5c MO fluorescence activated cell sorting 4|cultivar:not applicable|ecotype:not applicable|age:1 year|sex:male and female|tissue:fli1a+ endothelium|BioSampleModel:Model organism or animal                 RNA seq of endothelial cells4 5c 20192 5c 20192 5c MO 2     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP197695     SCMO2.gz fastq 3909804300.0 26065362.0 SCMO2.gz 0:150 1:0 A:1033271905;C:928576644;G:928527559;T:1019420939;N:7253 150 0     1033271905 928576644 928527559 1019420939 7253 SRX5820653 SRS4749300 SRA885405 Chinese academy of sciences|institute of zoology Chinese academy of sciences 1 0.94475   0.096   0.7867   0.55845   150   B   usable mapping rate illumina novaseq_era unknown other unknown bulk unknown unknown   China 2020-01-17 Adult Adult Endothelium Cardiovascular 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");;