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run_metadata

8 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "Oligo-dT" and experiment.library_strategy = "miRNA-Seq"

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tissue_curation_coarse 1

tissue_curation 1

technology 1

experiment.platform 1

experiment.library_strategy 1

  • miRNA-Seq · 8 ✖

experiment.library_source 1

experiment.library_selection 1

  • Oligo-dT · 8 ✖

experiment.library_layout 1

  • PAIRED · 8 ✖

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
72366 72366 SRR22805212 SRX18764981 SRS16199877 SRP413700 PRJNA906294 Danio rerio Raw sequence reads PRJNA906294 Other Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity       44 BHbisPhenolF 10uM for ribosome profiling replicate 2   strain:AB|isolate:44|dev stage:48hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal                 BHbisPhenolF 10uM for ribosome profiling replicate 2 44 44 44     miRNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP413700     BHPF_10uM_for_ribosome_profiling_replicate_2_R1.fastq.gz BHPF_10uM_for_ribosome_profiling_replicate_2_R2.fastq.gz fastq fastq 14888679600.0 49628932.0 BHbisPhenolF 10uM for ribosome profiling replicate 2 R1.fastq.gz 0:150 1:150 A:2177600650;C:2419699560;G:8025893657;T:2265187698;N:298035 150 150     2177600650 2419699560 8025893657 2265187698 298035 SRX18764981 SRS16199877 SRA1560952 Zhejiang University|Institute of Genetics Zhejiang University 2 0.0 0.64018 0.0 0.06137 1.0 0.83913   0.80601 150 150 T B mate1 technical by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-12-19 Hatching Embryo Whole Organism All anatomical structures
72367 72367 SRR22805213 SRX18764980 SRS16199875 SRP413700 PRJNA906294 Danio rerio Raw sequence reads PRJNA906294 Other Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity       43 BHbisPhenolF 10uM for ribosome profiling replicate 1   strain:AB|isolate:43|dev stage:48hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal                 BHbisPhenolF 10uM for ribosome profiling replicate 1 43 43 43     miRNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP413700     BHPF_10uM_for_ribosome_profiling_replicate_1_R1.fastq.gz BHPF_10uM_for_ribosome_profiling_replicate_1_R2.fastq.gz fastq fastq 15098951400.0 50329838.0 BHbisPhenolF 10uM for ribosome profiling replicate 1 R1.fastq.gz 0:150 1:150 A:2096550012;C:2382609157;G:8321980233;T:2297312503;N:499495 150 150     2096550012 2382609157 8321980233 2297312503 499495 SRX18764980 SRS16199875 SRA1560952 Zhejiang University|Institute of Genetics Zhejiang University 2 4e-05 0.62435 0.0 0.06076 0.99993 0.84279 0.75 0.77804 150 150 T B mate1 technical by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-12-19 Hatching Embryo Whole Organism All anatomical structures
72368 72368 SRR22805214 SRX18764979 SRS16199876 SRP413700 PRJNA906294 Danio rerio Raw sequence reads PRJNA906294 Other Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity       42 DMSO control for ribosome profiling replicate 2   strain:AB|isolate:42|dev stage:48hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal                 DMSO control for ribosome profiling replicate 2 42 42 42     miRNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP413700     DMSO_control_for_ribosome_profiling_replicate_2_R1.fastq.gz DMSO_control_for_ribosome_profiling_replicate_2_R2.fastq.gz fastq fastq 13980558600.0 46601862.0 DMSO control for ribosome profiling replicate 2 R1.fastq.gz 0:150 1:150 A:2002344572;C:2128464587;G:7737629750;T:2111846347;N:273344 150 150     2002344572 2128464587 7737629750 2111846347 273344 SRX18764979 SRS16199876 SRA1560952 Zhejiang University|Institute of Genetics Zhejiang University 2 0.0 0.5747 0.0 0.04778 1.0 0.85411   0.72362 150 150 T B mate1 technical by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-12-19 Hatching Embryo Whole Organism All anatomical structures
72369 72369 SRR22805215 SRX18764978 SRS16199874 SRP413700 PRJNA906294 Danio rerio Raw sequence reads PRJNA906294 Other Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity       41 DMSO control for ribosome profiling replicate 1   strain:AB|isolate:41|dev stage:48hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal                 DMSO control for ribosome profiling replicate 1 41 41 41     miRNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP413700     DMSO_control_for_ribosome_profiling_replicate_1_R1.fastq.gz DMSO_control_for_ribosome_profiling_replicate_1_R2.fastq.gz fastq fastq 15802088100.0 52673627.0 DMSO control for ribosome profiling replicate 1 R1.fastq.gz 0:150 1:150 A:2301580863;C:2488100262;G:8575515119;T:2436818717;N:73139 150 150     2301580863 2488100262 8575515119 2436818717 73139 SRX18764978 SRS16199874 SRA1560952 Zhejiang University|Institute of Genetics Zhejiang University 2 0.0 0.59521 0.0 0.05092 1.0 0.84471   0.75944 150 150 T B mate1 technical by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-12-19 Hatching Embryo Whole Organism All anatomical structures
72375 72375 SRR22805221 SRX18764972 SRS16199868 SRP413700 PRJNA906294 Danio rerio Raw sequence reads PRJNA906294 Other Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity       36 36.ythdf2 MO for ribosome profiling replicate 2   strain:AB|isolate:36|dev stage:48hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal                 36.ythdf2 MO for ribosome profiling replicate 2 36 36 36     miRNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP413700     ythdf2_MO_for_ribosome_profiling_replicate_2_R1.fastq.gz ythdf2_MO_for_ribosome_profiling_replicate_2_R2.fastq.gz fastq fastq 17815545600.0 59385152.0 ythdf2 MO for ribosome profiling replicate 2 R1.fastq.gz 0:150 1:150 A:2527267522;C:2803112888;G:9669305830;T:2815502488;N:356872 150 150     2527267522 2803112888 9669305830 2815502488 356872 SRX18764972 SRS16199868 SRA1560952 Zhejiang University|Institute of Genetics Zhejiang University 2 0.0 0.6595 0.0 0.05763 1.0 0.82359   0.76446 150 150 T B mate1 technical by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-12-19 Hatching Embryo Whole Organism All anatomical structures
72376 72376 SRR22805222 SRX18764971 SRS16199867 SRP413700 PRJNA906294 Danio rerio Raw sequence reads PRJNA906294 Other Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity       35 35.ythdf2 MO for ribosome profiling replicate 1   strain:AB|isolate:35|dev stage:48hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal                 35.ythdf2 MO for ribosome profiling replicate 1 35 35 35     miRNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP413700     ythdf2_MO_for_ribosome_profiling_replicate_1_R1.fastq.gz ythdf2_MO_for_ribosome_profiling_replicate_1_R2.fastq.gz fastq fastq 14133373800.0 47111246.0 ythdf2 MO for ribosome profiling replicate 1 R1.fastq.gz 0:150 1:150 A:2066299382;C:2279837250;G:7718113208;T:2069058663;N:65297 150 150     2066299382 2279837250 7718113208 2069058663 65297 SRX18764971 SRS16199867 SRA1560952 Zhejiang University|Institute of Genetics Zhejiang University 2 0.0 0.68906 0.0 0.06024 1.0 0.81633   0.76663 150 150 T B mate1 technical by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-12-19 Hatching Embryo Whole Organism All anatomical structures
72377 72377 SRR22805223 SRX18764970 SRS16199866 SRP413700 PRJNA906294 Danio rerio Raw sequence reads PRJNA906294 Other Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity       34 34.Control knockdown for ribosome profiling replicate 2   strain:AB|isolate:34|dev stage:48hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal                 34.Control knockdown for ribosome profiling replicate 2 34 34 34     miRNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP413700     Control_knockdown_for_ribosome_profiling_replicate_2_R1.fastq.gz Control_knockdown_for_ribosome_profiling_replicate_2_R2.fastq.gz fastq fastq 15570048000.0 51900160.0 Control knockdown for ribosome profiling replicate 2 R1.fastq.gz 0:150 1:150 A:2253659984;C:2507376043;G:8463755127;T:2344938646;N:318200 150 150     2253659984 2507376043 8463755127 2344938646 318200 SRX18764970 SRS16199866 SRA1560952 Zhejiang University|Institute of Genetics Zhejiang University 2 0.0 0.57539 0.0 0.06254 1.0 0.86989   0.80447 150 150 T B mate1 technical by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-12-19 Hatching Embryo Whole Organism All anatomical structures
72378 72378 SRR22805224 SRX18764969 SRS16199865 SRP413700 PRJNA906294 Danio rerio Raw sequence reads PRJNA906294 Other Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity       33 33.Control knockdown for ribosome profiling replicate 1   strain:AB|isolate:33|dev stage:48hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal                 33.Control knockdown for ribosome profiling replicate 1 33 33 33     miRNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP413700     Control_knockdown_for_ribosome_profiling_replicate_1_R1.fastq.gz Control_knockdown_for_ribosome_profiling_replicate_1_R2.fastq.gz fastq fastq 21657503400.0 72191678.0 Control knockdown for ribosome profiling replicate 1 R1.fastq.gz 0:150 1:150 A:3052615137;C:3123462026;G:12407511554;T:3073813355;N:101328 150 150     3052615137 3123462026 12407511554 3073813355 101328 SRX18764969 SRS16199865 SRA1560952 Zhejiang University|Institute of Genetics Zhejiang University 2 0.0 0.51073 0.0 0.05546 1.0 0.88162   0.79972 150 150 T B mate1 technical by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-12-19 Hatching Embryo Whole Organism All anatomical structures

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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");;