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run_metadata

8 rows where experiment.library_selection = "Oligo-dT", experiment.library_strategy = "RIP-Seq" and tissue_curation_coarse = "All anatomical structures"

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tissue_curation_coarse 1

  • All anatomical structures · 8 ✖

tissue_curation 1

technology 1

experiment.platform 1

experiment.library_strategy 1

  • RIP-Seq · 8 ✖

experiment.library_source 1

experiment.library_selection 1

  • Oligo-dT · 8 ✖

experiment.library_layout 1

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
72384 72384 SRR22805230 SRX18764963 SRS16199859 SRP413700 PRJNA906294 Danio rerio Raw sequence reads PRJNA906294 Other Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity       28 28.ythdf2 MO m6A meRIP replicate 2   strain:AB|isolate:28|dev stage:34hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal                 28.ythdf2 MO m6A meRIP replicate 2 28 28 28     RIP-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP413700     ythdf2_MO_m6A_meRIP_replicate_2_R1.fastq.gz ythdf2_MO_m6A_meRIP_replicate_2_R2.fastq.gz fastq fastq 7361721649.0 26446542.0 ythdf2 MO m6A meRIP replicate 2 R1.fastq.gz 0:139.19 1:139.17 A:1963471349;C:1716978769;G:1713549467;T:1967688429;N:33635 139 139     1963471349 1716978769 1713549467 1967688429 33635 SRX18764963 SRS16199859 SRA1560952 Zhejiang University|Institute of Genetics Zhejiang University 2 0.95246 0.9547 0.1386 0.13796 0.69757 0.69593 0.44772 0.44911 138 138 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-12-19 Pharyngula Embryo Whole Organism All anatomical structures
72385 72385 SRR22805231 SRX18764962 SRS16199858 SRP413700 PRJNA906294 Danio rerio Raw sequence reads PRJNA906294 Other Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity       27 27.ythdf2 MO m6A meRIP replicate 1   strain:AB|isolate:27|dev stage:34hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal                 27.ythdf2 MO m6A meRIP replicate 1 27 27 27     RIP-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP413700     ythdf2_MO_m6A_meRIP_replicate_1_R1.fastq.gz ythdf2_MO_m6A_meRIP_replicate_1_R2.fastq.gz fastq fastq 7064658336.0 25169165.0 ythdf2 MO m6A meRIP replicate 1 R1.fastq.gz 0:140.35 1:140.33 A:1889792523;C:1642179006;G:1639348147;T:1893307582;N:31078 140 140     1889792523 1642179006 1639348147 1893307582 31078 SRX18764962 SRS16199858 SRA1560952 Zhejiang University|Institute of Genetics Zhejiang University 2 0.95312 0.95495 0.14782 0.14808 0.69856 0.69656 0.46053 0.45683 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-12-19 Pharyngula Embryo Whole Organism All anatomical structures
72386 72386 SRR22805232 SRX18764961 SRS16199857 SRP413700 PRJNA906294 Danio rerio Raw sequence reads PRJNA906294 Other Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity       26 26.Control knockdown m6A meRIP replicate 2   strain:AB|isolate:26|dev stage:34hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal                 26.Control knockdown m6A meRIP replicate 2 26 26 26     RIP-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP413700     Control_knockdown_m6A_meRIP_replicate_2_R1.fastq.gz Control_knockdown_m6A_meRIP_replicate_2_R2.fastq.gz fastq fastq 6960835520.0 25210812.0 Control knockdown m6A meRIP replicate 2 R1.fastq.gz 0:138.06 1:138.04 A:1851748550;C:1628253635;G:1624430306;T:1856371475;N:31554 138 138     1851748550 1628253635 1624430306 1856371475 31554 SRX18764961 SRS16199857 SRA1560952 Zhejiang University|Institute of Genetics Zhejiang University 2 0.95077 0.95337 0.12974 0.13019 0.69846 0.69737 0.45561 0.45724 134 134 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-12-19 Pharyngula Embryo Whole Organism All anatomical structures
72387 72387 SRR22805233 SRX18764960 SRS16199856 SRP413700 PRJNA906294 Danio rerio Raw sequence reads PRJNA906294 Other Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity       25 25.Control knockdown m6A meRIP replicate 1   strain:AB|isolate:25|dev stage:34hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal                 25.Control knockdown m6A meRIP replicate 1 25 25 25     RIP-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP413700     Control_knockdown_m6A_meRIP_replicate_1_R1.fastq.gz Control_knockdown_m6A_meRIP_replicate_1_R2.fastq.gz fastq fastq 7116588450.0 25626978.0 Control knockdown m6A meRIP replicate 1 R1.fastq.gz 0:138.86 1:138.84 A:1872021500;C:1685125220;G:1683152373;T:1876257768;N:31589 138 138     1872021500 1685125220 1683152373 1876257768 31589 SRX18764960 SRS16199856 SRA1560952 Zhejiang University|Institute of Genetics Zhejiang University 2 0.95363 0.95468 0.05483 0.05373 0.76777 0.76648 0.4523 0.45215 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-12-19 Pharyngula Embryo Whole Organism All anatomical structures
72393 72393 SRR22805239 SRX18764954 SRS16199850 SRP413700 PRJNA906294 Danio rerio Raw sequence reads PRJNA906294 Other Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity       20 20.BHbisPhenolF 10uM m6A meRIP replicate 2   strain:AB|isolate:20|dev stage:34hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal                 20.BHbisPhenolF 10uM m6A meRIP replicate 2 20 20 20     RIP-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP413700     BHPF_10uM_m6A_meRIP_replicate_2_R1.fastq.gz BHPF_10uM_m6A_meRIP_replicate_2_R2.fastq.gz fastq fastq 7491317369.0 26658666.0 BHbisPhenolF 10uM m6A meRIP replicate 2 R1.fastq.gz 0:140.51 1:140.49 A:1978702731;C:1766538897;G:1763052208;T:1982989954;N:33579 140 140     1978702731 1766538897 1763052208 1982989954 33579 SRX18764954 SRS16199850 SRA1560952 Zhejiang University|Institute of Genetics Zhejiang University 2 0.9529 0.95443 0.08298 0.08205 0.68891 0.68846 0.47278 0.47013 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-12-19 Pharyngula Embryo Whole Organism All anatomical structures
72394 72394 SRR22805240 SRX18764953 SRS16199849 SRP413700 PRJNA906294 Danio rerio Raw sequence reads PRJNA906294 Other Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity       19 19.BHbisPhenolF 10uM m6A meRIP replicate 1   strain:AB|isolate:19|dev stage:34hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal                 19.BHbisPhenolF 10uM m6A meRIP replicate 1 19 19 19     RIP-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP413700     BHPF_10uM_m6A_meRIP_replicate_1_R1.fastq.gz BHPF_10uM_m6A_meRIP_replicate_1_R2.fastq.gz fastq fastq 7103220388.0 25558854.0 BHbisPhenolF 10uM m6A meRIP replicate 1 R1.fastq.gz 0:138.97 1:138.95 A:1882505135;C:1667796740;G:1665421739;T:1887465071;N:31703 138 138     1882505135 1667796740 1665421739 1887465071 31703 SRX18764953 SRS16199849 SRA1560952 Zhejiang University|Institute of Genetics Zhejiang University 2 0.95261 0.95474 0.09233 0.09094 0.69794 0.6966 0.46269 0.46455 111 111 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-12-19 Pharyngula Embryo Whole Organism All anatomical structures
72395 72395 SRR22805241 SRX18764952 SRS16199848 SRP413700 PRJNA906294 Danio rerio Raw sequence reads PRJNA906294 Other Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity       18 18.DMSO control m6A meRIP replicate 2   strain:AB|isolate:18|dev stage:34hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal                 18.DMSO control m6A meRIP replicate 2 18 18 18     RIP-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP413700     DMSO_control_m6A_meRIP_replicate_2_R1.fastq.gz DMSO_control_m6A_meRIP_replicate_2_R2.fastq.gz fastq fastq 7608584716.0 27081562.0 DMSO control m6A meRIP replicate 2 R1.fastq.gz 0:140.48 1:140.47 A:2016159583;C:1788089257;G:1783486901;T:2020815087;N:33888 140 140     2016159583 1788089257 1783486901 2020815087 33888 SRX18764952 SRS16199848 SRA1560952 Zhejiang University|Institute of Genetics Zhejiang University 2 0.9526 0.95462 0.08497 0.08367 0.69822 0.69755 0.46646 0.4688 114 114 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-12-19 Pharyngula Embryo Whole Organism All anatomical structures
72396 72396 SRR22805242 SRX18764951 SRS16199847 SRP413700 PRJNA906294 Danio rerio Raw sequence reads PRJNA906294 Other Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity       17 17.DMSO control m6A meRIP replicate 1   strain:AB|isolate:17|dev stage:34hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal                 17.DMSO control m6A meRIP replicate 1 17 17 17     RIP-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP413700     DMSO_control_m6A_meRIP_replicate_1_R1.fastq.gz DMSO_control_m6A_meRIP_replicate_1_R2.fastq.gz fastq fastq 7394836277.0 26199072.0 DMSO control m6A meRIP replicate 1 R1.fastq.gz 0:141.14 1:141.12 A:1964011730;C:1732461692;G:1728237059;T:1970092128;N:33668 141 141     1964011730 1732461692 1728237059 1970092128 33668 SRX18764951 SRS16199847 SRA1560952 Zhejiang University|Institute of Genetics Zhejiang University 2 0.95315 0.95536 0.1083 0.1071 0.70694 0.70587 0.47144 0.47082 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-12-19 Pharyngula 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");;