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run_metadata

10 rows where experiment.library_source = "TRANSCRIPTOMIC", experiment.library_strategy = "WGS" and tissue_curation = "Undetermined"

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experiment.platform 2

experiment.library_selection 2

tissue_curation_coarse 1

tissue_curation 1

  • Undetermined · 10 ✖

technology 1

experiment.library_strategy 1

  • WGS · 10 ✖

experiment.library_source 1

  • TRANSCRIPTOMIC · 10 ✖

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
36214 36214 SRR33581822 SRX28811683 SRS25048556 SRP585544 PRJNA1263423 Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis PRJNA1263423 Other           Rg1 L3   strain:Not collected|isolate:Rg1 L3|cultivar:Not collected|ecotype:Not collected|age:8 dpf stage:Larvae|collection date:2024 06 03|geo loc name:Not collected|sex:Not collected|tissue:Larvae|tmp:9|BioSampleModel:Model organism or animal                 RNA seq of Zebrafish: Treatment Rg1 L3 Rg1 L3 Treatment     WGS TRANSCRIPTOMIC PolyA PAIRED DNBSEQ DNBSEQ-G400   SRP585544     D4_1.fq.gz D4_2.fq.gz fastq fastq 6696495000.0 22321650.0 D4 1.fq.gz 0:150 1:150 A:1846856660;C:1513002602;G:1504866522;T:1831769216;N:0 150 150     1846856660 1513002602 1504866522 1831769216 0 SRX28811683 SRS25048556 SRA2130283 Hubei University of Medicine|Graduate school Hubei University of Medicine                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2025-05-15 Larval Larval Undetermined Undetermined
36215 36215 SRR33581823 SRX28811682 SRS25048555 SRP585544 PRJNA1263423 Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis PRJNA1263423 Other           Rg1 L7   strain:Not collected|isolate:Rg1 L7|cultivar:Not collected|ecotype:Not collected|age:8 dpf stage:Larvae|collection date:2024 06 03|geo loc name:Not collected|sex:Not collected|tissue:Larvae|tmp:8|BioSampleModel:Model organism or animal                 RNA seq of Zebrafish: Treatment Rg1 L7 Rg1 L7 Treatment     WGS TRANSCRIPTOMIC PolyA PAIRED DNBSEQ DNBSEQ-G400   SRP585544     D2_1.fq.gz D2_2.fq.gz fastq fastq 6666041700.0 22220139.0 D2 1.fq.gz 0:150 1:150 A:1845276816;C:1500512488;G:1492917547;T:1827334849;N:0 150 150     1845276816 1500512488 1492917547 1827334849 0 SRX28811682 SRS25048555 SRA2130283 Hubei University of Medicine|Graduate school Hubei University of Medicine                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2025-05-15 Larval Larval Undetermined Undetermined
36216 36216 SRR33581824 SRX28811681 SRS25048554 SRP585544 PRJNA1263423 Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis PRJNA1263423 Other           Rg1 L5   strain:Not collected|isolate:Rg1 L5|cultivar:Not collected|ecotype:Not collected|age:8 dpf stage:Larvae|collection date:2024 06 03|geo loc name:Not collected|sex:Not collected|tissue:Larvae|tmp:7|BioSampleModel:Model organism or animal                 RNA seq of Zebrafish: Treatment Rg1 L5 Rg1 L5 Treatment     WGS TRANSCRIPTOMIC PolyA PAIRED DNBSEQ DNBSEQ-G400   SRP585544     D1_1.fq.gz D1_2.fq.gz fastq fastq 6698296200.0 22327654.0 D1 1.fq.gz 0:150 1:150 A:1843962508;C:1518208646;G:1509450148;T:1826674898;N:0 150 150     1843962508 1518208646 1509450148 1826674898 0 SRX28811681 SRS25048554 SRA2130283 Hubei University of Medicine|Graduate school Hubei University of Medicine                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2025-05-15 Larval Larval Undetermined Undetermined
36217 36217 SRR33581825 SRX28811680 SRS25048553 SRP585544 PRJNA1263423 Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis PRJNA1263423 Other           PN L7   strain:Not collected|isolate:PN L7|cultivar:Not collected|ecotype:Not collected|age:8 dpf stage:Larvae|collection date:2024 06 03|geo loc name:Not collected|sex:Not collected|tissue:Larvae|tmp:6|BioSampleModel:Model organism or animal                 RNA seq of Zebrafish: Model PN L7 PN L7 Model     WGS TRANSCRIPTOMIC PolyA PAIRED DNBSEQ DNBSEQ-G400   SRP585544     B3_1.fq.gz B3_2.fq.gz fastq fastq 6611023200.0 22036744.0 B3 1.fq.gz 0:150 1:150 A:1823488173;C:1492231000;G:1485521400;T:1809782627;N:0 150 150     1823488173 1492231000 1485521400 1809782627 0 SRX28811680 SRS25048553 SRA2130283 Hubei University of Medicine|Graduate school Hubei University of Medicine                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2025-05-15 Larval Larval Undetermined Undetermined
36218 36218 SRR33581826 SRX28811679 SRS25048552 SRP585544 PRJNA1263423 Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis PRJNA1263423 Other           PN L2   strain:Not collected|isolate:PN L2|cultivar:Not collected|ecotype:Not collected|age:8 dpf stage:Larvae|collection date:2024 06 03|geo loc name:Not collected|sex:Not collected|tissue:Larvae|tmp:5|BioSampleModel:Model organism or animal                 RNA seq of Zebrafish: Model PN L2 PN L2 Model     WGS TRANSCRIPTOMIC PolyA PAIRED DNBSEQ DNBSEQ-G400   SRP585544     B2_1.fq.gz B2_2.fq.gz fastq fastq 6673419600.0 22244732.0 B2 1.fq.gz 0:150 1:150 A:1853555661;C:1496204062;G:1487686506;T:1835973371;N:0 150 150     1853555661 1496204062 1487686506 1835973371 0 SRX28811679 SRS25048552 SRA2130283 Hubei University of Medicine|Graduate school Hubei University of Medicine                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2025-05-15 Larval Larval Undetermined Undetermined
36219 36219 SRR33581827 SRX28811678 SRS25048551 SRP585544 PRJNA1263423 Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis PRJNA1263423 Other           PN L4   strain:Not collected|isolate:PN L4|cultivar:Not collected|ecotype:Not collected|age:8 dpf stage:Larvae|collection date:2024 06 03|geo loc name:Not collected|sex:Not collected|tissue:Larvae|tmp:4|BioSampleModel:Model organism or animal                 RNA seq of Zebrafish: Model PN L4 PN L4 Model     WGS TRANSCRIPTOMIC PolyA PAIRED DNBSEQ DNBSEQ-G400   SRP585544     B1_1.fq.gz B1_2.fq.gz fastq fastq 6654915300.0 22183051.0 B1 1.fq.gz 0:150 1:150 A:1864666474;C:1477163584;G:1469026869;T:1844058373;N:0 150 150     1864666474 1477163584 1469026869 1844058373 0 SRX28811678 SRS25048551 SRA2130283 Hubei University of Medicine|Graduate school Hubei University of Medicine                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2025-05-15 Larval Larval Undetermined Undetermined
36220 36220 SRR33581828 SRX28811677 SRS25048550 SRP585544 PRJNA1263423 Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis PRJNA1263423 Other           Con L1   strain:Not collected|isolate:Con L1|cultivar:Not collected|ecotype:Not collected|age:8 dpf stage:Larvae|collection date:2024 06 03|geo loc name:Not collected|sex:Not collected|tissue:Larvae|tmp:3|BioSampleModel:Model organism or animal                 RNA seq of Zebrafish: Control Con L1 Con L1 Control     WGS TRANSCRIPTOMIC PolyA PAIRED DNBSEQ DNBSEQ-G400   SRP585544     A3_1.fq.gz A3_2.fq.gz fastq fastq 6805948200.0 22686494.0 A3 1.fq.gz 0:150 1:150 A:1865806598;C:1548653255;G:1540767459;T:1850720888;N:0 150 150     1865806598 1548653255 1540767459 1850720888 0 SRX28811677 SRS25048550 SRA2130283 Hubei University of Medicine|Graduate school Hubei University of Medicine                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2025-05-15 Larval Larval Undetermined Undetermined
36221 36221 SRR33581829 SRX28811676 SRS25048549 SRP585544 PRJNA1263423 Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis PRJNA1263423 Other           Con Lb   strain:Not collected|isolate:Con Lb|cultivar:Not collected|ecotype:Not collected|age:8 dpf stage:Larvae|collection date:2024 06 03|geo loc name:Not collected|sex:Not collected|tissue:Larvae|tmp:2|BioSampleModel:Model organism or animal                 RNA seq of Zebrafish: Control Con Lb Con Lb Control     WGS TRANSCRIPTOMIC PolyA PAIRED DNBSEQ DNBSEQ-G400   SRP585544     A2_1.fq.gz A2_2.fq.gz fastq fastq 6807123600.0 22690412.0 A2 1.fq.gz 0:150 1:150 A:1868554012;C:1546467202;G:1539322143;T:1852780243;N:0 150 150     1868554012 1546467202 1539322143 1852780243 0 SRX28811676 SRS25048549 SRA2130283 Hubei University of Medicine|Graduate school Hubei University of Medicine                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2025-05-15 Larval Larval Undetermined Undetermined
36222 36222 SRR33581830 SRX28811675 SRS25048548 SRP585544 PRJNA1263423 Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis PRJNA1263423 Other           Con La   strain:Not collected|isolate:Con La|cultivar:Not collected|ecotype:Not collected|age:8 dpf stage:Larvae|collection date:2024 06 03|geo loc name:Not collected|sex:Not collected|tissue:Larvae|tmp:1|BioSampleModel:Model organism or animal                 RNA seq of Zebrafish: Control Con La Con La       WGS TRANSCRIPTOMIC PolyA PAIRED DNBSEQ DNBSEQ-G400   SRP585544     A1_1.fq.gz A1_2.fq.gz fastq fastq 6782914200.0 22609714.0 A1 1.fq.gz 0:150 1:150 A:1857557307;C:1544915899;G:1537431564;T:1843009430;N:0 150 150     1857557307 1544915899 1537431564 1843009430 0 SRX28811675 SRS25048548 SRA2130283 Hubei University of Medicine|Graduate school Hubei University of Medicine                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2025-05-15 Larval Larval Undetermined Undetermined
60823 60823 SRR12494407 SRX8985926 SRS7239898 SRP278434 PRJNA658611 zebrafish starvation stress PRJNA658611 Other RNA Seq Analysis Reveals the Molecular Response Mechanisms in Zebrafish Larvae Undergoing Starvation During the Mouth opening Stage         sszf   strain:AB line|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:8 days|dev stage:larval fish|sex:not determined|tissue:not collected|BioSampleModel:Model organism or animal                 Transcriptome analysis reveals the role of exogenous feeding in regulating antioxidant defenses during the mouth opening stage in zebrafish larvae 821 821 RNA sequencing     WGS TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP278434     Starved2-R2.R2.clean.fastq.gz Starved2-R1.R1.clean.fastq.gz Starved1-R2.R2.clean.fastq.gz Starved1-R1.R1.clean.fastq.gz Control2-R2.R2.clean.fastq.gz Control2-R1.R1.clean.fastq.gz Control1-R2.R2.clean.fastq.gz Control1-R1.R1.clean.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq 11815834250.0 47263337.0 Control1 R1.R1.clean.fastq.gz 0:125 1:125 A:2985063485;C:2935671076;G:2921346976;T:2973732805;N:19908 125 125     2985063485 2935671076 2921346976 2973732805 19908 SRX8985926 SRS7239898 SRA1115895 Southwest University|College of Animal Science and Technolgoy Southwest University 2 0.9663 0.96526 0.05986 0.06116 0.70889 0.71108 0.50789 0.50441 125 125 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-08-21 Larval Larval Undetermined Undetermined

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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");;