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run_metadata

6 rows where experiment.library_selection = "PolyA", experiment.platform = "DNBSEQ" and tissue_curation = "Liver"

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tissue_curation_coarse 1

tissue_curation 1

  • Liver · 6 ✖

technology 1

experiment.platform 1

  • DNBSEQ · 6 ✖

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • PolyA · 6 ✖

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
31980 31980 SRR28892728 SRX24451189 SRS21204958 SRP505641 PRJNA1107713 Tea polyphenols induce hepatotoxicity by interfering with adult zebrafish lipid metabolism and gut microbiota through the gut liver axis PRJNA1107713 Other High dose tea polyphenols may promote fatty acid absorption by hepatocytes by up regulating FABP CD36 and SRB1 genes inhibiting fatty acid efflux by down regulating ABCA1 genes and inhibiting fatty acid beta oxidation by down regulating CPT1 and ACAA2 genes resulting in fat accumulation in hepatocytes upregulation of inflammatory pathways and increased expression of pro inflammatory factors TNF a and IL1 b.         TP3   strain:not applicable|isolate:not applicable|breed:not collected|cultivar:not applicable|ecotype:AB ecotype|age:5 month|collection date:2022 11 24|geo loc name:China|sex:male|tissue:liver|replicate:replicate=biological replicate 6|BioSampleModel:Model organism or animal                 Adult zebrafish liver TP3 TP3 mRNAseq of zebrafish liver replication 3 of TP     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED DNBSEQ DNBSEQ-T7   SRP505641     TP3_1.fq.gz TP3_2.fq.gz fastq fastq 6657069900.0 22190233.0 TP3 1.fq.gz 0:150 1:150 A:1808410149;C:1512668682;G:1536153888;T:1799837181;N:0 150 150     1808410149 1512668682 1536153888 1799837181 0 SRX24451189 SRS21204958 SRA1858747 Beibu Gulf University|college of Food Engineering Beibu Gulf University                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Adult Adult Liver Liver and Biliary System
31981 31981 SRR28892729 SRX24451188 SRS21204959 SRP505641 PRJNA1107713 Tea polyphenols induce hepatotoxicity by interfering with adult zebrafish lipid metabolism and gut microbiota through the gut liver axis PRJNA1107713 Other High dose tea polyphenols may promote fatty acid absorption by hepatocytes by up regulating FABP CD36 and SRB1 genes inhibiting fatty acid efflux by down regulating ABCA1 genes and inhibiting fatty acid beta oxidation by down regulating CPT1 and ACAA2 genes resulting in fat accumulation in hepatocytes upregulation of inflammatory pathways and increased expression of pro inflammatory factors TNF a and IL1 b.         TP2   strain:not applicable|isolate:not applicable|breed:not collected|cultivar:not applicable|ecotype:AB ecotype|age:5 month|collection date:2022 11 24|geo loc name:China|sex:male|tissue:liver|replicate:replicate=biological replicate 5|BioSampleModel:Model organism or animal                 Adult zebrafish liver TP2 TP2 mRNAseq of zebrafish liver replication 2 of TP     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED DNBSEQ DNBSEQ-T7   SRP505641     TP2_1.fq.gz TP2_2.fq.gz fastq fastq 6617368500.0 22057895.0 TP2 1.fq.gz 0:150 1:150 A:1799646726;C:1503407966;G:1523443584;T:1790870224;N:0 150 150     1799646726 1503407966 1523443584 1790870224 0 SRX24451188 SRS21204959 SRA1858747 Beibu Gulf University|college of Food Engineering Beibu Gulf University                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Adult Adult Liver Liver and Biliary System
31982 31982 SRR28892730 SRX24451187 SRS21204956 SRP505641 PRJNA1107713 Tea polyphenols induce hepatotoxicity by interfering with adult zebrafish lipid metabolism and gut microbiota through the gut liver axis PRJNA1107713 Other High dose tea polyphenols may promote fatty acid absorption by hepatocytes by up regulating FABP CD36 and SRB1 genes inhibiting fatty acid efflux by down regulating ABCA1 genes and inhibiting fatty acid beta oxidation by down regulating CPT1 and ACAA2 genes resulting in fat accumulation in hepatocytes upregulation of inflammatory pathways and increased expression of pro inflammatory factors TNF a and IL1 b.         TP1   strain:not applicable|isolate:not applicable|breed:not collected|cultivar:not applicable|ecotype:AB ecotype|age:5 month|collection date:2022 11 24|geo loc name:China|sex:male|tissue:liver|replicate:replicate=biological replicate 4|BioSampleModel:Model organism or animal                 Adult zebrafish liver TP1 TP1 mRNAseq of zebrafish liver replication 1 of TP     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED DNBSEQ DNBSEQ-T7   SRP505641     TP1_1.fq.gz TP1_2.fq.gz fastq fastq 6432586800.0 21441956.0 TP1 1.fq.gz 0:150 1:150 A:1743341515;C:1465440262;G:1488109144;T:1735695879;N:0 150 150     1743341515 1465440262 1488109144 1735695879 0 SRX24451187 SRS21204956 SRA1858747 Beibu Gulf University|college of Food Engineering Beibu Gulf University                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Adult Adult Liver Liver and Biliary System
31983 31983 SRR28892731 SRX24451186 SRS21204957 SRP505641 PRJNA1107713 Tea polyphenols induce hepatotoxicity by interfering with adult zebrafish lipid metabolism and gut microbiota through the gut liver axis PRJNA1107713 Other High dose tea polyphenols may promote fatty acid absorption by hepatocytes by up regulating FABP CD36 and SRB1 genes inhibiting fatty acid efflux by down regulating ABCA1 genes and inhibiting fatty acid beta oxidation by down regulating CPT1 and ACAA2 genes resulting in fat accumulation in hepatocytes upregulation of inflammatory pathways and increased expression of pro inflammatory factors TNF a and IL1 b.         CONT3   strain:not applicable|isolate:not applicable|breed:not collected|cultivar:not applicable|ecotype:AB ecotype|age:5 month|collection date:2022 11 24|geo loc name:China|sex:male|tissue:liver|replicate:replicate=biological replicate 3|BioSampleModel:Model organism or animal                 Adult zebrafish liver CON3 CON3 mRNAseq of zebrafish liver replication 3 of CONT     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED DNBSEQ DNBSEQ-T7   SRP505641     CONT3_1.fq.gz CONT3_2.fq.gz fastq fastq 6595768200.0 21985894.0 CONT3 1.fq.gz 0:150 1:150 A:1762107185;C:1525175684;G:1547321856;T:1761163475;N:0 150 150     1762107185 1525175684 1547321856 1761163475 0 SRX24451186 SRS21204957 SRA1858747 Beibu Gulf University|college of Food Engineering Beibu Gulf University                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Adult Adult Liver Liver and Biliary System
31984 31984 SRR28892732 SRX24451185 SRS21204954 SRP505641 PRJNA1107713 Tea polyphenols induce hepatotoxicity by interfering with adult zebrafish lipid metabolism and gut microbiota through the gut liver axis PRJNA1107713 Other High dose tea polyphenols may promote fatty acid absorption by hepatocytes by up regulating FABP CD36 and SRB1 genes inhibiting fatty acid efflux by down regulating ABCA1 genes and inhibiting fatty acid beta oxidation by down regulating CPT1 and ACAA2 genes resulting in fat accumulation in hepatocytes upregulation of inflammatory pathways and increased expression of pro inflammatory factors TNF a and IL1 b.         CONT2   strain:not applicable|isolate:not applicable|breed:not collected|cultivar:not applicable|ecotype:AB ecotype|age:5 month|collection date:2022 11 24|geo loc name:China|sex:male|tissue:liver|replicate:replicate=biological replicate 2|BioSampleModel:Model organism or animal                 Adult zebrafish liver CON2 CON2 mRNAseq of zebrafish liver replication 2 of CONT     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED DNBSEQ DNBSEQ-T7   SRP505641     CONT2_1.fq.gz CONT2_2.fq.gz fastq fastq 6175346400.0 20584488.0 CONT2 1.fq.gz 0:150 1:150 A:1656546719;C:1421990443;G:1442409824;T:1654399414;N:0 150 150     1656546719 1421990443 1442409824 1654399414 0 SRX24451185 SRS21204954 SRA1858747 Beibu Gulf University|college of Food Engineering Beibu Gulf University                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Adult Adult Liver Liver and Biliary System
31985 31985 SRR28892733 SRX24451184 SRS21204955 SRP505641 PRJNA1107713 Tea polyphenols induce hepatotoxicity by interfering with adult zebrafish lipid metabolism and gut microbiota through the gut liver axis PRJNA1107713 Other High dose tea polyphenols may promote fatty acid absorption by hepatocytes by up regulating FABP CD36 and SRB1 genes inhibiting fatty acid efflux by down regulating ABCA1 genes and inhibiting fatty acid beta oxidation by down regulating CPT1 and ACAA2 genes resulting in fat accumulation in hepatocytes upregulation of inflammatory pathways and increased expression of pro inflammatory factors TNF a and IL1 b.         CONT1   strain:not applicable|isolate:not applicable|breed:not collected|cultivar:not applicable|ecotype:AB ecotype|age:5 month|collection date:2022 11 24|geo loc name:China|sex:male|tissue:liver|replicate:replicate=biological replicate 1|BioSampleModel:Model organism or animal                 Adult zebrafish liver CON1 CON1 mRNAseq of zebrafish liver replication 1 of CONT     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED DNBSEQ DNBSEQ-T7   SRP505641     CONT1_1.fq.gz CONT1_2.fq.gz fastq fastq 6342828300.0 21142761.0 CONT1 1.fq.gz 0:150 1:150 A:1698306803;C:1464261565;G:1482929449;T:1697330483;N:0 150 150     1698306803 1464261565 1482929449 1697330483 0 SRX24451184 SRS21204955 SRA1858747 Beibu Gulf University|college of Food Engineering Beibu Gulf University                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Adult Adult Liver Liver and Biliary 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");;