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run_metadata

6 rows where experiment.library_selection = "RT-PCR", technology = "unknown" and tissue_curation_coarse = "Respiratory System"

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tissue_curation_coarse 1

  • Respiratory System · 6 ✖

tissue_curation 1

technology 1

  • unknown · 6 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • RT-PCR · 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
56335 56335 SRR10948646 SRX7615730 SRS6049033 SRP243861 PRJNA602594 cold induce zebrafish gill transcriptome sequence PRJNA602594 Other The zebrafish gill RNA seq data for different temperature     mutant3 D16gill 16 D16 8 16a   strain:not applicable|isolate:not collected|breed:not collected|cultivar:not applicable|ecotype:not applicable|age:6 months|sex:pooled male and female|tissue:gill|sample type:tissue sample|treatment:cold 12h|BioSampleModel:Model organism or animal                 RNA Seq of dusp zebrafish:adult pooled male and female adductor gill D 16 D 16 polyT enrichment     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP243861     20-D16gill_R1.fq.gz 20-D16gill_R2.fq.gz fastq fastq 7507019400.0 25023398.0 20 D16gill R1.fq.gz 0:150 1:150 A:2047788807;C:1697151831;G:1707927470;T:2054037909;N:113383 150 150     2047788807 1697151831 1707927470 2054037909 113383 SRX7615730 SRS6049033 SRA1029833 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 2 0.9234 0.92482 0.13264 0.13155 0.69426 0.69457 0.49876 0.50169 150 150 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2020-01-22 Adult Adult Gill Respiratory System
56336 56336 SRR10948647 SRX7615729 SRS6049036 SRP243861 PRJNA602594 cold induce zebrafish gill transcriptome sequence PRJNA602594 Other The zebrafish gill RNA seq data for different temperature     mutant2 D10gill 10 D10 8 10a   strain:not applicable|isolate:not collected|breed:not collected|cultivar:not applicable|ecotype:not applicable|age:6 months|sex:pooled male and female|tissue:gill|sample type:tissue sample|treatment:cold 6h|BioSampleModel:Model organism or animal                 RNA Seq of dusp zebrafish:adult pooled male and female adductor gill D 10 D 10 polyT enrichment     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP243861     19-D10gill_R1.fq.gz 19-D10gill_R2.fq.gz fastq fastq 7509639600.0 25032132.0 19 D10gill R1.fq.gz 0:150 1:150 A:2041498757;C:1701842925;G:1706997255;T:2059186235;N:114428 150 150     2041498757 1701842925 1706997255 2059186235 114428 SRX7615729 SRS6049036 SRA1029833 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 2 0.92824 0.92909 0.12654 0.12581 0.68765 0.68734 0.48967 0.48161 150 150 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2020-01-22 Adult Adult Gill Respiratory System
56337 56337 SRR10948648 SRX7615728 SRS6049034 SRP243861 PRJNA602594 cold induce zebrafish gill transcriptome sequence PRJNA602594 Other The zebrafish gill RNA seq data for different temperature     mutant1 Dgill 28 D 28 a   strain:not applicable|isolate:not collected|breed:not collected|cultivar:not applicable|ecotype:not applicable|age:6 months|sex:pooled male and female|tissue:gill|sample type:tissue sample|treatment:no cold|BioSampleModel:Model organism or animal                 RNA Seq of dusp zebrafish:adult pooled male and female adductor gill D 28 D 28 polyT enrichment     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP243861     17-Dgill_R1.fq.gz 17-Dgill_R2.fq.gz fastq fastq 15464885400.0 51549618.0 17 Dgill R1.fq.gz 0:150 1:150 A:4239813270;C:3475699051;G:3496941841;T:4252196734;N:234504 150 150     4239813270 3475699051 3496941841 4252196734 234504 SRX7615728 SRS6049034 SRA1029833 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 2 0.91861 0.91958 0.12044 0.1182 0.67456 0.67393 0.49751 0.496 150 150 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2020-01-22 Adult Adult Gill Respiratory System
56338 56338 SRR10948649 SRX7615727 SRS6049032 SRP243861 PRJNA602594 cold induce zebrafish gill transcriptome sequence PRJNA602594 Other The zebrafish gill RNA seq data for different temperature     WT3 w16gill 16 W16 8 16a   strain:not applicable|isolate:not collected|breed:not collected|cultivar:not applicable|ecotype:not applicable|age:6 months|sex:pooled male and female|tissue:gill|sample type:tissue sample|treatment:8 cold 12h|BioSampleModel:Model organism or animal                 RNA Seq of wt zebrafish:adult pooled male and female adductor gill W 16 W 16 polyT enrichment     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP243861     8-W16gill_R2.fq.gz 8-W16gill_R1.fq.gz fastq fastq 4257006300.0 14190021.0 8 W16gill R1.fq.gz 0:150 1:150 A:1178956453;C:941379863;G:962238308;T:1174367386;N:64290 150 150     1178956453 941379863 962238308 1174367386 64290 SRX7615727 SRS6049032 SRA1029833 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 2 0.91201 0.91293 0.14747 0.14512 0.70138 0.70193 0.51012 0.50331 150 150 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2020-01-22 Adult Adult Gill Respiratory System
56339 56339 SRR10948650 SRX7615726 SRS6049035 SRP243861 PRJNA602594 cold induce zebrafish gill transcriptome sequence PRJNA602594 Other The zebrafish gill RNA seq data for different temperature     WT2 w10gill 10 W10 8 10a   strain:not applicable|isolate:not collected|breed:not collected|cultivar:not applicable|ecotype:not applicable|age:6 months|sex:pooled male and female|tissue:gill|sample type:tissue sample|treatment:8 cold 6h|BioSampleModel:Model organism or animal                 RNA Seq of wt zebrafish:adult pooled male and female adductor gill W 10 W 10 polyT enrichment     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP243861     7-W10gill_R1.fq.gz 7-W10gill_R2.fq.gz fastq fastq 5491391700.0 18304639.0 7 W10gill R1.fq.gz 0:150 1:150 A:1515889569;C:1220781777;G:1237527823;T:1517109229;N:83302 150 150     1515889569 1220781777 1237527823 1517109229 83302 SRX7615726 SRS6049035 SRA1029833 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 2 0.90595 0.90718 0.13983 0.13717 0.69406 0.69416 0.50316 0.50561 150 150 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2020-01-22 Adult Adult Gill Respiratory System
56340 56340 SRR10948651 SRX7615725 SRS6049031 SRP243861 PRJNA602594 cold induce zebrafish gill transcriptome sequence PRJNA602594 Other The zebrafish gill RNA seq data for different temperature     WT1 wgill 28 W 28 a   strain:not applicable|isolate:not collected|breed:not collected|cultivar:not applicable|ecotype:not applicable|age:6 months|sex:pooled male and female|tissue:gill|sample type:tissue sample|treatment:28 room temperature|BioSampleModel:Model organism or animal                 RNA Seq of wt zebrafish:adult pooled male and female adductor gill W 28 W 28 polyT enrichment     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP243861     5-Wgill_R1.fq.gz 5-Wgill_R2.fq.gz fastq fastq 6212437800.0 20708126.0 5 Wgill R1.fq.gz 0:150 1:150 A:1688481589;C:1407576242;G:1424513662;T:1691771107;N:95200 150 150     1688481589 1407576242 1424513662 1691771107 95200 SRX7615725 SRS6049031 SRA1029833 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 2 0.92094 0.92314 0.10403 0.10188 0.68444 0.68347 0.49471 0.49287 150 150 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2020-01-22 Adult Adult Gill Respiratory 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");;