RNAquarium Metadata Server
Institute Website Terms of Use Privacy Policy

run_metadata

8 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "size fractionation" and tissue_curation = "Undetermined"

✎ View and edit SQL

This data as json, CSV (advanced)

tissue_curation_coarse 1

tissue_curation 1

  • Undetermined · 8 ✖

technology 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • size fractionation · 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
31514 31514 SRR28435337 SRX24039257 SRS20832031 SRP497569 PRJNA1090643 Danio rerio Raw sequence reads PRJNA1090643 Other The transcriptome of WT and cry dash / mutant are tested at CT 4 and CT 16.     cry dash / group 2 at CT 16 Cryd CT16G2 Unknown BA023 04T0008.fq.gz   isolate:The second group of cry dash / fish collected at CT 16.|age:120 hpf|collection date:2023 06 10|geo loc name:China:Suzhou|sex:not determined|tissue:larvae|biomaterial provider:Han Wang|birth date:2023 06 05|genotype:cry dash / |health state:Health|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: larvae Unknown BA023 04T0008.fq.gz Unknown BA023 04T0008.fq.gz CT16 cry dash group2     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA HiSeq X Five   SRP497569     Unknown_BA023-04T0008_good_2.fq.gz Unknown_BA023-04T0008_good_1.fq.gz fastq fastq 6928082472.0 23162452.0 Unknown BA023 04T0008 good 1.fq.gz 0:149.55 1:149.55 A:1783381005;C:1671764458;G:1686432861;T:1786331460;N:172688 149 149     1783381005 1671764458 1686432861 1786331460 172688 SRX24039257 SRS20832031 SRA1832685 Soochow University|School of Biology & Basic Medical Sciences Soochow University 2 0.96107 0.96048 0.06638 0.06578 0.68546 0.68582 0.46626 0.45803 150 150 B B biological fallback assumption illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Unknown 2024-03-25 Larval Larval Undetermined Undetermined
31515 31515 SRR28435338 SRX24039256 SRS20832030 SRP497569 PRJNA1090643 Danio rerio Raw sequence reads PRJNA1090643 Other The transcriptome of WT and cry dash / mutant are tested at CT 4 and CT 16.     cry dash / group 1 at CT 16 Cryd CT16G1 Unknown BA023 04T0007.fq.gz   isolate:The first group of cry dash / fish collected at CT 16.|age:120 hpf|collection date:2023 06 10|geo loc name:China:Suzhou|sex:not determined|tissue:larvae|biomaterial provider:Han Wang|birth date:2023 06 05|genotype:cry dash / |health state:Health|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: larvae Unknown BA023 04T0007.fq.gz Unknown BA023 04T0007.fq.gz CT16 cry dash group1     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA HiSeq X Five   SRP497569     Unknown_BA023-04T0007_good_2.fq.gz Unknown_BA023-04T0007_good_1.fq.gz fastq fastq 7247045982.0 24239568.0 Unknown BA023 04T0007 good 1.fq.gz 0:149.49 1:149.49 A:1868252704;C:1747715656;G:1761213537;T:1869681292;N:182793 149 149     1868252704 1747715656 1761213537 1869681292 182793 SRX24039256 SRS20832030 SRA1832685 Soochow University|School of Biology & Basic Medical Sciences Soochow University 2 0.95954 0.95937 0.0624 0.06218 0.68809 0.68765 0.47347 0.47429 150 150 B B biological fallback assumption illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Unknown 2024-03-25 Larval Larval Undetermined Undetermined
31516 31516 SRR28435339 SRX24039255 SRS20832029 SRP497569 PRJNA1090643 Danio rerio Raw sequence reads PRJNA1090643 Other The transcriptome of WT and cry dash / mutant are tested at CT 4 and CT 16.     cry dash / group 2 at CT 4 Cryd CT4G2 Unknown BA023 04T0006.fq.gz   isolate:The second group of cry dash / fish collected at CT 4.|age:120 hpf|collection date:2023 06 10|geo loc name:China:Suzhou|sex:not determined|tissue:larvae|biomaterial provider:Han Wang|birth date:2023 06 05|genotype:cry dash / |health state:Health|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: larvae Unknown BA023 04T0006.fq.gz Unknown BA023 04T0006.fq.gz CT4 cry dash group2     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA HiSeq X Five   SRP497569     Unknown_BA023-04T0006_good_1.fq.gz Unknown_BA023-04T0006_good_2.fq.gz fastq fastq 7467294282.0 24985127.0 Unknown BA023 04T0006 good 1.fq.gz 0:149.43 1:149.43 A:1940430660;C:1790773066;G:1798765445;T:1937139187;N:185924 149 149     1940430660 1790773066 1798765445 1937139187 185924 SRX24039255 SRS20832029 SRA1832685 Soochow University|School of Biology & Basic Medical Sciences Soochow University 2 0.95702 0.95753 0.08848 0.08877 0.6829 0.68199 0.49417 0.49443 150 150 B B biological fallback assumption illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Unknown 2024-03-25 Larval Larval Undetermined Undetermined
31517 31517 SRR28435340 SRX24039254 SRS20832028 SRP497569 PRJNA1090643 Danio rerio Raw sequence reads PRJNA1090643 Other The transcriptome of WT and cry dash / mutant are tested at CT 4 and CT 16.     cry dash / group 1 at CT 4 Cryd CT4G1 Unknown BA023 04T0005.fq.gz   isolate:The first group of cry dash / fish collected at CT 4.|age:120 hpf|collection date:2023 06 10|geo loc name:China:Suzhou|sex:not determined|tissue:larvae|biomaterial provider:Han Wang|birth date:2023 06 05|genotype:cry dash / |health state:Health|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: larvae Unknown BA023 04T0005.fq.gz Unknown BA023 04T0005.fq.gz CT4 cry dash group1     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA HiSeq X Five   SRP497569     Unknown_BA023-04T0005_good_1.fq.gz Unknown_BA023-04T0005_good_2.fq.gz fastq fastq 6766310740.0 22646274.0 Unknown BA023 04T0005 good 1.fq.gz 0:149.39 1:149.39 A:1762324132;C:1615995203;G:1625767974;T:1762055354;N:168077 149 149     1762324132 1615995203 1625767974 1762055354 168077 SRX24039254 SRS20832028 SRA1832685 Soochow University|School of Biology & Basic Medical Sciences Soochow University 2 0.95588 0.95587 0.06663 0.06633 0.67911 0.67888 0.46701 0.47626 150 150 B B biological fallback assumption illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Unknown 2024-03-25 Larval Larval Undetermined Undetermined
31518 31518 SRR28435341 SRX24039253 SRS20832027 SRP497569 PRJNA1090643 Danio rerio Raw sequence reads PRJNA1090643 Other The transcriptome of WT and cry dash / mutant are tested at CT 4 and CT 16.     WT group 2 at CT 16 WT CT16G2 Unknown BA023 04T0004.fq.gz   isolate:The second group of WT fish collected at CT 16.|age:120 hpf|collection date:2023 06 10|geo loc name:China:Suzhou|sex:not determined|tissue:larvae|biomaterial provider:Han Wang|birth date:2023 06 05|genotype:wildtype|health state:Health|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: larvae Unknown BA023 04T0004.fq.gz Unknown BA023 04T0004.fq.gz CT6 WT group2     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA HiSeq X Five   SRP497569     Unknown_BA023-04T0004_good_2.fq.gz Unknown_BA023-04T0004_good_1.fq.gz fastq fastq 6830283170.0 22847843.0 Unknown BA023 04T0004 good 1.fq.gz 0:149.47 1:149.47 A:1791839697;C:1618554485;G:1627518993;T:1792199298;N:170697 149 149     1791839697 1618554485 1627518993 1792199298 170697 SRX24039253 SRS20832027 SRA1832685 Soochow University|School of Biology & Basic Medical Sciences Soochow University 2 0.9515 0.94997 0.08493 0.08422 0.67178 0.67316 0.47915 0.48187 150 150 B B biological fallback assumption illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Unknown 2024-03-25 Larval Larval Undetermined Undetermined
31519 31519 SRR28435342 SRX24039252 SRS20832026 SRP497569 PRJNA1090643 Danio rerio Raw sequence reads PRJNA1090643 Other The transcriptome of WT and cry dash / mutant are tested at CT 4 and CT 16.     WT group 1 at CT 16 WT CT16G1 Unknown BA023 04T0003.fq.gz   isolate:The first group of WT fish collected at CT 16.|age:120 hpf|collection date:2023 06 10|geo loc name:China:Suzhou|sex:not determined|tissue:larvae|biomaterial provider:Han Wang|birth date:2023 06 05|genotype:wildtype|health state:Health|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: larvae Unknown BA023 04T0003.fq.gz Unknown BA023 04T0003.fq.gz CT6 WT group1     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA HiSeq X Five   SRP497569     Unknown_BA023-04T0003_good_1.fq.gz Unknown_BA023-04T0003_good_2.fq.gz fastq fastq 6430546584.0 21512133.0 Unknown BA023 04T0003 good 1.fq.gz 0:149.46 1:149.46 A:1678015842;C:1530296350;G:1541505212;T:1680568743;N:160437 149 149     1678015842 1530296350 1541505212 1680568743 160437 SRX24039252 SRS20832026 SRA1832685 Soochow University|School of Biology & Basic Medical Sciences Soochow University 2 0.94974 0.95051 0.08145 0.0819 0.6775 0.67848 0.47999 0.47986 150 150 B B biological fallback assumption illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Unknown 2024-03-25 Larval Larval Undetermined Undetermined
31520 31520 SRR28435343 SRX24039251 SRS20832025 SRP497569 PRJNA1090643 Danio rerio Raw sequence reads PRJNA1090643 Other The transcriptome of WT and cry dash / mutant are tested at CT 4 and CT 16.     WT group 2 at CT 4 WT CT4G2 Unknown BA023 04T0002.fq.gz   isolate:The second group of WT fish collected at CT 4.|age:120 hpf|collection date:2023 06 10|geo loc name:China:Suzhou|sex:not determined|tissue:larvae|biomaterial provider:Han Wang|birth date:2023 06 05|genotype:wildtype|health state:Health|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: larvae Unknown BA023 04T0002.fq.gz Unknown BA023 04T0002.fq.gz CT4 WT group2     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA HiSeq X Five   SRP497569     Unknown_BA023-04T0002_good_1.fq.gz Unknown_BA023-04T0002_good_2.fq.gz fastq fastq 7084078326.0 23701315.0 Unknown BA023 04T0002 good 1.fq.gz 0:149.44 1:149.44 A:1855453089;C:1679520129;G:1688607029;T:1860319577;N:178502 149 149     1855453089 1679520129 1688607029 1860319577 178502 SRX24039251 SRS20832025 SRA1832685 Soochow University|School of Biology & Basic Medical Sciences Soochow University 2 0.95393 0.95431 0.07799 0.07802 0.66728 0.66835 0.46237 0.47322 150 150 B B biological fallback assumption illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Unknown 2024-03-25 Larval Larval Undetermined Undetermined
31521 31521 SRR28435344 SRX24039250 SRS20832024 SRP497569 PRJNA1090643 Danio rerio Raw sequence reads PRJNA1090643 Other The transcriptome of WT and cry dash / mutant are tested at CT 4 and CT 16.     WT group 1 at CT 4 WT CT4G1 Unknown BA023 04T0001.fq.gz   isolate:The first group of WT fish collected at CT 4.|age:120 hpf|collection date:2023 06 10|geo loc name:China:Suzhou|sex:not determined|tissue:larvae|biomaterial provider:Han Wang|birth date:2023 06 05|genotype:wildtype|health state:Health|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: larvae Unknown BA023 04T0001.fq.gz Unknown BA023 04T0001.fq.gz CT4 WT group1     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA HiSeq X Five   SRP497569     Unknown_BA023-04T0001_good_2.fq.gz Unknown_BA023-04T0001_good_1.fq.gz fastq fastq 7360015710.0 24625447.0 Unknown BA023 04T0001 good 1.fq.gz 0:149.44 1:149.44 A:1931324589;C:1743134275;G:1748699685;T:1936672740;N:184421 149 149     1931324589 1743134275 1748699685 1936672740 184421 SRX24039250 SRS20832024 SRA1832685 Soochow University|School of Biology & Basic Medical Sciences Soochow University 2 0.954 0.95301 0.08257 0.08182 0.66772 0.66906 0.47505 0.47577 150 150 B B biological fallback assumption illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Unknown 2024-03-25 Larval Larval Undetermined Undetermined

Advanced export

JSON shape: default, array, newline-delimited

CSV options: 

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");;