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run_metadata

12 rows where experiment.library_selection = "PCR", experiment.library_strategy = "RNA-Seq" and tissue_curation_coarse = "Undetermined"

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devstage_curation_coarse 2

devstage_curation 2

tissue_curation_coarse 1

  • Undetermined · 12 ✖

tissue_curation 1

technology 1

experiment.platform 1

experiment.library_strategy 1

  • RNA-Seq · 12 ✖

experiment.library_source 1

experiment.library_selection 1

  • PCR · 12 ✖

experiment.library_layout 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
30250 30250 SRR27756860 SRX23421865 SRS20276790 SRP486416 PRJNA1069604 Danio rerio strain:TL | breed:Danio rerio Raw sequence reads PRJNA1069604 Other To study the effect of a gene deletion in zebrafish       Model organism or animal sample from danio rerio cobll1a   ecotype:missing|dev stage:missing|collection date:2023 02 21|geo loc name:missing|sex:neuter|tissue:FISH|biomaterial provider:missing|z:1000|BioSampleModel:Model organism or animal                 Sample A 1 1 common method     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP486416     cobll1a1.R2.fq.gz cobll1a1.R1.fq.gz fastq fastq 7119566009.0 24893517.0 cobll1a1.R1.fq.gz 0:143.02 1:142.98 A:1899718926;C:1652762152;G:1669973661;T:1897092278;N:18992 143 142     1899718926 1652762152 1669973661 1897092278 18992 SRX23421865 SRS20276790 SRA1792726 Hunan Normal University|Hunan Normal University Hunan Normal University Hunan Normal University Hunan Normal University 2 0.95825 0.95956 0.0788 0.07795 0.67894 0.67884 0.48342 0.48268 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-01-29 Undetermined Undetermined Undetermined Undetermined
30251 30251 SRR27756861 SRX23421864 SRS20276789 SRP486416 PRJNA1069604 Danio rerio strain:TL | breed:Danio rerio Raw sequence reads PRJNA1069604 Other To study the effect of a gene deletion in zebrafish       MIMARKS Specimen sample from Danio rerio WT   strain:WT|collection date:2023 02 28|depth:missing|elev:missing|env broad scale:missing|env local scale:missing|env medium:missing|geo loc name:missing|isol growth condt:missing|lat lon:missing|BioSampleModel:MIMARKS.specimen|BioSampleModel:MIGS/MIMS/MIMARKS.microbial                 Sample L 11 11 common method     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP486416     tu3.R1.fq.gz tu3.R2.fq.gz fastq fastq 6881670461.0 24208326.0 tu3.R1.fq.gz 0:142.15 1:142.12 A:1820714788;C:1612866668;G:1629078247;T:1818992861;N:17897 142 142     1820714788 1612866668 1629078247 1818992861 17897 SRX23421864 SRS20276789 SRA1792726 Hunan Normal University|Hunan Normal University Hunan Normal University Hunan Normal University Hunan Normal University 2 0.95713 0.95821 0.07191 0.07071 0.67801 0.67726 0.48591 0.48501 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-01-29 Undetermined Undetermined Undetermined Undetermined
30252 30252 SRR27756862 SRX23421863 SRS20276790 SRP486416 PRJNA1069604 Danio rerio strain:TL | breed:Danio rerio Raw sequence reads PRJNA1069604 Other To study the effect of a gene deletion in zebrafish       Model organism or animal sample from danio rerio cobll1a   ecotype:missing|dev stage:missing|collection date:2023 02 21|geo loc name:missing|sex:neuter|tissue:FISH|biomaterial provider:missing|z:1000|BioSampleModel:Model organism or animal                 Sample C 3 3 common method     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP486416     cobll1a2.R1.fq.gz cobll1a2.R2.fq.gz fastq fastq 6639076778.0 23213579.0 cobll1a2.R1.fq.gz 0:143.02 1:142.98 A:1799749408;C:1513051586;G:1530064901;T:1796193421;N:17462 143 142     1799749408 1513051586 1530064901 1796193421 17462 SRX23421863 SRS20276790 SRA1792726 Hunan Normal University|Hunan Normal University Hunan Normal University Hunan Normal University Hunan Normal University 2 0.95695 0.95781 0.091 0.0896 0.68199 0.68075 0.49051 0.49057 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-01-29 Undetermined Undetermined Undetermined Undetermined
30253 30253 SRR27756863 SRX23421862 SRS20276790 SRP486416 PRJNA1069604 Danio rerio strain:TL | breed:Danio rerio Raw sequence reads PRJNA1069604 Other To study the effect of a gene deletion in zebrafish       Model organism or animal sample from danio rerio cobll1a   ecotype:missing|dev stage:missing|collection date:2023 02 21|geo loc name:missing|sex:neuter|tissue:FISH|biomaterial provider:missing|z:1000|BioSampleModel:Model organism or animal                 Sample E 5 5 common method     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP486416     cobll1a3.R2.fq.gz cobll1a3.R1.fq.gz fastq fastq 6697695084.0 23490214.0 cobll1a3.R1.fq.gz 0:142.58 1:142.55 A:1755043056;C:1586242926;G:1602146148;T:1754245480;N:17474 142 142     1755043056 1586242926 1602146148 1754245480 17474 SRX23421862 SRS20276790 SRA1792726 Hunan Normal University|Hunan Normal University Hunan Normal University Hunan Normal University Hunan Normal University 2 0.96007 0.96224 0.06487 0.06404 0.66939 0.66906 0.48829 0.48765 130 130 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-01-29 Undetermined Undetermined Undetermined Undetermined
30254 30254 SRR27756864 SRX23421861 SRS20276789 SRP486416 PRJNA1069604 Danio rerio strain:TL | breed:Danio rerio Raw sequence reads PRJNA1069604 Other To study the effect of a gene deletion in zebrafish       MIMARKS Specimen sample from Danio rerio WT   strain:WT|collection date:2023 02 28|depth:missing|elev:missing|env broad scale:missing|env local scale:missing|env medium:missing|geo loc name:missing|isol growth condt:missing|lat lon:missing|BioSampleModel:MIMARKS.specimen|BioSampleModel:MIGS/MIMS/MIMARKS.microbial                 Sample G 7 7 common method     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP486416     tu1.R1.fq.gz tu1.R2.fq.gz fastq fastq 7124072376.0 25020568.0 tu1.R1.fq.gz 0:142.38 1:142.35 A:1889928651;C:1664950324;G:1681768417;T:1887406325;N:18659 142 142     1889928651 1664950324 1681768417 1887406325 18659 SRX23421861 SRS20276789 SRA1792726 Hunan Normal University|Hunan Normal University Hunan Normal University Hunan Normal University Hunan Normal University 2 0.96032 0.96145 0.07398 0.07359 0.68503 0.6843 0.48524 0.48933 116 116 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-01-29 Undetermined Undetermined Undetermined Undetermined
30255 30255 SRR27756865 SRX23421860 SRS20276789 SRP486416 PRJNA1069604 Danio rerio strain:TL | breed:Danio rerio Raw sequence reads PRJNA1069604 Other To study the effect of a gene deletion in zebrafish       MIMARKS Specimen sample from Danio rerio WT   strain:WT|collection date:2023 02 28|depth:missing|elev:missing|env broad scale:missing|env local scale:missing|env medium:missing|geo loc name:missing|isol growth condt:missing|lat lon:missing|BioSampleModel:MIMARKS.specimen|BioSampleModel:MIGS/MIMS/MIMARKS.microbial                 Sample J 9 9 common method     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP486416     tu2.R1.fq.gz tu2.R2.fq.gz fastq fastq 7024719799.0 24627933.0 tu2.R1.fq.gz 0:142.63 1:142.60 A:1841519314;C:1662861553;G:1679614735;T:1840705226;N:18971 142 142     1841519314 1662861553 1679614735 1840705226 18971 SRX23421860 SRS20276789 SRA1792726 Hunan Normal University|Hunan Normal University Hunan Normal University Hunan Normal University Hunan Normal University 2 0.96006 0.96141 0.06713 0.06631 0.67464 0.67426 0.48684 0.48648 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-01-29 Undetermined Undetermined Undetermined Undetermined
68548 68548 SRR18056674 SRX14208687 SRS12030730 SRP360305 PRJNA806354 Danio rerio Raw sequence reads PRJNA806354 Whole Genome Sequencing Danio rerio RNA seq reads       Model organism or animal sample from Danio rerio sample 001   breed:AB|age:50dpf|sex:not collected|tissue:b1|BioSampleModel:Model organism or animal                 SS3WT6 6 6 commen method     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP360305     SS3WT6.R1.fq.gz SS3WT6.R2.fq.gz fastq fastq 7174164397.0 25400980.0 SS3WT6.R1.fq.gz 0:141.31 1:141.13 A:1934605412;C:1644763885;G:1664938935;T:1929811138;N:45027 141 141     1934605412 1644763885 1664938935 1929811138 45027 SRX14208687 SRS12030730 SRA1373545 Shanghai Ocean University|College of Fisheries and life Shanghai Ocean University 2 0.94928 0.94948 0.09187 0.09099 0.68765 0.68769 0.50435 0.50363 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2022-02-22 Juvenile Juvenile Undetermined Undetermined
68549 68549 SRR18056675 SRX14208686 SRS12030730 SRP360305 PRJNA806354 Danio rerio Raw sequence reads PRJNA806354 Whole Genome Sequencing Danio rerio RNA seq reads       Model organism or animal sample from Danio rerio sample 001   breed:AB|age:50dpf|sex:not collected|tissue:b1|BioSampleModel:Model organism or animal                 SS3WT5 5 5 commen method     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP360305     SS3WT5.R1.fq.gz SS3WT5.R2.fq.gz fastq fastq 7159028081.0 25133913.0 SS3WT5.R1.fq.gz 0:142.50 1:142.33 A:1905921436;C:1664337487;G:1683294939;T:1905427825;N:46394 142 142     1905921436 1664337487 1683294939 1905427825 46394 SRX14208686 SRS12030730 SRA1373545 Shanghai Ocean University|College of Fisheries and life Shanghai Ocean University 2 0.94917 0.95027 0.09384 0.09347 0.6594 0.65894 0.49218 0.49202 122 122 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2022-02-22 Juvenile Juvenile Undetermined Undetermined
68550 68550 SRR18056676 SRX14208685 SRS12030730 SRP360305 PRJNA806354 Danio rerio Raw sequence reads PRJNA806354 Whole Genome Sequencing Danio rerio RNA seq reads       Model organism or animal sample from Danio rerio sample 001   breed:AB|age:50dpf|sex:not collected|tissue:b1|BioSampleModel:Model organism or animal                 SS3WT4 4 4 commen method     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP360305     SS3WT4.R1.fq.gz SS3WT4.R2.fq.gz fastq fastq 6985092696.0 24360978.0 SS3WT4.R1.fq.gz 0:143.44 1:143.29 A:1858629258;C:1624045323;G:1642960060;T:1859412787;N:45268 143 143     1858629258 1624045323 1642960060 1859412787 45268 SRX14208685 SRS12030730 SRA1373545 Shanghai Ocean University|College of Fisheries and life Shanghai Ocean University 2 0.94221 0.94208 0.1047 0.1038 0.66231 0.66251 0.49213 0.49128 113 112 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2022-02-22 Juvenile Juvenile Undetermined Undetermined
68551 68551 SRR18056677 SRX14208684 SRS12030730 SRP360305 PRJNA806354 Danio rerio Raw sequence reads PRJNA806354 Whole Genome Sequencing Danio rerio RNA seq reads       Model organism or animal sample from Danio rerio sample 001   breed:AB|age:50dpf|sex:not collected|tissue:b1|BioSampleModel:Model organism or animal                 SS3WT3 3 3 commen method     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP360305     SS3WT3.R1.fq.gz SS3WT3.R2.fq.gz fastq fastq 6604271936.0 23189546.0 SS3WT3.R1.fq.gz 0:142.47 1:142.32 A:1765899330;C:1527534084;G:1543609939;T:1767186572;N:42011 142 142     1765899330 1527534084 1543609939 1767186572 42011 SRX14208684 SRS12030730 SRA1373545 Shanghai Ocean University|College of Fisheries and life Shanghai Ocean University 2 0.94017 0.94088 0.10254 0.10225 0.65163 0.65167 0.47798 0.47707 131 131 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2022-02-22 Juvenile Juvenile Undetermined Undetermined
68552 68552 SRR18056678 SRX14208683 SRS12030730 SRP360305 PRJNA806354 Danio rerio Raw sequence reads PRJNA806354 Whole Genome Sequencing Danio rerio RNA seq reads       Model organism or animal sample from Danio rerio sample 001   breed:AB|age:50dpf|sex:not collected|tissue:b1|BioSampleModel:Model organism or animal                 SS3WT2 2 2 commen method     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP360305     SS3WT2.R1.fq.gz SS3WT2.R2.fq.gz fastq fastq 6674317073.0 23265242.0 SS3WT2.R1.fq.gz 0:143.52 1:143.36 A:1768071045;C:1560492667;G:1576548690;T:1769161220;N:43451 143 143     1768071045 1560492667 1576548690 1769161220 43451 SRX14208683 SRS12030730 SRA1373545 Shanghai Ocean University|College of Fisheries and life Shanghai Ocean University 2 0.94677 0.9473 0.08956 0.08902 0.66559 0.66557 0.48058 0.48136 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2022-02-22 Juvenile Juvenile Undetermined Undetermined
68553 68553 SRR18056679 SRX14208682 SRS12030730 SRP360305 PRJNA806354 Danio rerio Raw sequence reads PRJNA806354 Whole Genome Sequencing Danio rerio RNA seq reads       Model organism or animal sample from Danio rerio sample 001   breed:AB|age:50dpf|sex:not collected|tissue:b1|BioSampleModel:Model organism or animal                 SS3WT1 1 1 commen method     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP360305     SS3WT1.R1.fq.gz SS3WT1.R2.fq.gz fastq fastq 6848211264.0 23787995.0 SS3WT1.R1.fq.gz 0:144.06 1:143.82 A:1825907736;C:1587014566;G:1607121352;T:1828122105;N:45505 144 143     1825907736 1587014566 1607121352 1828122105 45505 SRX14208682 SRS12030730 SRA1373545 Shanghai Ocean University|College of Fisheries and life Shanghai Ocean University 2 0.94226 0.94255 0.09053 0.08971 0.65807 0.65823 0.48525 0.48427 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2022-02-22 Juvenile Juvenile 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");;