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run_metadata

8 rows where devstage_curation_coarse = "Juvenile" and experiment.library_selection = "RANDOM"

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tissue_curation_coarse 2

tissue_curation 2

technology 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • RANDOM · 8 ✖

experiment.library_layout 1

devstage_curation_coarse 1

  • Juvenile · 8 ✖

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
42301 42301 SRR5579865 SRX2837982 SRS2212147 SRP107584 PRJNA387320 Danio rerio 1207 Raw sequence reads PRJNA387320 Other           1207 2   breed:not applicable|strain:not applicable|age:1 month|biomaterial provider:not applicable|sex:not collected|tissue:Embyro|treatment:1207 2|BioSampleModel:Model organism or animal                 2002 2 1207 2 S1 L001 1207 2 S1 L001 The embryos were subjected to RNA isolation. Ten embryos per group n = 10 from wild type control embryos n = 10 from mibnn2002 mutants and n = 10 from mibta52b mutants were used to prepare a pooled RNA sample. Three biological replicates per group were prepared. Total RNA from pooled samples was extracted by using the mirVanaTM RNA isolation kit Applied Biosystems according to the manufacturer’s protocol as previously described. RNA quality was assessed by using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina MiSeq   SRP107584         1531873131.0 5203504.0 1207 2 S2 L001 2 paired.fq.gz 0:148.34 1:146.06 A:384469512;C:380138079;G:381661689;T:385603823;N:28 148 146     384469512 380138079 381661689 385603823 28 SRX2837982 SRS2212147 SRA563090 The Chinese University of Hong Kong|School of Life Sciences The Chinese University of Hong Kong 2 0.97313 0.97391 0.03931 0.03966 0.73675 0.74186 0.47243 0.47819 151 150 B B biological fallback assumption illumina miseq unknown random_priming unknown bulk unknown unknown   China 2017-05-20 Juvenile Juvenile Embryo Imprecise All anatomical structures
42302 42302 SRR5579866 SRX2837981 SRS2212146 SRP107584 PRJNA387320 Danio rerio 1207 Raw sequence reads PRJNA387320 Other           1207 1   breed:not applicable|strain:not applicable|age:1 month|biomaterial provider:not applicable|sex:not collected|tissue:Embyro|treatment:1207 1|BioSampleModel:Model organism or animal                 2002 1 1207 1 S1 L001 1207 1 S1 L001 The embryos were subjected to RNA isolation. Ten embryos per group n = 10 from wild type control embryos n = 10 from mibnn2002 mutants and n = 10 from mibta52b mutants were used to prepare a pooled RNA sample. Three biological replicates per group were prepared. Total RNA from pooled samples was extracted by using the mirVanaTM RNA isolation kit Applied Biosystems according to the manufacturer’s protocol as previously described. RNA quality was assessed by using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina MiSeq   SRP107584         1250178633.0 4243308.0 1207 1 S1 L001 2 paired.fq.gz 0:148.83 1:145.79 A:314820390;C:308887372;G:310674271;T:315796566;N:34 148 145     314820390 308887372 310674271 315796566 34 SRX2837981 SRS2212146 SRA563090 The Chinese University of Hong Kong|School of Life Sciences The Chinese University of Hong Kong 2 0.97174 0.9719 0.04506 0.04505 0.73154 0.73683 0.4817 0.48252 150 148 B B biological fallback assumption illumina miseq unknown random_priming unknown bulk unknown unknown   China 2017-05-20 Juvenile Juvenile Embryo Imprecise All anatomical structures
42303 42303 SRR5579867 SRX2837980 SRS2212145 SRP107584 PRJNA387320 Danio rerio 1207 Raw sequence reads PRJNA387320 Other           AB 1   breed:not applicable|strain:not applicable|age:1 month|biomaterial provider:not applicable|sex:not collected|tissue:Embyro|treatment:AB1|BioSampleModel:Model organism or animal                 WT1 AB1 S1 L001 AB1 S1 L001 The embryos were subjected to RNA isolation. Ten embryos per group n = 10 from wild type control embryos n = 10 from mibnn2002 mutants and n = 10 from mibta52b mutants were used to prepare a pooled RNA sample. Three biological replicates per group were prepared. Total RNA from pooled samples was extracted by using the mirVanaTM RNA isolation kit Applied Biosystems according to the manufacturer’s protocol as previously described. RNA quality was assessed by using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina MiSeq   SRP107584         1819768909.0 6190653.0 AB1 S1 L001 2 paired.fq.gz 0:148.08 1:145.88 A:465877977;C:442905762;G:444673127;T:466312043;N:0 148 145     465877977 442905762 444673127 466312043 0 SRX2837980 SRS2212145 SRA563090 The Chinese University of Hong Kong|School of Life Sciences The Chinese University of Hong Kong 2 0.97169 0.97078 0.03527 0.03575 0.72823 0.73338 0.48283 0.48226 151 151 B B biological fallback assumption illumina miseq unknown random_priming unknown bulk unknown unknown   China 2017-05-20 Juvenile Juvenile Embryo Imprecise All anatomical structures
42304 42304 SRR5579868 SRX2837979 SRS2212143 SRP107584 PRJNA387320 Danio rerio 1207 Raw sequence reads PRJNA387320 Other           1207 3   breed:not applicable|strain:not applicable|age:1 month|biomaterial provider:not applicable|sex:not collected|tissue:Embyro|treatment:1207 3|BioSampleModel:Model organism or animal                 2002 3 1207 3 S1 L001 1207 3 S1 L001 The embryos were subjected to RNA isolation. Ten embryos per group n = 10 from wild type control embryos n = 10 from mibnn2002 mutants and n = 10 from mibta52b mutants were used to prepare a pooled RNA sample. Three biological replicates per group were prepared. Total RNA from pooled samples was extracted by using the mirVanaTM RNA isolation kit Applied Biosystems according to the manufacturer’s protocol as previously described. RNA quality was assessed by using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina MiSeq   SRP107584         1045991851.0 3554741.0 1207 3 S3 L001 2 paired.fq.gz 0:148.38 1:145.87 A:263998819;C:257909132;G:259440555;T:264643331;N:14 148 145     263998819 257909132 259440555 264643331 14 SRX2837979 SRS2212143 SRA563090 The Chinese University of Hong Kong|School of Life Sciences The Chinese University of Hong Kong 2 0.97252 0.97273 0.0409 0.04037 0.74213 0.74574 0.48248 0.48634 151 151 B B biological fallback assumption illumina miseq unknown random_priming unknown bulk unknown unknown   China 2017-05-20 Juvenile Juvenile Embryo Imprecise All anatomical structures
42305 42305 SRR5579869 SRX2837978 SRS2212142 SRP107584 PRJNA387320 Danio rerio 1207 Raw sequence reads PRJNA387320 Other           AB 3   breed:not applicable|strain:not applicable|age:1 month|biomaterial provider:not applicable|sex:not collected|tissue:Embyro|treatment:AB3|BioSampleModel:Model organism or animal                 WT3 AB3 S1 L001 AB3 S1 L001 The embryos were subjected to RNA isolation. Ten embryos per group n = 10 from wild type control embryos n = 10 from mibnn2002 mutants and n = 10 from mibta52b mutants were used to prepare a pooled RNA sample. Three biological replicates per group were prepared. Total RNA from pooled samples was extracted by using the mirVanaTM RNA isolation kit Applied Biosystems according to the manufacturer’s protocol as previously described. RNA quality was assessed by using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina MiSeq   SRP107584         1126218531.0 3826972.0 AB3 S3 L001 1 paired.fq.gz 0:148.46 1:145.83 A:285650942;C:276774884;G:276765238;T:287027467;N:0 148 145     285650942 276774884 276765238 287027467 0 SRX2837978 SRS2212142 SRA563090 The Chinese University of Hong Kong|School of Life Sciences The Chinese University of Hong Kong 2 0.97355 0.97389 0.03977 0.04012 0.71999 0.72506 0.47576 0.4728 149 151 B B biological fallback assumption illumina miseq unknown random_priming unknown bulk unknown unknown   China 2017-05-20 Juvenile Juvenile Embryo Imprecise All anatomical structures
42306 42306 SRR5579870 SRX2837977 SRS2212144 SRP107584 PRJNA387320 Danio rerio 1207 Raw sequence reads PRJNA387320 Other           AB 2   breed:not applicable|strain:not applicable|age:1 month|biomaterial provider:not applicable|sex:not collected|tissue:Embyro|treatment:AB2|BioSampleModel:Model organism or animal                 WT2 AB2 S1 L001 AB2 S1 L001 The embryos were subjected to RNA isolation. Ten embryos per group n = 10 from wild type control embryos n = 10 from mibnn2002 mutants and n = 10 from mibta52b mutants were used to prepare a pooled RNA sample. Three biological replicates per group were prepared. Total RNA from pooled samples was extracted by using the mirVanaTM RNA isolation kit Applied Biosystems according to the manufacturer’s protocol as previously described. RNA quality was assessed by using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina MiSeq   SRP107584         1716453669.0 5815815.0 AB2 S2 L001 1 paired.fq.gz 0:148.63 1:146.50 A:430519895;C:426826400;G:426635292;T:432472082;N:0 148 146     430519895 426826400 426635292 432472082 0 SRX2837977 SRS2212144 SRA563090 The Chinese University of Hong Kong|School of Life Sciences The Chinese University of Hong Kong 2 0.97735 0.97725 0.02854 0.02833 0.73196 0.73484 0.48256 0.4861 151 151 B B biological fallback assumption illumina miseq unknown random_priming unknown bulk unknown unknown   China 2017-05-20 Juvenile Juvenile Embryo Imprecise All anatomical structures
74633 74633 SRR23884658 SRX19696514 SRS17065387 SRP427793 PRJNA945580 Danio rerio strain:AB Raw sequence reads PRJNA945580 Other The Raw sequence reads of WT and miR 184 KO zebrafish eyes         210508902   strain:AB|age:2 month|sex:pooled male and female|tissue:eyes|ID:2|BioSampleModel:Model organism or animal                 WT 2 210508902 210508902 NEBNext Ultra RNA Library Prep Kit for Illumina     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 1000   SRP427793     WT_2_1.fq.gz WT_2_2.fq.gz fastq fastq 6735894000.0 22452980.0 WT 2 1.fq.gz 0:150 1:150 A:1829468826;C:1562022082;G:1548721920;T:1795640273;N:40899 150 150     1829468826 1562022082 1548721920 1795640273 40899 SRX19696514 SRS17065387 SRA1605997 Henan university|Joint National Laboratory for Antibody Drug Engine Henan university 2 0.94008 0.9398 0.10958 0.11001 0.69907 0.70088 0.46448 0.46026 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming nebnext bulk unknown unknown   China 2023-03-17 Juvenile Juvenile Eye Sensory System
74634 74634 SRR23884659 SRX19696513 SRS17065384 SRP427793 PRJNA945580 Danio rerio strain:AB Raw sequence reads PRJNA945580 Other The Raw sequence reads of WT and miR 184 KO zebrafish eyes         210508901   strain:AB|age:1 month|sex:pooled male and female|tissue:eyes|ID:1|BioSampleModel:Model organism or animal                 WT 1 210508901 210508901 NEBNext Ultra RNA Library Prep Kit for Illumina     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 1000   SRP427793     WT_1_1.fq.gz WT_1_2.fq.gz fastq fastq 6733134600.0 22443782.0 WT 1 1.fq.gz 0:150 1:150 A:1819908990;C:1568144240;G:1555637420;T:1789402357;N:41593 150 150     1819908990 1568144240 1555637420 1789402357 41593 SRX19696513 SRS17065384 SRA1605997 Henan university|Joint National Laboratory for Antibody Drug Engine Henan university 2 0.94058 0.94013 0.10559 0.10527 0.69676 0.69627 0.46962 0.46888 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming nebnext bulk unknown unknown   China 2023-03-17 Juvenile Juvenile Eye Sensory 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");;