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run_metadata

12 rows where devstage_curation_coarse = "Juvenile" and tissue_curation = "Skin"

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experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Skin · 12 ✖

technology 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

devstage_curation_coarse 1

  • Juvenile · 12 ✖

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
67576 67576 SRR17224787 SRX13404154 SRS11307153 SRP350669 PRJNA788440 Danio rerio Raw sequence reads PRJNA788440 Whole Genome Sequencing Danio rerio Raw sequence reads of eyes and skin         zebrafishskin   breed:AB|age:30days|sex:pooled male and female|tissue:skin|BioSampleModel:Model organism or animal                 RNAseq of zebrafish skin mut 3 30dpf skin mut 3 30dpf RNAseq of skin     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP350669     skin-mut_3_30dpf.R1.fq.gz skin-mut_3_30dpf.R2.fq.gz fastq fastq 8025414600.0 26751382.0 skin mut 3 30dpf.R1.fq.gz 0:150 1:150 A:1973620738;C:1947874868;G:2125741877;T:1978157854;N:19263 150 150     1973620738 1947874868 2125741877 1978157854 19263 SRX13404154 SRS11307153 SRA1343194 Huazhong Agricultural University|College of Fisheries Huazhong Agricultural University 2 0.92241 0.9178 0.03287 0.03164 0.74951 0.75258 0.53912 0.5384 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-14 Juvenile Juvenile Skin Surface Structure
67577 67577 SRR17224788 SRX13404153 SRS11307153 SRP350669 PRJNA788440 Danio rerio Raw sequence reads PRJNA788440 Whole Genome Sequencing Danio rerio Raw sequence reads of eyes and skin         zebrafishskin   breed:AB|age:30days|sex:pooled male and female|tissue:skin|BioSampleModel:Model organism or animal                 RNAseq of zebrafish skin mut 2 30dpf skin mut 2 30dpf RNAseq of skin     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP350669     skin-mut_2_30dpf.R1.fq.gz skin-mut_2_30dpf.R2.fq.gz fastq fastq 6098938800.0 20329796.0 skin mut 2 30dpf.R1.fq.gz 0:150 1:150 A:1520021563;C:1474526796;G:1582813467;T:1521562690;N:14284 150 150     1520021563 1474526796 1582813467 1521562690 14284 SRX13404153 SRS11307153 SRA1343194 Huazhong Agricultural University|College of Fisheries Huazhong Agricultural University 2 0.92872 0.92431 0.0312 0.02974 0.75426 0.7567 0.50003 0.50362 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-14 Juvenile Juvenile Skin Surface Structure
67578 67578 SRR17224789 SRX13404152 SRS11307153 SRP350669 PRJNA788440 Danio rerio Raw sequence reads PRJNA788440 Whole Genome Sequencing Danio rerio Raw sequence reads of eyes and skin         zebrafishskin   breed:AB|age:30days|sex:pooled male and female|tissue:skin|BioSampleModel:Model organism or animal                 RNAseq of zebrafish skin mut 1 30dpf skin mut 1 30dpf RNAseq of skin     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP350669     skin-mut_1_30dpf.R1.fq.gz skin-mut_1_30dpf.R2.fq.gz fastq fastq 5827766700.0 19425889.0 skin mut 1 30dpf.R1.fq.gz 0:150 1:150 A:1447618390;C:1412402925;G:1523986527;T:1443745018;N:13840 150 150     1447618390 1412402925 1523986527 1443745018 13840 SRX13404152 SRS11307153 SRA1343194 Huazhong Agricultural University|College of Fisheries Huazhong Agricultural University 2 0.93283 0.92736 0.02677 0.02568 0.77477 0.77731 0.45528 0.53231 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-14 Juvenile Juvenile Skin Surface Structure
67579 67579 SRR17224790 SRX13404151 SRS11307153 SRP350669 PRJNA788440 Danio rerio Raw sequence reads PRJNA788440 Whole Genome Sequencing Danio rerio Raw sequence reads of eyes and skin         zebrafishskin   breed:AB|age:30days|sex:pooled male and female|tissue:skin|BioSampleModel:Model organism or animal                 RNAseq of zebrafish skin wt 3 30dpf skin wt 3 30dpf RNAseq of skin     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP350669     skin-wt_3_30dpf.R1.fq.gz skin-wt_3_30dpf.R2.fq.gz fastq fastq 7180880434.0 25043295.0 skin wt 3 30dpf.R1.fq.gz 0:143.99 1:142.74 A:1774318367;C:1783613777;G:1819466761;T:1803467054;N:14475 143 142     1774318367 1783613777 1819466761 1803467054 14475 SRX13404151 SRS11307153 SRA1343194 Huazhong Agricultural University|College of Fisheries Huazhong Agricultural University 2 0.95299 0.94655 0.0347 0.03421 0.74426 0.74649 0.55044 0.54733 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-14 Juvenile Juvenile Skin Surface Structure
67582 67582 SRR17224793 SRX13404148 SRS11307153 SRP350669 PRJNA788440 Danio rerio Raw sequence reads PRJNA788440 Whole Genome Sequencing Danio rerio Raw sequence reads of eyes and skin         zebrafishskin   breed:AB|age:30days|sex:pooled male and female|tissue:skin|BioSampleModel:Model organism or animal                 RNAseq of zebrafish skin wt 2 30dpf skin wt 2 30dpf RNAseq of skin     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP350669     skin-wt_2_30dpf.R1.fq.gz skin-wt_2_30dpf.R2.fq.gz fastq fastq 5568886770.0 19196789.0 skin wt 2 30dpf.R1.fq.gz 0:145.60 1:144.50 A:1392028598;C:1367410036;G:1394084093;T:1415353000;N:11043 145 144     1392028598 1367410036 1394084093 1415353000 11043 SRX13404148 SRS11307153 SRA1343194 Huazhong Agricultural University|College of Fisheries Huazhong Agricultural University 2 0.95518 0.94706 0.03299 0.0324 0.75124 0.75294 0.50897 0.50693 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-14 Juvenile Juvenile Skin Surface Structure
67583 67583 SRR17224794 SRX13404147 SRS11307153 SRP350669 PRJNA788440 Danio rerio Raw sequence reads PRJNA788440 Whole Genome Sequencing Danio rerio Raw sequence reads of eyes and skin         zebrafishskin   breed:AB|age:30days|sex:pooled male and female|tissue:skin|BioSampleModel:Model organism or animal                 RNAseq of zebrafish skin wt 1 30dpf skin wt 1 30dpf RNAseq of skin     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP350669     skin-wt_1_30dpf.R1.fq.gz skin-wt_1_30dpf.R2.fq.gz fastq fastq 5296036598.0 18327020.0 skin wt 1 30dpf.R1.fq.gz 0:145.04 1:143.94 A:1317620766;C:1308908827;G:1332788335;T:1336708189;N:10481 145 143     1317620766 1308908827 1332788335 1336708189 10481 SRX13404147 SRS11307153 SRA1343194 Huazhong Agricultural University|College of Fisheries Huazhong Agricultural University 2 0.95731 0.94905 0.02784 0.02784 0.77222 0.7738 0.52941 0.58327 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-14 Juvenile Juvenile Skin Surface Structure
67674 67674 SRR17247007 SRX13426044 SRS11327036 SRP351072 PRJNA789095 Danio rerio Raw sequence reads PRJNA789095 Whole Genome Sequencing normal of RNA seq of danio rerio         C3   isolate:not collected|age:41dpf|sex:pooled male and female|tissue:scaly skin|replicate:replicate=biological replicate C3|BioSampleModel:Model organism or animal                 RNAseq of danio rerio S340 S340 normal RNA seq of danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP351072     c3_R1.fq.gz c3_R2.fq.gz fastq fastq 4841497500.0 16138325.0 c3 R1.fq.gz 0:150 1:150 A:1386818341;C:1017922211;G:1041712160;T:1394940280;N:104508 150 150     1386818341 1017922211 1041712160 1394940280 104508 SRX13426044 SRS11327036 SRA1344321 shanghai ocean university|college of marine sciences shanghai ocean university 2 0.90078 0.9042 0.12147 0.12291 0.73184 0.73497 0.57479 0.5555 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-16 Juvenile Juvenile Skin Surface Structure
67675 67675 SRR17247008 SRX13426043 SRS11327037 SRP351072 PRJNA789095 Danio rerio Raw sequence reads PRJNA789095 Whole Genome Sequencing normal of RNA seq of danio rerio         C2   isolate:not collected|age:41dpf|sex:pooled male and female|tissue:scaly skin|replicate:replicate=biological replicate C2|BioSampleModel:Model organism or animal                 RNAseq of danio rerio S339 S339 normal RNA seq of danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP351072     c2_R1.fq.gz c2_R2.fq.gz fastq fastq 7688124900.0 25627083.0 c2 R1.fq.gz 0:150 1:150 A:2102172030;C:1722525598;G:1752732030;T:2110524143;N:171099 150 150     2102172030 1722525598 1752732030 2110524143 171099 SRX13426043 SRS11327037 SRA1344321 shanghai ocean university|college of marine sciences shanghai ocean university 2 0.8669 0.86816 0.08761 0.08688 0.70725 0.71145 0.49101 0.48619 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-16 Juvenile Juvenile Skin Surface Structure
67676 67676 SRR17247009 SRX13426042 SRS11327035 SRP351072 PRJNA789095 Danio rerio Raw sequence reads PRJNA789095 Whole Genome Sequencing normal of RNA seq of danio rerio         C1   isolate:not collected|age:41dpf|sex:pooled male and female|tissue:scaly skin|replicate:replicate=biological replicate C1|BioSampleModel:Model organism or animal                 RNAseq of danio rerio S338 S338 normal RNA seq of danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP351072     c1_R1.fq.gz c1_R2.fq.gz fastq fastq 7456776900.0 24855923.0 c1 R1.fq.gz 0:150 1:150 A:2051878608;C:1656315578;G:1687161312;T:2061254398;N:167004 150 150     2051878608 1656315578 1687161312 2061254398 167004 SRX13426042 SRS11327035 SRA1344321 shanghai ocean university|college of marine sciences shanghai ocean university 2 0.82556 0.82709 0.09055 0.08946 0.70471 0.70857 0.48138 0.4916 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-16 Juvenile Juvenile Skin Surface Structure
67677 67677 SRR17247010 SRX13426041 SRS11327033 SRP351072 PRJNA789095 Danio rerio Raw sequence reads PRJNA789095 Whole Genome Sequencing normal of RNA seq of danio rerio         B3   isolate:not collected|age:33dpf|sex:pooled male and female|tissue:scaly skin|replicate:replicate=biological replicate B3|BioSampleModel:Model organism or animal                 RNAseq of danio rerio S337 S337 normal RNA seq of danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP351072     b3_R1.fq.gz b3_R2.fq.gz fastq fastq 9228717900.0 30762393.0 b3 R1.fq.gz 0:150 1:150 A:2487982964;C:2099691030;G:2134638107;T:2506202131;N:203668 150 150     2487982964 2099691030 2134638107 2506202131 203668 SRX13426041 SRS11327033 SRA1344321 shanghai ocean university|college of marine sciences shanghai ocean university 2 0.66624 0.66885 0.06853 0.06779 0.71887 0.72066 0.4895 0.49681 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-16 Juvenile Juvenile Skin Surface Structure
67678 67678 SRR17247011 SRX13426040 SRS11327034 SRP351072 PRJNA789095 Danio rerio Raw sequence reads PRJNA789095 Whole Genome Sequencing normal of RNA seq of danio rerio         B2   isolate:not collected|age:33dpf|sex:pooled male and female|tissue:scaly skin|replicate:replicate=biological replicate B2|BioSampleModel:Model organism or animal                 RNAseq of danio rerio S336 S336 normal RNA seq of danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP351072     b2_R1.fq.gz b2_R2.fq.gz fastq fastq 6040557600.0 20135192.0 b2 R1.fq.gz 0:150 1:150 A:1664821294;C:1338719408;G:1359251973;T:1677628310;N:136615 150 150     1664821294 1338719408 1359251973 1677628310 136615 SRX13426040 SRS11327034 SRA1344321 shanghai ocean university|college of marine sciences shanghai ocean university 2 0.93426 0.93571 0.10066 0.10055 0.69631 0.69897 0.47588 0.46263 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-16 Juvenile Juvenile Skin Surface Structure
67679 67679 SRR17247012 SRX13426039 SRS11327032 SRP351072 PRJNA789095 Danio rerio Raw sequence reads PRJNA789095 Whole Genome Sequencing normal of RNA seq of danio rerio         B1   isolate:not collected|age:33dpf|sex:pooled male and female|tissue:scaly skin|replicate:replicate=biological replicate B1|BioSampleModel:Model organism or animal                 RNAseq of danio rerio S335 S335 normal RNA seq of danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP351072     b1_R1.fq.gz b1_R2.fq.gz fastq fastq 6368555100.0 21228517.0 b1 R1.fq.gz 0:150 1:150 A:1748027301;C:1419234076;G:1440533749;T:1760617536;N:142438 150 150     1748027301 1419234076 1440533749 1760617536 142438 SRX13426039 SRS11327032 SRA1344321 shanghai ocean university|college of marine sciences shanghai ocean university 2 0.93385 0.93455 0.09654 0.09586 0.70031 0.70274 0.4679 0.47428 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-16 Juvenile Juvenile Skin Surface Structure

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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");;