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run_metadata

6 rows where experiment.library_selection = "RANDOM PCR", experiment.platform = "ILLUMINA" and tissue_curation = "Gonad"

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tissue_curation_coarse 1

tissue_curation 1

  • Gonad · 6 ✖

technology 1

experiment.platform 1

  • ILLUMINA · 6 ✖

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • RANDOM 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
76464 76464 SRR24957216 SRX20715257 SRS18006806 SRP444571 PRJNA984937 Danio rerio Raw sequence reads PRJNA984937 Whole Genome Sequencing To further elucidate the mechanism of ovulatory dysfunction in the cyp21a2 gene knockout model we first performed a transcriptome analysis on the ovaries.         WT1   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:4 to 5 mpf|collection date:not collected|geo loc name:China|sex:female|tissue:ovary|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: female WT1 WT1 355bp     RNA-Seq TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP444571     WT_3_1.fq.gz WT_3_2.fq.gz fastq fastq 7193246700.0 23977489.0 WT 3 1.fq.gz 0:150 1:150 A:1899215463;C:1704365793;G:1700125063;T:1889255858;N:284523 150 150     1899215463 1704365793 1700125063 1889255858 284523 SRX20715257 SRS18006806 SRA1657875 Chinese Academy of Fishery Sciences|Chinese Academy of Fishery Sciences Chinese Academy of Fishery Sciences 2 0.96018 0.95972 0.02154 0.02156 0.74783 0.74752 0.47659 0.4779 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-06-19 Adult Adult Gonad Reproductive System
76465 76465 SRR24957217 SRX20715256 SRS18006805 SRP444571 PRJNA984937 Danio rerio Raw sequence reads PRJNA984937 Whole Genome Sequencing To further elucidate the mechanism of ovulatory dysfunction in the cyp21a2 gene knockout model we first performed a transcriptome analysis on the ovaries.         WT2   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:4 to 5 mpf|collection date:not collected|geo loc name:China|sex:female|tissue:ovary|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: female WT2 WT2 354bp     RNA-Seq TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP444571     WT_2_1.fq.gz WT_2_2.fq.gz fastq fastq 6692745000.0 22309150.0 WT 2 1.fq.gz 0:150 1:150 A:1754867143;C:1599183933;G:1593183572;T:1745248372;N:261980 150 150     1754867143 1599183933 1593183572 1745248372 261980 SRX20715256 SRS18006805 SRA1657875 Chinese Academy of Fishery Sciences|Chinese Academy of Fishery Sciences Chinese Academy of Fishery Sciences 2 0.95144 0.95135 0.02095 0.02093 0.74783 0.74797 0.47881 0.48019 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-06-19 Adult Adult Gonad Reproductive System
76466 76466 SRR24957218 SRX20715255 SRS18006804 SRP444571 PRJNA984937 Danio rerio Raw sequence reads PRJNA984937 Whole Genome Sequencing To further elucidate the mechanism of ovulatory dysfunction in the cyp21a2 gene knockout model we first performed a transcriptome analysis on the ovaries.         WT3   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:4 to 5 mpf|collection date:not collected|geo loc name:China|sex:female|tissue:ovary|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: female WT3 WT3 353bp     RNA-Seq TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP444571     WT_1_1.fq.gz WT_1_2.fq.gz fastq fastq 6063572400.0 20211908.0 WT 1 1.fq.gz 0:150 1:150 A:1587049845;C:1452167103;G:1446522880;T:1577597629;N:234943 150 150     1587049845 1452167103 1446522880 1577597629 234943 SRX20715255 SRS18006804 SRA1657875 Chinese Academy of Fishery Sciences|Chinese Academy of Fishery Sciences Chinese Academy of Fishery Sciences 2 0.95503 0.95566 0.0198 0.0198 0.75189 0.75205 0.48404 0.48544 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-06-19 Adult Adult Gonad Reproductive System
76467 76467 SRR24957219 SRX20715254 SRS18006803 SRP444571 PRJNA984937 Danio rerio Raw sequence reads PRJNA984937 Whole Genome Sequencing To further elucidate the mechanism of ovulatory dysfunction in the cyp21a2 gene knockout model we first performed a transcriptome analysis on the ovaries.         cyp21a2 1   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:4 to 5 mpf|collection date:not collected|geo loc name:China|sex:female|tissue:ovary|replicate:biological replicate 4|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: female cyp21a2 1 cyp21a2 1 352bp     RNA-Seq TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP444571     cyp21a_3_1.fq.gz cyp21a_3_2.fq.gz fastq fastq 6995989200.0 23319964.0 cyp21a 3 1.fq.gz 0:150 1:150 A:1835165397;C:1669847288;G:1667209860;T:1823520176;N:246479 150 150     1835165397 1669847288 1667209860 1823520176 246479 SRX20715254 SRS18006803 SRA1657875 Chinese Academy of Fishery Sciences|Chinese Academy of Fishery Sciences Chinese Academy of Fishery Sciences 2 0.95816 0.95833 0.02281 0.02265 0.74823 0.7487 0.47417 0.47569 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-06-19 Adult Adult Gonad Reproductive System
76468 76468 SRR24957220 SRX20715253 SRS18006802 SRP444571 PRJNA984937 Danio rerio Raw sequence reads PRJNA984937 Whole Genome Sequencing To further elucidate the mechanism of ovulatory dysfunction in the cyp21a2 gene knockout model we first performed a transcriptome analysis on the ovaries.         cyp21a2 2   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:4 to 5 mpf|collection date:not collected|geo loc name:China|sex:female|tissue:ovary|replicate:biological replicate 5|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: female cyp21a2 2 cyp21a2 2 351bp     RNA-Seq TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP444571     cyp21a_2_1.fq.gz cyp21a_2_2.fq.gz fastq fastq 7468139100.0 24893797.0 cyp21a 2 1.fq.gz 0:150 1:150 A:1948988233;C:1794014163;G:1789429610;T:1935404071;N:303023 150 150     1948988233 1794014163 1789429610 1935404071 303023 SRX20715253 SRS18006802 SRA1657875 Chinese Academy of Fishery Sciences|Chinese Academy of Fishery Sciences Chinese Academy of Fishery Sciences 2 0.95662 0.95647 0.01866 0.01855 0.75067 0.75043 0.48064 0.48347 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-06-19 Adult Adult Gonad Reproductive System
76469 76469 SRR24957221 SRX20715252 SRS18006801 SRP444571 PRJNA984937 Danio rerio Raw sequence reads PRJNA984937 Whole Genome Sequencing To further elucidate the mechanism of ovulatory dysfunction in the cyp21a2 gene knockout model we first performed a transcriptome analysis on the ovaries.         cyp21a2 3   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:4 to 5 mpf|collection date:not collected|geo loc name:China|sex:female|tissue:ovary|replicate:biological replicate 6|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: female cyp21a2 3 cyp21a2 3 350bp     RNA-Seq TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP444571     cyp21a_1_1.fq.gz cyp21a_1_2.fq.gz fastq fastq 6687974400.0 22293248.0 cyp21a 1 1.fq.gz 0:150 1:150 A:1760782650;C:1592288096;G:1584534831;T:1750325587;N:43236 150 150     1760782650 1592288096 1584534831 1750325587 43236 SRX20715252 SRS18006801 SRA1657875 Chinese Academy of Fishery Sciences|Chinese Academy of Fishery Sciences Chinese Academy of Fishery Sciences 2 0.95394 0.95415 0.02019 0.0204 0.74921 0.74834 0.47901 0.47809 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-06-19 Adult Adult Gonad Reproductive 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");;