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run_metadata

6 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "Oligo-dT" and tissue_curation = "Eye"

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tissue_curation_coarse 1

tissue_curation 1

technology 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • Oligo-dT · 6 ✖

experiment.library_layout 1

  • SINGLE · 6 ✖

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
67572 67572 SRR17224783 SRX13404158 SRS11307154 SRP350669 PRJNA788440 Danio rerio Raw sequence reads PRJNA788440 Whole Genome Sequencing Danio rerio Raw sequence reads of eyes and skin         zebrafisheye   breed:AB|age:30days|sex:pooled male and female|tissue:eyes|BioSampleModel:Model organism or animal                 RNAseq of zebrafish eye mut 1 30dpf eye mut 1 30dpf RNAseq of eye     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP350669     eye_mut_1_30dpf.R1.fastq.gz eye_mut_1_30dpf.R2.fastq.gz fastq fastq 6647236232.0 22010716.0 eye mut 1 30dpf.R1.fastq.gz 0:151 1:151 A:1828748374;C:1496039359;G:1520471614;T:1801966254;N:10631 151 151     1828748374 1496039359 1520471614 1801966254 10631 SRX13404158 SRS11307154 SRA1343194 Huazhong Agricultural University|College of Fisheries Huazhong Agricultural University 2 0.91773 0.91812 0.11227 0.11178 0.6687 0.66931 0.47877 0.47805 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-14 Juvenile Juvenile Eye Sensory System
67573 67573 SRR17224784 SRX13404157 SRS11307154 SRP350669 PRJNA788440 Danio rerio Raw sequence reads PRJNA788440 Whole Genome Sequencing Danio rerio Raw sequence reads of eyes and skin         zebrafisheye   breed:AB|age:30days|sex:pooled male and female|tissue:eyes|BioSampleModel:Model organism or animal                 RNAseq of zebrafish eye wt 3 30dpf eye wt 3 30dpf RNAseq of eye     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP350669     eye_wt_3_30dpf.R1.fastq.gz eye_wt_3_30dpf.R2.fastq.gz fastq fastq 6665043964.0 22069682.0 eye wt 3 30dpf.R1.fastq.gz 0:151 1:151 A:1837907813;C:1496332954;G:1517206099;T:1813585697;N:11401 151 151     1837907813 1496332954 1517206099 1813585697 11401 SRX13404157 SRS11307154 SRA1343194 Huazhong Agricultural University|College of Fisheries Huazhong Agricultural University 2 0.92328 0.92376 0.11972 0.11905 0.69002 0.69039 0.48654 0.48588 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-14 Juvenile Juvenile Eye Sensory System
67574 67574 SRR17224785 SRX13404156 SRS11307154 SRP350669 PRJNA788440 Danio rerio Raw sequence reads PRJNA788440 Whole Genome Sequencing Danio rerio Raw sequence reads of eyes and skin         zebrafisheye   breed:AB|age:30days|sex:pooled male and female|tissue:eyes|BioSampleModel:Model organism or animal                 RNAseq of zebrafish eye wt 2 30dpf eye wt 2 30dpf RNAseq of eye     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP350669     eye_wt_2_30dpf.R1.fastq.gz eye_wt_2_30dpf.R2.fastq.gz fastq fastq 7313252536.0 24216068.0 eye wt 2 30dpf.R1.fastq.gz 0:151 1:151 A:2005760880;C:1644712229;G:1691008059;T:1971759242;N:12126 151 151     2005760880 1644712229 1691008059 1971759242 12126 SRX13404156 SRS11307154 SRA1343194 Huazhong Agricultural University|College of Fisheries Huazhong Agricultural University 2 0.92458 0.92267 0.11276 0.11098 0.68834 0.6939 0.48994 0.48977 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-14 Juvenile Juvenile Eye Sensory System
67575 67575 SRR17224786 SRX13404155 SRS11307154 SRP350669 PRJNA788440 Danio rerio Raw sequence reads PRJNA788440 Whole Genome Sequencing Danio rerio Raw sequence reads of eyes and skin         zebrafisheye   breed:AB|age:30days|sex:pooled male and female|tissue:eyes|BioSampleModel:Model organism or animal                 RNAseq of zebrafish eye wt 1 30dpf eye wt 1 30dpf RNAseq of eye     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP350669     eye_wt_1_30dpf.R1.fastq.gz eye_wt_1_30dpf.R2.fastq.gz fastq fastq 7374231470.0 24417985.0 eye wt 1 30dpf.R1.fastq.gz 0:151 1:151 A:2032283041;C:1657026689;G:1681898985;T:2003011689;N:11066 151 151     2032283041 1657026689 1681898985 2003011689 11066 SRX13404155 SRS11307154 SRA1343194 Huazhong Agricultural University|College of Fisheries Huazhong Agricultural University 2 0.92217 0.92217 0.11433 0.11344 0.69045 0.69087 0.48935 0.47534 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-14 Juvenile Juvenile Eye Sensory System
67580 67580 SRR17224791 SRX13404150 SRS11307154 SRP350669 PRJNA788440 Danio rerio Raw sequence reads PRJNA788440 Whole Genome Sequencing Danio rerio Raw sequence reads of eyes and skin         zebrafisheye   breed:AB|age:30days|sex:pooled male and female|tissue:eyes|BioSampleModel:Model organism or animal                 RNAseq of zebrafish eye mut 3 30dpf eye mut 3 30dpf RNAseq of eye     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP350669     eye_mut_3_30dpf.R1.fastq.gz eye_mut_3_30dpf.R2.fastq.gz fastq fastq 7370863566.0 24406833.0 eye mut 3 30dpf.R1.fastq.gz 0:151 1:151 A:2035593457;C:1650415961;G:1678944830;T:2005897248;N:12070 151 151     2035593457 1650415961 1678944830 2005897248 12070 SRX13404150 SRS11307154 SRA1343194 Huazhong Agricultural University|College of Fisheries Huazhong Agricultural University 2 0.9169 0.91717 0.11546 0.11616 0.66249 0.66312 0.47895 0.47697 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-14 Juvenile Juvenile Eye Sensory System
67581 67581 SRR17224792 SRX13404149 SRS11307154 SRP350669 PRJNA788440 Danio rerio Raw sequence reads PRJNA788440 Whole Genome Sequencing Danio rerio Raw sequence reads of eyes and skin         zebrafisheye   breed:AB|age:30days|sex:pooled male and female|tissue:eyes|BioSampleModel:Model organism or animal                 RNAseq of zebrafish eye mut 2 30dpf eye mut 2 30dpf RNAseq of eye     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP350669     eye_mut_2_30dpf.R1.fastq.gz eye_mut_2_30dpf.R2.fastq.gz fastq fastq 6025971496.0 19953548.0 eye mut 2 30dpf.R1.fastq.gz 0:151 1:151 A:1659612510;C:1355527081;G:1377376165;T:1633446020;N:9720 151 151     1659612510 1355527081 1377376165 1633446020 9720 SRX13404149 SRS11307154 SRA1343194 Huazhong Agricultural University|College of Fisheries Huazhong Agricultural University 2 0.91909 0.92042 0.11187 0.11181 0.66884 0.66985 0.48856 0.49166 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-14 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");;