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run_metadata

5 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "RT-PCR" and tissue_curation = "Head"

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tissue_curation_coarse 1

tissue_curation 1

  • Head · 5 ✖

technology 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • RT-PCR · 5 ✖

experiment.library_layout 1

  • PAIRED · 5 ✖

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
52285 52285 SRR9077089 SRX5852368 SRS4776361 SRP198708 PRJNA543385 mRNA sequence of zebrafish head and body PRJNA543385 Other RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing       head1 mock s1   breed:zebrafish|dev stage:adult|sex:NA|tissue:head1|BioSampleModel:Model organism or animal                 head1 mock WC TC 041 WC TC 041 TRUEseq standardised protocol     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP198708     WC_TC_041_S8.R1.fastq.gz WC_TC_041_S8.R2.fastq.gz fastq fastq 5480620528.0 36056714.0 WC TC 041 S8.R1.fastq.gz 0:101 1:51 A:1456079218;C:1286879398;G:1250199115;T:1487095432;N:367365 101 51     1456079218 1286879398 1250199115 1487095432 367365 SRX5852368 SRS4776361 SRA887738 Southern University of Science and Technology|Department of Biology Southern University of Science and Technology 2 0.96102 0.95396 0.09057 0.09452 0.70285 0.70573 0.474 0.47396 101 51 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk unknown unknown   China 2019-10-08 Adult Adult Head Nervous System
52286 52286 SRR9077090 SRX5852367 SRS4776360 SRP198708 PRJNA543385 mRNA sequence of zebrafish head and body PRJNA543385 Other RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing       head1 control s2   breed:zebrafish|dev stage:adult|sex:NA|tissue:head2|BioSampleModel:Model organism or animal                 head1 control WC TC 042 WC TC 042 TRUEseq standardised protocol     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP198708     WC_TC_042_S9.R1.fastq.gz WC_TC_042_S9.R2.fastq.gz fastq fastq 5011160472.0 32968161.0 WC TC 042 S9.R1.fastq.gz 0:101 1:51 A:1328768028;C:1179737412;G:1141948263;T:1360371072;N:335697 101 51     1328768028 1179737412 1141948263 1360371072 335697 SRX5852367 SRS4776360 SRA887738 Southern University of Science and Technology|Department of Biology Southern University of Science and Technology 2 0.96134 0.95488 0.09183 0.09597 0.70203 0.70398 0.4719 0.46265 101 51 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk unknown unknown   China 2019-10-08 Adult Adult Head Nervous System
52287 52287 SRR9077091 SRX5852366 SRS4776359 SRP198708 PRJNA543385 mRNA sequence of zebrafish head and body PRJNA543385 Other RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing       head1 kd s3   breed:zebrafish|dev stage:adult|sex:NA|tissue:head3|BioSampleModel:Model organism or animal                 head1 kd WC TC 043 WC TC 043 TRUEseq standardised protocol     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP198708     WC_TC_043_S10.R1.fastq.gz WC_TC_043_S10.R2.fastq.gz fastq fastq 5709609744.0 37563222.0 WC TC 043 S10.R1.fastq.gz 0:101 1:51 A:1517831332;C:1339538042;G:1299421324;T:1552434811;N:384235 101 51     1517831332 1339538042 1299421324 1552434811 384235 SRX5852366 SRS4776359 SRA887738 Southern University of Science and Technology|Department of Biology Southern University of Science and Technology 2 0.95768 0.95177 0.10352 0.10892 0.69209 0.69556 0.4693 0.47272 101 51 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk unknown unknown   China 2019-10-08 Adult Adult Head Nervous System
52288 52288 SRR9077092 SRX5852365 SRS4776358 SRP198708 PRJNA543385 mRNA sequence of zebrafish head and body PRJNA543385 Other RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing       head1 kd+wt s4   breed:zebrafish|dev stage:adult|sex:NA|tissue:head4|BioSampleModel:Model organism or animal                 head1 kd+wt WC TC 044 WC TC 044 TRUEseq standardised protocol     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP198708     WC_TC_044_S11.R2.fastq.gz WC_TC_044_S11.R1.fastq.gz fastq fastq 4776327920.0 31423210.0 WC TC 044 S11.R1.fastq.gz 0:101 1:51 A:1272079335;C:1117051709;G:1087240750;T:1299640784;N:315342 101 51     1272079335 1117051709 1087240750 1299640784 315342 SRX5852365 SRS4776358 SRA887738 Southern University of Science and Technology|Department of Biology Southern University of Science and Technology 2 0.9572 0.95024 0.10519 0.11173 0.69412 0.69621 0.47948 0.46528 101 51 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk unknown unknown   China 2019-05-17 Adult Adult Head Nervous System
52292 52292 SRR9077096 SRX5852361 SRS4776354 SRP198708 PRJNA543385 mRNA sequence of zebrafish head and body PRJNA543385 Other RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing       head1 kd+mt s5   breed:zebrafish|dev stage:adult|sex:NA|tissue:head5|BioSampleModel:Model organism or animal                 head1 kd+mt WC TC 045 WC TC 045 TRUEseq standardised protocol     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP198708     WC_TC_045_S12.R1.fastq.gz WC_TC_045_S12.R2.fastq.gz fastq fastq 4914615696.0 32332998.0 WC TC 045 S12.R1.fastq.gz 0:101 1:51 A:1304784949;C:1154087581;G:1119502459;T:1335912697;N:328010 101 51     1304784949 1154087581 1119502459 1335912697 328010 SRX5852361 SRS4776354 SRA887738 Southern University of Science and Technology|Department of Biology Southern University of Science and Technology 2 0.95742 0.95094 0.10146 0.1069 0.69686 0.69978 0.47629 0.469 101 51 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk unknown unknown   China 2019-10-08 Adult Adult Head Nervous 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");;