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run_metadata

6 rows where experiment.library_selection = "RANDOM", technology = "unknown" and tissue_curation = "Muscle"

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experiment.platform 2

tissue_curation_coarse 1

tissue_curation 1

  • Muscle · 6 ✖

technology 1

  • unknown · 6 ✖

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • RANDOM · 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
37105 37105 SRR891510 SRX298190 SRS673880 SRP024369 PRJNA207719 Tissue specific transcriptome profiling of zebrafish PRJNA207719 Other Tissue specific transcriptome profiling of zebrafish.         Danio rerio muscle   sex:missing|strain:wild type|tissue:muscle|health state:normal|collection date:2013|geo loc name:India|biomaterial provider:CSIR Institute of Genomics and Integrative Biology|age:adult|BioSampleModel:Model organism or animal                 Tissue specific transcriptome of zebrafish Transcriptome of zebrafish Danio rerio muscle zebrafish muscle 1     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP024369     lane4_NoIndex_L004_R1_cat.fastq lane4_NoIndex_L004_R2_cat.fastq fastq fastq 1895673468.0 18585034.0 Transcriptome of zebrafish Danio rerio muscle 0:51 1:51 A:461627994;C:495899684;G:489490468;T:448396921;N:258401 51 51     461627994 495899684 489490468 448396921 258401 SRX298190 SRS673880 SRA089174 CSIR-IGIB CSIR-Institute of Genomics and Integrative Biology CSIR-Institute of Genomics and Integrative Biology 2 0.90619 0.93507 0.0338 0.03473 0.79267 0.78683 0.45256 0.45438 51 51 B B biological fallback assumption illumina early_illumina unknown random_priming unknown bulk unknown unknown   India 2013-10-10 Adult Adult Muscle Muscular System
55987 55987 SRR10895893 SRX7564586 SRS6001801 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 006   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Muscle|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100103858 L02 11 CL100103858 L02 11       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100103858_L02_517_1.fq.gz CL100103858_L02_517_2.fq.gz fastq fastq 8506603800.0 85066038.0 CL100103858 L02 517 1.fq.gz 0:100 1:100 A:2292801692;C:1923556878;G:1974694874;T:2303714790;N:11835566 100 100     2292801692 1923556878 1974694874 2303714790 11835566 SRX7564586 SRS6001801 SRA1026516 BGI|BGI-Research BGI 1 0.96138   0.03993   0.82976   0.64498   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Muscle Muscular System
55988 55988 SRR10895894 SRX7564585 SRS6001801 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 006   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Muscle|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100103858 L01 13 CL100103858 L01 13       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100103858_L01_514_2.fq.gz CL100103858_L01_514_1.fq.gz fastq fastq 7391075800.0 73910758.0 CL100103858 L01 514 1.fq.gz 0:100 1:100 A:1927614555;C:1731326620;G:1786947018;T:1932511997;N:12675610 100 100     1927614555 1731326620 1786947018 1932511997 12675610 SRX7564585 SRS6001801 SRA1026516 BGI|BGI-Research BGI 1 0.93702   0.04631   0.77985   0.53119   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Muscle Muscular System
55989 55989 SRR10895895 SRX7564584 SRS6001801 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 006   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Muscle|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100103858 L01 12 CL100103858 L01 12       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100103858_L01_515_1.fq.gz CL100103858_L01_515_2.fq.gz fastq fastq 8374057600.0 83740576.0 CL100103858 L01 515 1.fq.gz 0:100 1:100 A:2230542787;C:1917435448;G:1965561976;T:2246062032;N:14455357 100 100     2230542787 1917435448 1965561976 2246062032 14455357 SRX7564584 SRS6001801 SRA1026516 BGI|BGI-Research BGI 1 0.94954   0.04127   0.78589   0.61201   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Muscle Muscular System
55990 55990 SRR10895896 SRX7564583 SRS6001801 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 006   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Muscle|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100103858 L01 11 CL100103858 L01 11       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100103858_L01_516_1.fq.gz CL100103858_L01_516_2.fq.gz fastq fastq 7909115600.0 79091156.0 CL100103858 L01 516 1.fq.gz 0:100 1:100 A:2073091675;C:1842299453;G:1898493755;T:2081930446;N:13300271 100 100     2073091675 1842299453 1898493755 2081930446 13300271 SRX7564583 SRS6001801 SRA1026516 BGI|BGI-Research BGI 1 0.95755   0.02912   0.83483   0.61158   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Muscle Muscular System
55991 55991 SRR10895897 SRX7564582 SRS6001801 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 006   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Muscle|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100103858 L02 10 CL100103858 L02 10       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100103858_L02_518_1.fq.gz CL100103858_L02_518_2.fq.gz fastq fastq 9462489200.0 94624892.0 CL100103858 L02 518 1.fq.gz 0:100 1:100 A:2473166981;C:2213506014;G:2273238020;T:2489490295;N:13087890 100 100     2473166981 2213506014 2273238020 2489490295 13087890 SRX7564582 SRS6001801 SRA1026516 BGI|BGI-Research BGI 1 0.95581   0.04117   0.79784   0.53207   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Muscle Muscular 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");;