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run_metadata

4 rows where experiment.library_selection = "other", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation = "Fin"

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tissue_curation_coarse 1

tissue_curation 1

technology 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

  • TRANSCRIPTOMIC · 4 ✖

experiment.library_selection 1

  • other · 4 ✖

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
36617 36617 SRR941753 SRX326770 SRS463196 SRP027598 PRJNA187413 Danio rerio strain:EK Transcriptome or Gene expression PRJNA187413 Transcriptome Analysis Gene expression across the anteroposterior axis of the zebrafish pectoral fin.     tissue comprising posterior most 2 fin rays Posterior pectoral fin replicate 2 Pos2   strain:EK|isolate:4|age:6 Month|sex:female                 RNA seq posterior pectoral fin replicate 2 Pectoral Posterior 2 1 1     RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP027598     Pos_R2.fastq fastq 2119489050.0 42389781.0 Pos R2 0:50 A:551122430;C:507870866;G:499494183;T:555469321;N:5532250 50       551122430 507870866 499494183 555469321 5532250 SRX326770 SRS463196 SRA065677 Duke Cell Biology|Poss Poss Lab, Duke Cell Biology 1 0.90238   0.08924   0.71303   0.43405   50   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   United States 2013-07-19 Adult Adult Fin Surface Structure
36618 36618 SRR941754 SRX326769 SRS463195 SRP027598 PRJNA187413 Danio rerio strain:EK Transcriptome or Gene expression PRJNA187413 Transcriptome Analysis Gene expression across the anteroposterior axis of the zebrafish pectoral fin.     tissue comprising posterior most 2 fin rays Posterior pectoral fin replicate 1 Pos1   strain:EK|isolate:3|age:6 Month|sex:female                 RNA seq posterior pectoral fin replicate 1 Pectoral Fin Posterior 1 1 1     RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP027598         1839141950.0 36782839.0 Pos R1 0:50 A:461313296;C:455413049;G:451484067;T:466101993;N:4829545 50       461313296 455413049 451484067 466101993 4829545 SRX326769 SRS463195 SRA065677 Duke Cell Biology|Poss Poss Lab, Duke Cell Biology 1 0.91205   0.06923   0.71656   0.42651   50   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   United States 2013-07-19 Adult Adult Fin Surface Structure
36619 36619 SRR941751 SRX326756 SRS463187 SRP027598 PRJNA187413 Danio rerio strain:EK Transcriptome or Gene expression PRJNA187413 Transcriptome Analysis Gene expression across the anteroposterior axis of the zebrafish pectoral fin.     tissue comprising anterior most 2 fin rays Anterior pectoral fin replicate 2 Ant2   strain:EK|isolate:2|age:6 Month|sex:female                 RNA seq anterior pectoral fin replicate 2 Pectoral Fin Anterior 2 1 1     RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP027598     Ant_R2.fastq fastq 2146396250.0 42927925.0 Ant R2 0:50 A:562140204;C:509390346;G:501995610;T:567232459;N:5637631 50       562140204 509390346 501995610 567232459 5637631 SRX326756 SRS463187 SRA065677 Duke Cell Biology|Poss Poss Lab, Duke Cell Biology 1 0.89956   0.09279   0.70997   0.44847   50   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   United States 2013-07-19 Adult Adult Fin Surface Structure
36620 36620 SRR941749 SRX326754 SRS463185 SRP027598 PRJNA187413 Danio rerio strain:EK Transcriptome or Gene expression PRJNA187413 Transcriptome Analysis Gene expression across the anteroposterior axis of the zebrafish pectoral fin.     tissue comprising anterior most 2 fin rays Anterior pectoral fin replicate 1 Ant1   strain:EK|isolate:1|age:6 Month|sex:female                 RNA seq anterior pectoral fin replicate 1 Pectoral Fin Anterior 1 1 1     RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP027598     Ant_R1.fastq fastq 2178096950.0 43561939.0 Ant R1 0:50 A:568580441;C:517705965;G:509551928;T:576519788;N:5738828 50       568580441 517705965 509551928 576519788 5738828 SRX326754 SRS463185 SRA065677 Duke Cell Biology|Poss Poss Lab, Duke Cell Biology 1 0.89833   0.08959   0.71494   0.44088   50   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   United States 2013-07-19 Adult Adult Fin 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");;