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run_metadata

3 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "size fractionation" and tissue_curation_coarse = "Surface Structure"

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devstage_curation 3

tissue_curation_coarse 1

  • Surface Structure · 3 ✖

tissue_curation 1

technology 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • size fractionation · 3 ✖

experiment.library_layout 1

  • PAIRED · 3 ✖

devstage_curation_coarse 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
48627 48627 SRR7280654 SRX4184228 SRS3395608 SRP149913 PRJNA474911 Origin and Evolution of Neural Microexons PRJNA474911 Other Our study focuses on the origin of the neural microexon program.We discover that neural microexon programs are present in non vertebrate speciesand trace their origin to bilaterian ancestors through the emergenceof a previously uncharacterized "enhancer of microexon" eMIC protein domain     Pool of one hundred 2hpf embryos 2hpf embryos Embr 2hpf   strain:AB|dev stage:2hpf|sex:pooled male and female|tissue:whole body|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: 2hpf embryos Embr 2hpf Embr 2hpf RNA extracted from a pool of one hundred embryos     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 2500   SRP149913     Embr_2hpf_R2-125.fq.gz Embr_2hpf_R1-125.fq.gz fastq fastq 17109578000.0 68438312.0 Embr 2hpf R1 125.fq.gz 0:125 1:125 A:4536550134;C:4009266695;G:4076560218;T:4484964079;N:2236874 125 125     4536550134 4009266695 4076560218 4484964079 2236874 SRX4184228 SRS3395608 SRA717220 Centre for Genomic Regulation|Systems Biology Department Centre for Genomic Regulation 2 0.96221 0.96458 0.02765 0.02716 0.77116 0.77325 0.48649 0.4853 125 125 B B biological fallback assumption illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Spain 2019-01-22 Cleavage Embryo Trunk Surface Structure
48628 48628 SRR7280655 SRX4184227 SRS3395607 SRP149913 PRJNA474911 Origin and Evolution of Neural Microexons PRJNA474911 Other Our study focuses on the origin of the neural microexon program.We discover that neural microexon programs are present in non vertebrate speciesand trace their origin to bilaterian ancestors through the emergenceof a previously uncharacterized "enhancer of microexon" eMIC protein domain     Pool of one hundred 8hpf embryos 8hpf embryos Embr 8hpf   strain:AB|dev stage:8hpf|sex:pooled male and female|tissue:whole body|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: 8hpf embryos Embr 8hpf Embr 8hpf RNA extracted from a pool of one hundred embryos     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 2500   SRP149913     Embr_8hpf_R1-125.fq.gz Embr_8hpf_R2-125.fq.gz fastq fastq 20486524750.0 81946099.0 Embr 8hpf R2 125.fq.gz 0:125 1:125 A:5437735333;C:4808439456;G:4859422420;T:5377132981;N:3794560 125 125     5437735333 4808439456 4859422420 5377132981 3794560 SRX4184227 SRS3395607 SRA717220 Centre for Genomic Regulation|Systems Biology Department Centre for Genomic Regulation 2 0.96373 0.95763 0.07096 0.0702 0.75937 0.75866 0.48455 0.484 125 125 B B biological fallback assumption illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Spain 2019-01-22 Gastrula Embryo Trunk Surface Structure
48629 48629 SRR7280656 SRX4184226 SRS3395606 SRP149913 PRJNA474911 Origin and Evolution of Neural Microexons PRJNA474911 Other Our study focuses on the origin of the neural microexon program.We discover that neural microexon programs are present in non vertebrate speciesand trace their origin to bilaterian ancestors through the emergenceof a previously uncharacterized "enhancer of microexon" eMIC protein domain     Pool of one hundred 12hpf embryos 12hpf embryos Embr 12hpf   strain:AB|dev stage:12hpf|sex:pooled male and female|tissue:whole body|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: 12hpf embryos Embr 12hpf Embr 12hpf RNA extracted from a pool of one hundred embryos     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 2500   SRP149913     Embr_12hpf_R2-125.fq.gz Embr_12hpf_R1-125.fq.gz fastq fastq 22366284500.0 89465138.0 Embr 12hpf R1 125.fq.gz 0:125 1:125 A:5886492098;C:5284016845;G:5382041408;T:5809628253;N:4105896 125 125     5886492098 5284016845 5382041408 5809628253 4105896 SRX4184226 SRS3395606 SRA717220 Centre for Genomic Regulation|Systems Biology Department Centre for Genomic Regulation 2 0.96226 0.96763 0.06393 0.06451 0.74355 0.74472 0.48233 0.48387 125 125 B B biological fallback assumption illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Spain 2019-01-22 Segmentation Embryo Trunk 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");;