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run_metadata

3 rows where experiment.library_selection = "RANDOM", experiment.platform = "ILLUMINA" and tissue_curation_coarse = "Cardiovascular System"

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tissue_curation_coarse 1

  • Cardiovascular System · 3 ✖

tissue_curation 1

technology 1

experiment.platform 1

  • ILLUMINA · 3 ✖

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • RANDOM · 3 ✖

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
37107 37107 SRR891495 SRX298188 SRS673878 SRP024369 PRJNA207719 Tissue specific transcriptome profiling of zebrafish PRJNA207719 Other Tissue specific transcriptome profiling of zebrafish.         Danio rerio heart   sex:missing|strain:wild type|tissue:heart|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 Danio rerio Transcriptome of zebrafish Danio rerio heart Zebrafish heart mRNA sequencing via poly A enrichment using poly A beads Illumina mRNA seq protocol     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     lane1_NoIndex_L001_R1_cat.fastq lane1_NoIndex_L001_R2_cat.fastq fastq fastq 2757807456.0 27037328.0 Transcriptome of zebrafish Danio rerio heart 0:51 1:51 A:685519386;C:693864326;G:733553235;T:643916122;N:954387 51 51     685519386 693864326 733553235 643916122 954387 SRX298188 SRS673878 SRA089174 CSIR-IGIB CSIR-Institute of Genomics and Integrative Biology CSIR-Institute of Genomics and Integrative Biology 2 0.789 0.79038 0.05666 0.05598 0.76982 0.77441 0.45627 0.46617 51 51 B B biological fallback assumption illumina early_illumina unknown random_priming unknown bulk unknown unknown   India 2013-10-10 Adult Adult Heart Cardiovascular System
39857 39857 SRR2293665 SRX1158743 SRS1039790 SRP062585 PRJNA293269 Danio rerio bigheart mutant transcriptome PRJNA293269 Whole Genome Sequencing Zebrafish cardiac transcriptome of big heart mutant. The Bigheart mutant is generated by random mutagenesis in zebrafish ASWT strain by using gene breaking trap GBT PX vector       Bigheart mutant cardiac transcriptome from Danio rerio Bigheart   breed:ASWT|age:Adult|sex:pooled male and female|tissue:Heart|biomaterial provider:CSIR IGIB|disease:Cardiac hypertrophy|geo loc name:India|BioSampleModel:Model organism or animal                 zebrafish Bigheart homozygous cardiac mutant Bigheart homozygous cardiac mutant Bigheart homozygous Truseq RNA seq with ribozero gold     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062585     ZF_24F_homo_ATGTCA_R1_cat.fastq.gz ZF_24F_homo_ATGTCA_R2_cat.fastq.gz fastq fastq 3375458178.0 16710189.0 Zebrafish bigheart homozygous mutant cardiac transcriptome 0:101 1:101 A:914068294;C:764700320;G:768182746;T:927976744;N:530074 101 101     914068294 764700320 768182746 927976744 530074 SRX1158743 SRS1039790 SRA290009 CSIR-IGIB CSIR- Institute of Genomics and Integrative Biology 2 0.90592 0.90808 0.24934 0.24544 0.73206 0.73316 0.50089 0.50209 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming ribozero bulk unknown unknown   India 2016-08-19 Adult Adult Heart Cardiovascular System
39858 39858 SRR2293664 SRX1158742 SRS1039790 SRP062585 PRJNA293269 Danio rerio bigheart mutant transcriptome PRJNA293269 Whole Genome Sequencing Zebrafish cardiac transcriptome of big heart mutant. The Bigheart mutant is generated by random mutagenesis in zebrafish ASWT strain by using gene breaking trap GBT PX vector       Bigheart mutant cardiac transcriptome from Danio rerio Bigheart   breed:ASWT|age:Adult|sex:pooled male and female|tissue:Heart|biomaterial provider:CSIR IGIB|disease:Cardiac hypertrophy|geo loc name:India|BioSampleModel:Model organism or animal                 ZEBRAFISH Bigheart hetrozygous cardiac transcriptome Bigheart hetrozygous cardiac transcriptome Bigheart heterozygous Truseq RNA seq with robozero gold     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062585     ZF_24F_hetero_CCGTCC_R2_cat.fastq.gz ZF_24F_hetero_CCGTCC_R1_cat.fastq.gz fastq fastq 17775105746.0 87995573.0 Transcriptome of zebrafish Bigheart heterozygous mutant cardiac transcriptome 0:101 1:101 A:4910552704;C:3934124661;G:3958965970;T:4968643725;N:2818686 101 101     4910552704 3934124661 3958965970 4968643725 2818686 SRX1158742 SRS1039790 SRA290009 CSIR-IGIB CSIR- Institute of Genomics and Integrative Biology 2 0.89569 0.89916 0.30152 0.30176 0.73598 0.73641 0.4892 0.49332 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   India 2016-08-19 Adult Adult Heart Cardiovascular 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");;