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run_metadata

3 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "unspecified" 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

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • unspecified · 3 ✖

experiment.library_layout 1

  • PAIRED · 3 ✖

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
39824 39824 SRR2168748 SRX1153634 SRS1036568 SRP062468 PRJNA293022 Danio rerio heart chamber specific transcriptome PRJNA293022 Whole Genome Sequencing Chamber specific transcriptome of zebrafish namely atrium ventricle and bulbus arteriosus         ASWT Heart chamber transcriptome   breed:ASWT|age:2 years|dev stage:Adult|sex:not applicable|tissue:Heart Chambers|BioSampleModel:Model organism or animal                 Zebrafish ASWT heart bulbus arteriosus transcriptome Zebrafish bulbus arteriosus Bulbus arteriosus 1     RNA-Seq TRANSCRIPTOMIC unspecified 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> SRP062468     ZFBulbouse_cat_R1.fastq.gz ZFBulbouse_cat_R2.fastq.gz fastq fastq 31137941450.0 154148225.0 Zebrafish bulbus arteriosus 0:101 1:101 A:8841038901;C:6663109706;G:6831238323;T:8799856408;N:2698112 101 101     8841038901 6663109706 6831238323 8799856408 2698112 SRX1153634 SRS1036568 SRA289351 CSIR-IGIB CSIR- Institute of Genomics and Integrative Biology 2 0.81876 0.77794 0.54672 0.51003 0.7162 0.72752 0.54114 0.5421 101 101 B B biological fallback assumption illumina hiseq_era unknown unknown unknown bulk unknown unknown   India 2016-03-01 Adult Adult Heart Cardiovascular System
39825 39825 SRR2168740 SRX1153633 SRS1036568 SRP062468 PRJNA293022 Danio rerio heart chamber specific transcriptome PRJNA293022 Whole Genome Sequencing Chamber specific transcriptome of zebrafish namely atrium ventricle and bulbus arteriosus         ASWT Heart chamber transcriptome   breed:ASWT|age:2 years|dev stage:Adult|sex:not applicable|tissue:Heart Chambers|BioSampleModel:Model organism or animal                 Zebrafish ASWT atrium specific transcriptome Zebrafish Atrium Atrium 1     RNA-Seq TRANSCRIPTOMIC unspecified 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> SRP062468     ZFAtrium_GTGAAA_L006_cat_R2.fastq.gz ZFAtrium_GTGAAA_L006_cat_R1.fastq.gz fastq fastq 28208507150.0 139646075.0 Zebrafish Atrium 0:101 1:101 A:8151737615;C:5894384726;G:6027846905;T:8129189369;N:5348535 101 101     8151737615 5894384726 6027846905 8129189369 5348535 SRX1153633 SRS1036568 SRA289351 CSIR-IGIB CSIR- Institute of Genomics and Integrative Biology 2 0.83701 0.79433 0.58576 0.54496 0.72486 0.73766 0.55105 0.54713 101 101 B B biological fallback assumption illumina hiseq_era unknown unknown unknown bulk unknown unknown   India 2015-09-08 Adult Adult Heart Cardiovascular System
39826 39826 SRR2168750 SRX1153632 SRS1036568 SRP062468 PRJNA293022 Danio rerio heart chamber specific transcriptome PRJNA293022 Whole Genome Sequencing Chamber specific transcriptome of zebrafish namely atrium ventricle and bulbus arteriosus         ASWT Heart chamber transcriptome   breed:ASWT|age:2 years|dev stage:Adult|sex:not applicable|tissue:Heart Chambers|BioSampleModel:Model organism or animal                 Zebrafish Ventricle chamber specific transcriptome Zebrafish Ventricle chamber specific transcriptome Ventricle 1     RNA-Seq TRANSCRIPTOMIC unspecified 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> SRP062468     ZFVentricle_cat_R2.fastq.gz ZFVentricle_cat_R1.fastq.gz fastq fastq 30913187362.0 153035581.0 Zebrafish Ventricle chamber specific transcriptome 0:101 1:101 A:8230747947;C:7230918780;G:7381253230;T:8066864305;N:3403100 101 101     8230747947 7230918780 7381253230 8066864305 3403100 SRX1153632 SRS1036568 SRA289351 CSIR-IGIB CSIR- Institute of Genomics and Integrative Biology 2 0.92213 0.91404 0.22257 0.21715 0.76761 0.77193 0.54625 0.54332 101 101 B B biological fallback assumption illumina hiseq_era unknown unknown unknown bulk unknown unknown   India 2016-03-01 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");;