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run_metadata

4 rows where experiment.library_selection = "size fractionation", experiment.library_strategy = "RNA-Seq" and tissue_curation_coarse = "Digestive System"

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tissue_curation_coarse 1

  • Digestive System · 4 ✖

tissue_curation 1

technology 1

experiment.platform 1

experiment.library_strategy 1

  • RNA-Seq · 4 ✖

experiment.library_source 1

experiment.library_selection 1

  • size fractionation · 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
32923 32923 SRR29498567 SRX25008885 SRS21709104 SRP515416 PRJNA1127032 Zebrafish Tissue Mid Range RNA Sequencing PRJNA1127032 Other This project sequenced mid size ranged RNA from zebrafish liver brain and gut tissues using male and female parallel samples.         F2g   strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:female|tissue:gut|identifier:F2g|BioSampleModel:Model organism or animal                 midRNA seq Danio rerio 10 10 Total RNA was extracted from different zebrafish tissues using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina NovaSeq 6000   SRP515416     F2g_R2.fq.gz F2g_R1.fq.gz fastq fastq 9101949000.0 30339830.0 F2g R1.fq.gz 0:150 1:150 A:2052853923;C:2394247721;G:2773304460;T:1881440199;N:102697 150 150     2052853923 2394247721 2773304460 1881440199 102697 SRX25008885 SRS21709104 SRA1905460 Eotvos Lorand University|Genetics Eotvos Lorand University 2 0.65449 0.37434 0.04313 0.12258 0.99519 0.99527 0.61425 0.56139 150 150 B B mate2-mate1 similar by mapping diff illumina novaseq_era unknown size_fractionation unknown bulk unknown unknown   Hungary 2024-06-22 Adult Adult Gut Digestive System
32924 32924 SRR29498568 SRX25008884 SRS21709103 SRP515416 PRJNA1127032 Zebrafish Tissue Mid Range RNA Sequencing PRJNA1127032 Other This project sequenced mid size ranged RNA from zebrafish liver brain and gut tissues using male and female parallel samples.         F1g   strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:female|tissue:gut|identifier:F1g|BioSampleModel:Model organism or animal                 midRNA seq Danio rerio 09 09 Total RNA was extracted from different zebrafish tissues using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina NovaSeq 6000   SRP515416     F1g_R1.fq.gz F1g_R2.fq.gz fastq fastq 8132653500.0 27108845.0 F1g R1.fq.gz 0:150 1:150 A:1811779602;C:2095863397;G:2529881799;T:1695036688;N:92014 150 150     1811779602 2095863397 2529881799 1695036688 92014 SRX25008884 SRS21709103 SRA1905460 Eotvos Lorand University|Genetics Eotvos Lorand University 2 0.53909 0.24181 0.01966 0.04797 0.99598 0.99624 0.59302 0.62038 150 150 B B mate2-mate1 similar by mapping diff illumina novaseq_era unknown size_fractionation unknown bulk unknown unknown   Hungary 2024-06-22 Adult Adult Gut Digestive System
32931 32931 SRR29498575 SRX25008877 SRS21709096 SRP515416 PRJNA1127032 Zebrafish Tissue Mid Range RNA Sequencing PRJNA1127032 Other This project sequenced mid size ranged RNA from zebrafish liver brain and gut tissues using male and female parallel samples.         M2g   strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:male|tissue:gut|identifier:M2g|BioSampleModel:Model organism or animal                 midRNA seq Danio rerio 12 12 Total RNA was extracted from different zebrafish tissues using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina NovaSeq 6000   SRP515416     M2g_R1.fq.gz M2g_R2.fq.gz fastq fastq 7106243100.0 23687477.0 M2g R1.fq.gz 0:150 1:150 A:1567154123;C:1866065312;G:2213286944;T:1459656676;N:80045 150 150     1567154123 1866065312 2213286944 1459656676 80045 SRX25008877 SRS21709096 SRA1905460 Eotvos Lorand University|Genetics Eotvos Lorand University 2 0.56476 0.25026 0.02259 0.04481 0.99667 0.99701 0.63277 0.65693 150 150 B B mate2-mate1 similar by mapping diff illumina novaseq_era unknown size_fractionation unknown bulk unknown unknown   Hungary 2024-06-22 Adult Adult Gut Digestive System
32932 32932 SRR29498576 SRX25008876 SRS21709095 SRP515416 PRJNA1127032 Zebrafish Tissue Mid Range RNA Sequencing PRJNA1127032 Other This project sequenced mid size ranged RNA from zebrafish liver brain and gut tissues using male and female parallel samples.         M1g   strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:male|tissue:gut|identifier:M1g|BioSampleModel:Model organism or animal                 midRNA seq Danio rerio 11 11 Total RNA was extracted from different zebrafish tissues using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina NovaSeq 6000   SRP515416     M1g_R2.fq.gz M1g_R1.fq.gz fastq fastq 7351182000.0 24503940.0 M1g R1.fq.gz 0:150 1:150 A:1623685246;C:1858847576;G:2315396486;T:1553169371;N:83321 150 150     1623685246 1858847576 2315396486 1553169371 83321 SRX25008876 SRS21709095 SRA1905460 Eotvos Lorand University|Genetics Eotvos Lorand University 2 0.96004 0.21521 0.16113 0.04578 0.92431 0.99143 0.61867 0.63432 150 150 B T mate2 technical by mapping diff illumina novaseq_era unknown size_fractionation unknown bulk unknown unknown   Hungary 2024-06-22 Adult Adult Gut Digestive 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");;