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run_metadata

4 rows where experiment.library_selection = "size fractionation", experiment.library_strategy = "RNA-Seq" and tissue_curation = "Liver"

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tissue_curation_coarse 1

tissue_curation 1

  • Liver · 4 ✖

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
32925 32925 SRR29498569 SRX25008883 SRS21709102 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.         M2l   strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:male|tissue:liver|identifier:M2l|BioSampleModel:Model organism or animal                 midRNA seq Danio rerio 08 08 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     M2l_R1.fq.gz M2l_R2.fq.gz fastq fastq 7733826600.0 25779422.0 M2l R1.fq.gz 0:150 1:150 A:1754773283;C:2022716836;G:2330439864;T:1625790112;N:106505 150 150     1754773283 2022716836 2330439864 1625790112 106505 SRX25008883 SRS21709102 SRA1905460 Eotvos Lorand University|Genetics Eotvos Lorand University 2 0.60941 0.31539 0.0377 0.09053 0.995 0.99478 0.50937 0.57123 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 Liver Liver and Biliary System
32927 32927 SRR29498571 SRX25008881 SRS21709100 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.         M1l   strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:male|tissue:liver|identifier:M1l|BioSampleModel:Model organism or animal                 midRNA seq Danio rerio 06 06 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     M1l_R2.fq.gz M1l_R1.fq.gz fastq fastq 8301268800.0 27670896.0 M1l R1.fq.gz 0:150 1:150 A:1856070257;C:2266693166;G:2413641098;T:1764769457;N:94822 150 150     1856070257 2266693166 2413641098 1764769457 94822 SRX25008881 SRS21709100 SRA1905460 Eotvos Lorand University|Genetics Eotvos Lorand University 2 0.8289 0.73852 0.21964 0.50932 0.99648 0.99701 0.57332 0.51129 150 150 B B biological fallback assumption illumina novaseq_era unknown size_fractionation unknown bulk unknown unknown   Hungary 2024-06-22 Adult Adult Liver Liver and Biliary System
32929 32929 SRR29498573 SRX25008879 SRS21709098 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.         F2l   strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:female|tissue:liver|identifier:F2l|BioSampleModel:Model organism or animal                 midRNA seq Danio rerio 04 04 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     F2l_R1.fq.gz F2l_R2.fq.gz fastq fastq 8701893900.0 29006313.0 F2l R1.fq.gz 0:150 1:150 A:1977580339;C:2299061131;G:2585058451;T:1840095650;N:98329 150 150     1977580339 2299061131 2585058451 1840095650 98329 SRX25008879 SRS21709098 SRA1905460 Eotvos Lorand University|Genetics Eotvos Lorand University 2 0.72425 0.57704 0.15111 0.37121 0.99744 0.99762 0.61161 0.55762 150 150 B B biological fallback assumption illumina novaseq_era unknown size_fractionation unknown bulk unknown unknown   Hungary 2024-06-22 Adult Adult Liver Liver and Biliary System
32933 32933 SRR29498577 SRX25008875 SRS21709094 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.         F1l   strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:female|tissue:liver|identifier:F1l|BioSampleModel:Model organism or animal                 midRNA seq Danio rerio 02 02 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     F1l_R2.fq.gz F1l_R1.fq.gz fastq fastq 4647564000.0 15491880.0 F1l R1.fq.gz 0:150 1:150 A:993332389;C:862184908;G:1814249126;T:977710185;N:87392 150 150     993332389 862184908 1814249126 977710185 87392 SRX25008875 SRS21709094 SRA1905460 Eotvos Lorand University|Genetics Eotvos Lorand University 2 0.88683 0.14922 0.24654 0.08178 0.9583 0.99819 0.70978 0.20254 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 Liver Liver and Biliary 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");;