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run_metadata

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

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tissue_curation_coarse 1

tissue_curation 1

  • Brain · 6 ✖

technology 1

experiment.platform 1

experiment.library_strategy 1

  • RNA-Seq · 6 ✖

experiment.library_source 1

experiment.library_selection 1

  • size fractionation · 6 ✖

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
32926 32926 SRR29498570 SRX25008882 SRS21709101 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.         M2b   strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:male|tissue:brain|identifier:M2b|BioSampleModel:Model organism or animal                 midRNA seq Danio rerio 07 07 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     M2b_R1.fq.gz M2b_R2.fq.gz fastq fastq 9324874800.0 31082916.0 M2b R1.fq.gz 0:150 1:150 A:2073617286;C:2382074775;G:2948687855;T:1920389281;N:105603 150 150     2073617286 2382074775 2948687855 1920389281 105603 SRX25008882 SRS21709101 SRA1905460 Eotvos Lorand University|Genetics Eotvos Lorand University 2 0.57388 0.29571 0.04187 0.10168 0.99506 0.99513 0.61677 0.60641 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 Brain Nervous System
32928 32928 SRR29498572 SRX25008880 SRS21709099 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.         M1b   strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:male|tissue:brain|identifier:M1b|BioSampleModel:Model organism or animal                 midRNA seq Danio rerio 05 05 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     M1b_R1.fq.gz M1b_R2.fq.gz fastq fastq 7947472800.0 26491576.0 M1b R1.fq.gz 0:150 1:150 A:1764190500;C:1937842699;G:2595509352;T:1649839967;N:90282 150 150     1764190500 1937842699 2595509352 1649839967 90282 SRX25008880 SRS21709099 SRA1905460 Eotvos Lorand University|Genetics Eotvos Lorand University 2 0.96542 0.21476 0.17288 0.05982 0.97289 0.99711 0.57845 0.611 150 150 B T mate2 technical by mapping diff illumina novaseq_era unknown size_fractionation unknown bulk unknown unknown   Hungary 2024-06-22 Adult Adult Brain Nervous System
32930 32930 SRR29498574 SRX25008878 SRS21709097 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.         F2b   strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:female|tissue:brain|identifier:F2b|BioSampleModel:Model organism or animal                 midRNA seq Danio rerio 03 03 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     F2b_R1.fq.gz F2b_R2.fq.gz fastq fastq 9249410100.0 30831367.0 F2b R1.fq.gz 0:150 1:150 A:2101671138;C:2272479255;G:2931272789;T:1943881150;N:105768 150 150     2101671138 2272479255 2931272789 1943881150 105768 SRX25008878 SRS21709097 SRA1905460 Eotvos Lorand University|Genetics Eotvos Lorand University 2 0.96654 0.19343 0.23127 0.08081 0.95272 0.99326 0.63762 0.64901 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 Brain Nervous System
32934 32934 SRR29498578 SRX25008874 SRS21709093 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.         F1b   strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:female|tissue:brain|identifier:F1b|BioSampleModel:Model organism or animal                 midRNA seq Danio rerio 01 01 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     F1b_R2.fq.gz F1b_R1.fq.gz fastq fastq 7995852300.0 26652841.0 F1b R1.fq.gz 0:150 1:150 A:1744452113;C:2053788787;G:2580416325;T:1617104387;N:90688 150 150     1744452113 2053788787 2580416325 1617104387 90688 SRX25008874 SRS21709093 SRA1905460 Eotvos Lorand University|Genetics Eotvos Lorand University 2 0.96107 0.17798 0.16452 0.02921 0.96759 0.99677 0.66455 0.62672 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 Brain Nervous System
48625 48625 SRR7280652 SRX4184230 SRS3395609 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       Telencephalon Brain Telenc   strain:AB|age:adult|sex:pooled male and female|tissue:Telencephalon|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: telencephalon Brain Telenc Brain Telenc RNA from dissociated telencephalons of males and females     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 2500   SRP149913     Brain_Telenc_R1-125.fq.gz Brain_Telenc_R2-125.fq.gz fastq fastq 71366993000.0 285467972.0 Brain Telenc R1 125.fq.gz 0:125 1:125 A:19965884492;C:15794543428;G:15865015134;T:19703234174;N:38315772 125 125     19965884492 15794543428 15865015134 19703234174 38315772 SRX4184230 SRS3395609 SRA717220 Centre for Genomic Regulation|Systems Biology Department Centre for Genomic Regulation 2 0.94146 0.94273 0.14194 0.14162 0.70167 0.70396 0.52125 0.51616 125 125 B B biological fallback assumption illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Spain 2019-01-22 Adult Adult Brain Nervous System
48626 48626 SRR7280653 SRX4184229 SRS3395610 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       Cerebellum Cerebellum   strain:AB|age:adult|sex:pooled male and female|tissue:Cerebellum|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: cerebellum Cerebellum Cerebellum RNA from dissociated cerebellum from males and females     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 2500   SRP149913     Cerebellum_R1-125.fq.gz Cerebellum_R2-125.fq.gz fastq fastq 34135866750.0 136543467.0 Cerebellum R2 125.fq.gz 0:125 1:125 A:9659073468;C:7434102293;G:7478952142;T:9549216912;N:14521935 125 125     9659073468 7434102293 7478952142 9549216912 14521935 SRX4184229 SRS3395610 SRA717220 Centre for Genomic Regulation|Systems Biology Department Centre for Genomic Regulation 2 0.93517 0.93417 0.16496 0.16457 0.73695 0.73476 0.47363 0.48287 125 125 B B biological fallback assumption illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Spain 2019-01-22 Adult Adult Brain Nervous 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");;