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run_metadata

6 rows where experiment.library_selection = "PolyA", technology = "bulk" and tissue_curation_coarse = "Nervous System"

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tissue_curation_coarse 1

  • Nervous System · 6 ✖

tissue_curation 1

technology 1

  • bulk · 6 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • PolyA · 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
34192 34192 SRR31443228 SRX26812023 SRS23296672 SRP546978 PRJNA1189474 Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf PRJNA1189474 Other The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses Total RNA was isolated for sequencing at 3 dpf         srrm4[y712] mutant replicate 3   strain:Tpfel long fin|age:3 dpf|collection date:2022 02|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous mutant|Replicate:mutant 3|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae srrm4[y712] mutant replicate 3 srrm4[y712] mutant replicate 3 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP546978   assembly:GRCz11 25938_mut3.pass2Aligned.sortedByCoord.out.bam bam 23466336192.0 117587529.0 25938 mut3.pass2Aligned.sortedByCoord.out.bam 0:100.13 1:100.08 A:6298034402;C:5433884683;G:5344985734;T:6388443446;N:987927 100 100     6298034402 5433884683 5344985734 6388443446 987927 SRX26812023 SRS23296672 SRA2019780 Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology Eunice Kennedy Shriver National Institute of Child Health and Human Development 2 0.95864 0.95894 0.10681 0.1052 0.65385 0.65403 0.46511 0.46252 99 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk bulk bulk   United States 2024-11-22 Larval Larval Head Nervous System
34193 34193 SRR31443229 SRX26812022 SRS23296671 SRP546978 PRJNA1189474 Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf PRJNA1189474 Other The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses Total RNA was isolated for sequencing at 3 dpf         srrm4[y712] wild type replicate 3   strain:Tpfel long fin|age:3 dpf|collection date:2022 02|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous wild type|Replicate:wild type 3|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae srrm4[y712] wild type replicate 3 srrm4[y712] wild type replicate 3 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP546978   assembly:GRCz11 25938_wt3.pass2Aligned.sortedByCoord.out.bam bam 23979171134.0 120156039.0 25938 wt3.pass2Aligned.sortedByCoord.out.bam 0:100.12 1:100.07 A:6398807397;C:5589997524;G:5503127729;T:6486232627;N:1005857 100 100     6398807397 5589997524 5503127729 6486232627 1005857 SRX26812022 SRS23296671 SRA2019780 Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology Eunice Kennedy Shriver National Institute of Child Health and Human Development 2 0.95941 0.96004 0.10323 0.10191 0.65451 0.6532 0.46396 0.46398 101 100 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk bulk bulk   United States 2024-11-22 Larval Larval Head Nervous System
34194 34194 SRR31443230 SRX26812021 SRS23296670 SRP546978 PRJNA1189474 Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf PRJNA1189474 Other The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses Total RNA was isolated for sequencing at 3 dpf         srrm4[y712] mutant replicate 2   strain:Tpfel long fin|age:3 dpf|collection date:2022 02|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous mutant|Replicate:mutant 2|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae srrm4[y712] mutant replicate 2 srrm4[y712] mutant replicate 2 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP546978   assembly:GRCz11 25938_mut2.pass2Aligned.sortedByCoord.out.bam bam 20256127500.0 101792067.0 25938 mut2.pass2Aligned.sortedByCoord.out.bam 0:100.05 1:100.00 A:5435798119;C:4683997479;G:4650293108;T:5485187428;N:851366 100 100     5435798119 4683997479 4650293108 5485187428 851366 SRX26812021 SRS23296670 SRA2019780 Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology Eunice Kennedy Shriver National Institute of Child Health and Human Development 2 0.96008 0.96049 0.10232 0.10156 0.66072 0.65932 0.4668 0.46817 95 95 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk bulk bulk   United States 2024-11-22 Larval Larval Head Nervous System
34195 34195 SRR31443231 SRX26812020 SRS23296669 SRP546978 PRJNA1189474 Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf PRJNA1189474 Other The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses Total RNA was isolated for sequencing at 3 dpf         srrm4[y712] wild type replicate 2   strain:Tpfel long fin|age:3 dpf|collection date:2022 02|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous wild type|Replicate:wild type 2|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae srrm4[y712] wild type replicate 2 srrm4[y712] wild type replicate 2 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP546978   assembly:GRCz11 25938_wt2.pass2Aligned.sortedByCoord.out.bam bam 22698373371.0 113599687.0 25938 wt2.pass2Aligned.sortedByCoord.out.bam 0:100.18 1:100.12 A:6063922145;C:5275724786;G:5212055837;T:6145709475;N:961128 100 100     6063922145 5275724786 5212055837 6145709475 961128 SRX26812020 SRS23296669 SRA2019780 Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology Eunice Kennedy Shriver National Institute of Child Health and Human Development 2 0.96129 0.96063 0.1003 0.09861 0.65744 0.65748 0.46167 0.46817 98 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk bulk bulk   United States 2024-11-22 Larval Larval Head Nervous System
34196 34196 SRR31443232 SRX26812019 SRS23296667 SRP546978 PRJNA1189474 Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf PRJNA1189474 Other The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses Total RNA was isolated for sequencing at 3 dpf         srrm4[y712] mutant replicate 1   strain:Tpfel long fin|age:3 dpf|collection date:2021 06|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous mutant|Replicate:mutant 1|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae srrm4[y712] mutant replicate 1 srrm4[y712] mutant replicate 1 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP546978   assembly:GRCz11 25938_mut.pass2Aligned.sortedByCoord.out.bam bam 11282501509.0 56702666.0 25938 mut.pass2Aligned.sortedByCoord.out.bam 0:99.65 1:99.55 A:2764745971;C:2868447715;G:2856237429;T:2792914545;N:155849 99 99     2764745971 2868447715 2856237429 2792914545 155849 SRX26812019 SRS23296667 SRA2019780 Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology Eunice Kennedy Shriver National Institute of Child Health and Human Development                       B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk bulk bulk   United States 2024-11-22 Larval Larval Head Nervous System
34197 34197 SRR31443233 SRX26812018 SRS23296668 SRP546978 PRJNA1189474 Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf PRJNA1189474 Other The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses Total RNA was isolated for sequencing at 3 dpf         srrm4[y712] wild type replicate 1   strain:Tpfel long fin|age:3 dpf|collection date:2021 06|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous wild type|Replicate:wild type 1|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae srrm4[y712] wild type replicate 1 srrm4[y712] wild type replicate 1 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP546978   assembly:GRCz11 25938_wt.pass2Aligned.sortedByCoord.out.bam bam 16346812838.0 82104499.0 25938 wt.pass2Aligned.sortedByCoord.out.bam 0:99.65 1:99.56 A:3996717287;C:4167381503;G:4130586142;T:4051899914;N:227992 99 99     3996717287 4167381503 4130586142 4051899914 227992 SRX26812018 SRS23296668 SRA2019780 Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology Eunice Kennedy Shriver National Institute of Child Health and Human Development 2 0.97776 0.97907 0.04095 0.04006 0.6702 0.67034 0.46611 0.46144 99 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk bulk bulk   United States 2024-11-22 Larval Larval Head 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");;