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run_metadata

8 rows where experiment.library_selection = "Oligo-dT", experiment.platform = "ILLUMINA" and tissue_curation = "Head"

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tissue_curation_coarse 1

tissue_curation 1

  • Head · 8 ✖

technology 1

experiment.platform 1

  • ILLUMINA · 8 ✖

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • Oligo-dT · 8 ✖

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
61716 61716 SRR13015574 SRX9466662 SRS7678788 SRP291905 PRJNA674002 A to I RNA editing in zebrafish during development PRJNA674002 Other Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.       zebrafish embryos 72hpf head single cross 2 72hpf head.rep2   strain:AB wildtype|dev stage:72 hpf|sex:unknown|tissue:head|embryos derived by cross:single cross 2|biological replicate:replicate 2|assay type:mRNA seq|BioSampleModel:Model organism or animal                 mRNA seq of whole zebrafish embryos wildtype AB 72 hpf head single cross 2 Rep2 lane2 PJ KH 025 2 PJ KH 025 2 stranded mRNA     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP291905     PJ_KH_025_S25_L004_R1_001.fastq.gz PJ_KH_025_S25_L004_R2_001.fastq.gz fastq fastq 6044277226.0 20014163.0 PJ KH 025 S25 L004 R1 001.fastq.gz 0:151 1:151 A:1592897775;C:1431102291;G:1483194415;T:1535949729;N:1133016 151 151     1592897775 1431102291 1483194415 1535949729 1133016 SRX9466662 SRS7678788 SRA1153075 MDC Berlin|BIMSB MDC Berlin 2 0.83797 0.8376 0.08415 0.08231 0.67734 0.67984 0.47005 0.47051 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Germany 2020-11-10 Larval Larval Head Nervous System
61717 61717 SRR13015575 SRX9466661 SRS7678788 SRP291905 PRJNA674002 A to I RNA editing in zebrafish during development PRJNA674002 Other Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.       zebrafish embryos 72hpf head single cross 2 72hpf head.rep2   strain:AB wildtype|dev stage:72 hpf|sex:unknown|tissue:head|embryos derived by cross:single cross 2|biological replicate:replicate 2|assay type:mRNA seq|BioSampleModel:Model organism or animal                 mRNA seq of whole zebrafish embryos wildtype AB 72 hpf head single cross 2 Rep2 lane1 PJ KH 025 1 PJ KH 025 1 stranded mRNA     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP291905     PJ_KH_025_S25_L003_R1_001.fastq.gz PJ_KH_025_S25_L003_R2_001.fastq.gz fastq fastq 5975225530.0 19785515.0 PJ KH 025 S25 L003 R1 001.fastq.gz 0:151 1:151 A:1575693310;C:1413843218;G:1467480556;T:1517391851;N:816595 151 151     1575693310 1413843218 1467480556 1517391851 816595 SRX9466661 SRS7678788 SRA1153075 MDC Berlin|BIMSB MDC Berlin 2 0.83685 0.83734 0.08376 0.08206 0.67452 0.67738 0.47208 0.46848 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Germany 2020-11-10 Larval Larval Head Nervous System
61720 61720 SRR13015578 SRX9466658 SRS7678785 SRP291905 PRJNA674002 A to I RNA editing in zebrafish during development PRJNA674002 Other Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.       zebrafish embryos 72hpf head single cross 2 72hpf head.rep1   strain:AB wildtype|dev stage:72 hpf|sex:unknown|tissue:head|embryos derived by cross:single cross 2|biological replicate:replicate 1|assay type:mRNA seq|BioSampleModel:Model organism or animal                 mRNA seq of whole zebrafish embryos wildtype AB 72 hpf head single cross 2 Rep1 lane2 PJ KH 023 2 PJ KH 023 2 stranded mRNA     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP291905     PJ_KH_023_S23_L004_R1_001.fastq.gz PJ_KH_023_S23_L004_R2_001.fastq.gz fastq fastq 6256736038.0 20717669.0 PJ KH 023 S23 L004 R1 001.fastq.gz 0:151 1:151 A:1682521012;C:1447539005;G:1492671488;T:1632844528;N:1160005 151 151     1682521012 1447539005 1492671488 1632844528 1160005 SRX9466658 SRS7678785 SRA1153075 MDC Berlin|BIMSB MDC Berlin 2 0.94403 0.94422 0.06806 0.06559 0.70849 0.71135 0.4781 0.47695 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Germany 2020-11-10 Larval Larval Head Nervous System
61722 61722 SRR13015580 SRX9466656 SRS7678785 SRP291905 PRJNA674002 A to I RNA editing in zebrafish during development PRJNA674002 Other Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.       zebrafish embryos 72hpf head single cross 2 72hpf head.rep1   strain:AB wildtype|dev stage:72 hpf|sex:unknown|tissue:head|embryos derived by cross:single cross 2|biological replicate:replicate 1|assay type:mRNA seq|BioSampleModel:Model organism or animal                 mRNA seq of whole zebrafish embryos wildtype AB 72 hpf head single cross 2 Rep1 lane1 PJ KH 023 1 PJ KH 023 1 stranded mRNA     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP291905     PJ_KH_023_S23_L003_R1_001.fastq.gz PJ_KH_023_S23_L003_R2_001.fastq.gz fastq fastq 6172422772.0 20438486.0 PJ KH 023 S23 L003 R1 001.fastq.gz 0:151 1:151 A:1661367824;C:1426239358;G:1473404055;T:1610579269;N:832266 151 151     1661367824 1426239358 1473404055 1610579269 832266 SRX9466656 SRS7678785 SRA1153075 MDC Berlin|BIMSB MDC Berlin 2 0.94408 0.94436 0.06817 0.06648 0.71074 0.71388 0.47742 0.47763 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Germany 2020-11-10 Larval Larval Head Nervous System
61727 61727 SRR13015585 SRX9466651 SRS7678782 SRP291905 PRJNA674002 A to I RNA editing in zebrafish during development PRJNA674002 Other Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.       zebrafish embryos 72hpf head single cross 1 72hpf head.rep2   strain:AB wildtype|dev stage:72 hpf|sex:unknown|tissue:head|embryos derived by cross:single cross 1|biological replicate:replicate 2|assay type:mRNA seq|BioSampleModel:Model organism or animal                 mRNA seq of whole zebrafish embryos wildtype AB 72 hpf head single cross 1 Rep2 lane2 PJ KH 020 2 PJ KH 020 2 stranded mRNA     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP291905     PJ_KH_020_S20_L004_R1_001.fastq.gz PJ_KH_020_S20_L004_R2_001.fastq.gz fastq fastq 6745348180.0 22335590.0 PJ KH 020 S20 L004 R1 001.fastq.gz 0:151 1:151 A:1776789651;C:1593504281;G:1638208135;T:1735588434;N:1257679 151 151     1776789651 1593504281 1638208135 1735588434 1257679 SRX9466651 SRS7678782 SRA1153075 MDC Berlin|BIMSB MDC Berlin 2 0.95721 0.96048 0.07705 0.07603 0.7109 0.71463 0.42624 0.41885 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Germany 2020-11-10 Larval Larval Head Nervous System
61728 61728 SRR13015586 SRX9466650 SRS7678782 SRP291905 PRJNA674002 A to I RNA editing in zebrafish during development PRJNA674002 Other Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.       zebrafish embryos 72hpf head single cross 1 72hpf head.rep2   strain:AB wildtype|dev stage:72 hpf|sex:unknown|tissue:head|embryos derived by cross:single cross 1|biological replicate:replicate 2|assay type:mRNA seq|BioSampleModel:Model organism or animal                 mRNA seq of whole zebrafish embryos wildtype AB 72 hpf head single cross 1 Rep2 lane1 PJ KH 020 1 PJ KH 020 1 stranded mRNA     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP291905     PJ_KH_020_S20_L003_R1_001.fastq.gz PJ_KH_020_S20_L003_R2_001.fastq.gz fastq fastq 6729174570.0 22282035.0 PJ KH 020 S20 L003 R1 001.fastq.gz 0:151 1:151 A:1774094248;C:1587891896;G:1635085296;T:1731190595;N:912535 151 151     1774094248 1587891896 1635085296 1731190595 912535 SRX9466650 SRS7678782 SRA1153075 MDC Berlin|BIMSB MDC Berlin 2 0.95736 0.96066 0.07726 0.07635 0.71082 0.71435 0.42984 0.42332 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Germany 2020-11-10 Larval Larval Head Nervous System
61729 61729 SRR13015587 SRX9466649 SRS7678781 SRP291905 PRJNA674002 A to I RNA editing in zebrafish during development PRJNA674002 Other Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.       zebrafish embryos 72hpf head single cross 1 72hpf head.rep1   strain:AB wildtype|dev stage:72 hpf|sex:unknown|tissue:head|embryos derived by cross:single cross 1|biological replicate:replicate 1|assay type:mRNA seq|BioSampleModel:Model organism or animal                 mRNA seq of whole zebrafish embryos wildtype AB 72 hpf head single cross 1 Rep1 lane2 PJ KH 019 2 PJ KH 019 2 stranded mRNA     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP291905     PJ_KH_019_S19_L004_R1_001.fastq.gz PJ_KH_019_S19_L004_R2_001.fastq.gz fastq fastq 6593199976.0 21831788.0 PJ KH 019 S19 L004 R1 001.fastq.gz 0:151 1:151 A:1810838908;C:1489027477;G:1536979505;T:1755131961;N:1222125 151 151     1810838908 1489027477 1536979505 1755131961 1222125 SRX9466649 SRS7678781 SRA1153075 MDC Berlin|BIMSB MDC Berlin 2 0.94258 0.94483 0.12584 0.12382 0.66048 0.66186 0.46479 0.46294 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Germany 2020-11-10 Larval Larval Head Nervous System
61730 61730 SRR13015588 SRX9466648 SRS7678781 SRP291905 PRJNA674002 A to I RNA editing in zebrafish during development PRJNA674002 Other Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.       zebrafish embryos 72hpf head single cross 1 72hpf head.rep1   strain:AB wildtype|dev stage:72 hpf|sex:unknown|tissue:head|embryos derived by cross:single cross 1|biological replicate:replicate 1|assay type:mRNA seq|BioSampleModel:Model organism or animal                 mRNA seq of whole zebrafish embryos wildtype AB 72 hpf head single cross 1 Rep1 lane1 PJ KH 019 1 PJ KH 019 1 stranded mRNA     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP291905     PJ_KH_019_S19_L003_R1_001.fastq.gz PJ_KH_019_S19_L003_R2_001.fastq.gz fastq fastq 6448860284.0 21353842.0 PJ KH 019 S19 L003 R1 001.fastq.gz 0:151 1:151 A:1772421932;C:1455472902;G:1504524766;T:1715573168;N:867516 151 151     1772421932 1455472902 1504524766 1715573168 867516 SRX9466648 SRS7678781 SRA1153075 MDC Berlin|BIMSB MDC Berlin 2 0.9419 0.9441 0.12553 0.12393 0.65963 0.66257 0.46785 0.46982 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Germany 2020-11-10 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");;