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run_metadata

12 rows where experiment.library_selection = "PCR", experiment.library_strategy = "Bisulfite-Seq" and technology = "unknown"

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tissue_curation_coarse 1

tissue_curation 1

technology 1

  • unknown · 12 ✖

experiment.platform 1

experiment.library_strategy 1

  • Bisulfite-Seq · 12 ✖

experiment.library_source 1

experiment.library_selection 1

  • PCR · 12 ✖

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
29641 29641 SRR27397714 SRX23073965 SRS20033317 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library10 PG2   strain:ab|age:adult|collection date:2023 02 02|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 10|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS10 RRBS10 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     PG2_L7_1.fq.gz PG2_L7_2.fq.gz fastq fastq 981695400.0 3272318.0 PG2 L7 1.fq.gz 0:150 1:150 A:253124715;C:152724975;G:341105704;T:234698202;N:41804 150 150     253124715 152724975 341105704 234698202 41804 SRX23073965 SRS20033317 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.0164 0.00047 0.01505 0.00036 0.9961 0.99965 0.58102 0.47058 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular System
29642 29642 SRR27397715 SRX23073964 SRS20033316 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library9 PG1   strain:ab|age:adult|collection date:2023 02 02|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 9|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS9 RRBS9 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     PG1_L7_1.fq.gz PG1_L7_2.fq.gz fastq fastq 1157067600.0 3856892.0 PG1 L7 1.fq.gz 0:150 1:150 A:278308283;C:162228777;G:432676687;T:283803806;N:50047 150 150     278308283 162228777 432676687 283803806 50047 SRX23073964 SRS20033316 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.02347 0.02319 0.02188 0.02162 0.99517 0.99519 0.50342 0.51027 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular System
29643 29643 SRR27397716 SRX23073963 SRS20033315 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library8 LG4   strain:ab|age:adult|collection date:2023 02 02|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 8|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS8 RRBS8 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     LG4_L7_1.fq.gz LG4_L7_2.fq.gz fastq fastq 1080684300.0 3602281.0 LG4 L7 1.fq.gz 0:150 1:150 A:270759422;C:159278390;G:387693215;T:262907381;N:45892 150 150     270759422 159278390 387693215 262907381 45892 SRX23073963 SRS20033315 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.01698 0.00033 0.01593 0.00026 0.99675 0.99979 0.4974 0.2 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular System
29644 29644 SRR27397717 SRX23073962 SRS20033314 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library7 LG3   strain:ab|age:adult|collection date:2023 02 02|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 7|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS7 RRBS7 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     LG3_L7_1.fq.gz LG3_L7_2.fq.gz fastq fastq 1223063700.0 4076879.0 LG3 L7 1.fq.gz 0:150 1:150 A:301167012;C:182106743;G:443329321;T:296409064;N:51560 150 150     301167012 182106743 443329321 296409064 51560 SRX23073962 SRS20033314 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.01787 0.01759 0.01644 0.01622 0.99545 0.99582 0.56826 0.56126 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular System
29645 29645 SRR27397718 SRX23073961 SRS20033313 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library6 LG2   strain:ab|age:adult|collection date:2023 02 07|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 6|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS6 RRBS6 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     LG2_L7_1.fq.gz LG2_L7_2.fq.gz fastq fastq 1188600300.0 3962001.0 LG2 L7 1.fq.gz 0:150 1:150 A:294477343;C:172669379;G:418732939;T:302669966;N:50673 150 150     294477343 172669379 418732939 302669966 50673 SRX23073961 SRS20033313 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.0205 0.02042 0.01903 0.01894 0.99584 0.99577 0.51685 0.51824 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular System
29646 29646 SRR27397719 SRX23073960 SRS20033312 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library5 LG1   strain:ab|age:adult|collection date:2023 02 06|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 5|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS5 RRBS5 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     LG1_L7_1.fq.gz LG1_L7_2.fq.gz fastq fastq 1048183200.0 3493944.0 LG1 L7 1.fq.gz 0:150 1:150 A:260330612;C:163890192;G:372783427;T:251133569;N:45400 150 150     260330612 163890192 372783427 251133569 45400 SRX23073960 SRS20033312 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.01999 0.00059 0.01851 0.00045 0.99563 0.99961 0.49816 0.36842 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular System
29647 29647 SRR27397720 SRX23073959 SRS20033311 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library4 CG4   strain:ab|age:adult|collection date:2023 02 05|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 4|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS4 RRBS4 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     CG4_L7_1.fq.gz CG4_L7_2.fq.gz fastq fastq 1547200200.0 5157334.0 CG4 L7 1.fq.gz 0:150 1:150 A:389261224;C:230650937;G:559928386;T:367293552;N:66101 150 150     389261224 230650937 559928386 367293552 66101 SRX23073959 SRS20033311 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.01121 0.00022 0.01024 0.00018 0.99713 0.99991 0.56111 1.0 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular System
29648 29648 SRR27397721 SRX23073958 SRS20033310 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library3 CG3   strain:ab|age:adult|collection date:2023 02 04|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 3|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS3 RRBS3 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     CG3_L7_1.fq.gz CG3_L7_2.fq.gz fastq fastq 1164022500.0 3880075.0 CG3 L7 1.fq.gz 0:150 1:150 A:281490630;C:172929357;G:423757698;T:285795200;N:49615 150 150     281490630 172929357 423757698 285795200 49615 SRX23073958 SRS20033310 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.0188 0.00046 0.01744 0.00039 0.99626 0.99981 0.55421 0.6 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular System
29649 29649 SRR27397722 SRX23073957 SRS20033309 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library12 PG4   strain:ab|age:adult|collection date:2023 02 02|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 12|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS12 RRBS12 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     PG4_L7_1.fq.gz PG4_L7_2.fq.gz fastq fastq 937521000.0 3125070.0 PG4 L7 1.fq.gz 0:150 1:150 A:230277419;C:145742183;G:328432893;T:233027715;N:40790 150 150     230277419 145742183 328432893 233027715 40790 SRX23073957 SRS20033309 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.01943 0.01926 0.01799 0.01786 0.99575 0.99588 0.51136 0.48062 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular System
29650 29650 SRR27397723 SRX23073956 SRS20033308 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library11 PG3   strain:ab|age:adult|collection date:2023 02 02|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 11|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS11 RRBS11 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     PG3_L7_1.fq.gz PG3_L7_2.fq.gz fastq fastq 1256812500.0 4189375.0 PG3 L7 1.fq.gz 0:150 1:150 A:318736087;C:194540494;G:434374337;T:309107761;N:53821 150 150     318736087 194540494 434374337 309107761 53821 SRX23073956 SRS20033308 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.01424 0.00046 0.01316 0.00036 0.99683 0.99975 0.49746 0.5 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular System
29651 29651 SRR27397724 SRX23073955 SRS20033307 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library2 CG2   strain:ab|age:adult|collection date:2023 02 03|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 2|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS2 RRBS2 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     CG2_L7_1.fq.gz CG2_L7_2.fq.gz fastq fastq 1157888400.0 3859628.0 CG2 L7 1.fq.gz 0:150 1:150 A:292628434;C:171796176;G:406707172;T:286706357;N:50261 150 150     292628434 171796176 406707172 286706357 50261 SRX23073955 SRS20033307 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.02036 0.02023 0.01903 0.01889 0.99616 0.99614 0.55102 0.57894 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular System
29652 29652 SRR27397725 SRX23073954 SRS20033306 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library1 CG1   strain:ab|age:adult|collection date:2023 02 02|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 1|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS1 RRBS1 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     CG1_L7_1.fq.gz CG1_L7_2.fq.gz fastq fastq 1004867700.0 3349559.0 CG1 L7 1.fq.gz 0:150 1:150 A:247727849;C:158203386;G:350367173;T:248526527;N:42765 150 150     247727849 158203386 350367173 248526527 42765 SRX23073954 SRS20033306 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.02764 0.00147 0.0252 0.00121 0.99233 0.99926 0.51541 0.5 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular 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");;