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run_metadata

12 rows where experiment.library_selection = "RANDOM", experiment.platform = "BGISEQ" and tissue_curation = "Whole Organism"

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tissue_curation_coarse 1

tissue_curation 1

  • Whole Organism · 12 ✖

technology 1

experiment.platform 1

  • BGISEQ · 12 ✖

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • RANDOM · 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
72445 72445 SRR22540104 SRX18504097 SRS15974727 SRP411489 PRJNA908883 Zebrafish PFHxS exposure RNA seq PRJNA908883 Other RAN seq of zebrafish embryos post 5 days PFHxS exposure       Model organism or animal sample from Danio rerio Treatment 3   strain:AB|dev stage:5dpf|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 RNA seq of zebrafish embryo T3/ T3/ effect of pfhxs     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE BGISEQ BGISEQ-500   SRP411489     T3.AddRG.Reorder.Sort.bam bam 4395695600.0 21978478.0 T3.AddRG.Reorder.Sort.bam 0:100 1:100 A:1142519361;C:1049796532;G:1054171464;T:1149208243;N:0 100 100     1142519361 1049796532 1054171464 1149208243 0 SRX18504097 SRS15974727 SRA1553988 Dr. William TSE/ Kyushu University|Faculty of Agriculture Dr. William TSE/ Kyushu University 2 0.95843 0.96189 0.05928 0.05837 0.66996 0.67022 0.48134 0.48129 100 100 B B biological fallback assumption bgi bgi unknown random_priming unknown bulk unknown unknown   Japan 2022-12-05 Larval Larval Whole Organism All anatomical structures
72446 72446 SRR22540105 SRX18504096 SRS15974726 SRP411489 PRJNA908883 Zebrafish PFHxS exposure RNA seq PRJNA908883 Other RAN seq of zebrafish embryos post 5 days PFHxS exposure       Model organism or animal sample from Danio rerio Treatment 2   strain:AB|dev stage:5dpf|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 RNA seq of zebrafish embryo T2/ T2/ effect of pfhxs     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE BGISEQ BGISEQ-500   SRP411489     T2.AddRG.Reorder.Sort.bam bam 4614912600.0 23074563.0 T2.AddRG.Reorder.Sort.bam 0:100 1:100 A:1188643000;C:1115164590;G:1120634369;T:1190470641;N:0 100 100     1188643000 1115164590 1120634369 1190470641 0 SRX18504096 SRS15974726 SRA1553988 Dr. William TSE/ Kyushu University|Faculty of Agriculture Dr. William TSE/ Kyushu University 2 0.95664 0.96166 0.05002 0.04822 0.68635 0.68554 0.47517 0.46481 100 100 B B biological fallback assumption bgi bgi unknown random_priming unknown bulk unknown unknown   Japan 2022-12-05 Larval Larval Whole Organism All anatomical structures
72447 72447 SRR22540106 SRX18504095 SRS15974725 SRP411489 PRJNA908883 Zebrafish PFHxS exposure RNA seq PRJNA908883 Other RAN seq of zebrafish embryos post 5 days PFHxS exposure       Model organism or animal sample from Danio rerio Treatment 1   strain:AB|dev stage:5dpf|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 RNA seq of zebrafish embryo T1/ T1/ effect of pfhxs     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE BGISEQ BGISEQ-500   SRP411489     T1.AddRG.Reorder.Sort.bam bam 4621886200.0 23109431.0 T1.AddRG.Reorder.Sort.bam 0:100 1:100 A:1193465655;C:1112344935;G:1119903386;T:1196172224;N:0 100 100     1193465655 1112344935 1119903386 1196172224 0 SRX18504095 SRS15974725 SRA1553988 Dr. William TSE/ Kyushu University|Faculty of Agriculture Dr. William TSE/ Kyushu University 2 0.95679 0.96088 0.05344 0.05139 0.67754 0.67598 0.462 0.46124 100 100 B B biological fallback assumption bgi bgi unknown random_priming unknown bulk unknown unknown   Japan 2022-12-05 Larval Larval Whole Organism All anatomical structures
72448 72448 SRR22540107 SRX18504094 SRS15974724 SRP411489 PRJNA908883 Zebrafish PFHxS exposure RNA seq PRJNA908883 Other RAN seq of zebrafish embryos post 5 days PFHxS exposure       Model organism or animal sample from Danio rerio Control 3   strain:AB|dev stage:5dpf|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 RNA seq of zebrafish embryo C3/ C3/ effect of pfhxs     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE BGISEQ BGISEQ-500   SRP411489     C3.AddRG.Reorder.Sort.bam bam 4617709400.0 23088547.0 C3.AddRG.Reorder.Sort.bam 0:100 1:100 A:1198527314;C:1106175441;G:1112503633;T:1200503012;N:0 100 100     1198527314 1106175441 1112503633 1200503012 0 SRX18504094 SRS15974724 SRA1553988 Dr. William TSE/ Kyushu University|Faculty of Agriculture Dr. William TSE/ Kyushu University 2 0.95798 0.96137 0.05412 0.05264 0.67223 0.67048 0.46376 0.46409 100 100 B B biological fallback assumption bgi bgi unknown random_priming unknown bulk unknown unknown   Japan 2022-12-05 Larval Larval Whole Organism All anatomical structures
72449 72449 SRR22540108 SRX18504093 SRS15974723 SRP411489 PRJNA908883 Zebrafish PFHxS exposure RNA seq PRJNA908883 Other RAN seq of zebrafish embryos post 5 days PFHxS exposure       Model organism or animal sample from Danio rerio Control 2   strain:AB|dev stage:5dpf|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 RNA seq of zebrafish embryo C2/ C2/ effect of pfhxs     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE BGISEQ BGISEQ-500   SRP411489     C2.AddRG.Reorder.Sort.bam bam 4871905600.0 24359528.0 C2.AddRG.Reorder.Sort.bam 0:100 1:100 A:1257717743;C:1172780375;G:1176887548;T:1264519934;N:0 100 100     1257717743 1172780375 1176887548 1264519934 0 SRX18504093 SRS15974723 SRA1553988 Dr. William TSE/ Kyushu University|Faculty of Agriculture Dr. William TSE/ Kyushu University 2 0.96005 0.96318 0.05702 0.05549 0.66789 0.66697 0.47093 0.46583 100 100 B B biological fallback assumption bgi bgi unknown random_priming unknown bulk unknown unknown   Japan 2022-12-05 Larval Larval Whole Organism All anatomical structures
72450 72450 SRR22540109 SRX18504092 SRS15974722 SRP411489 PRJNA908883 Zebrafish PFHxS exposure RNA seq PRJNA908883 Other RAN seq of zebrafish embryos post 5 days PFHxS exposure       Model organism or animal sample from Danio rerio Control 1   strain:AB|dev stage:5dpf|sex:not determined|tissue:whole embryo|BioSampleModel:Model organism or animal                 RNA seq of zebrafish embryo C1/ C1/ effect of pfhxs     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE BGISEQ BGISEQ-500   SRP411489     C1.AddRG.Reorder.Sort.bam bam 4632466800.0 23162334.0 C1.AddRG.Reorder.Sort.bam 0:100 1:100 A:1194920249;C:1116526905;G:1121202833;T:1199816813;N:0 100 100     1194920249 1116526905 1121202833 1199816813 0 SRX18504092 SRS15974722 SRA1553988 Dr. William TSE/ Kyushu University|Faculty of Agriculture Dr. William TSE/ Kyushu University 2 0.95802 0.96207 0.05444 0.05319 0.67371 0.67247 0.47155 0.46736 100 100 B B biological fallback assumption bgi bgi unknown random_priming unknown bulk unknown unknown   Japan 2022-12-05 Larval Larval Whole Organism All anatomical structures
72614 72614 SRR22891482 SRX18849297 SRS16280582 SRP414808 PRJNA915212 Danio rerio strain: 5dpf AB and sf3b4 / Raw sequence reads PRJNA915212 Whole Genome Sequencing A project that using 5dpf AB control and sf3b4 / mutant for RNA sequencing       Model organism or animal sample from Danio rerio Mutant3   strain:sf3b4|dev stage:5dpf|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 RNA seq of zebrafish embryo S3 S3 RNA seq of 5dpf     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE BGISEQ BGISEQ-500   SRP414808   assembly:GRCz11 S3.AddRG.Reorder.Sort.bam bam 4571163800.0 22855819.0 S3.AddRG.Reorder.Sort.bam 0:100 1:100 A:1194682262;C:1085195756;G:1103429751;T:1187856031;N:0 100 100     1194682262 1085195756 1103429751 1187856031 0 SRX18849297 SRS16280582 SRA1565404 Dr. William TSE/ Kyushu University|Faculty of Agriculture Dr. William TSE/ Kyushu University 2 0.93076 0.93744 0.0661 0.06566 0.67825 0.67675 0.46849 0.46581 100 100 B B biological fallback assumption bgi bgi unknown random_priming unknown bulk unknown unknown   Japan 2022-12-26 Larval Larval Whole Organism All anatomical structures
72615 72615 SRR22891483 SRX18849296 SRS16280581 SRP414808 PRJNA915212 Danio rerio strain: 5dpf AB and sf3b4 / Raw sequence reads PRJNA915212 Whole Genome Sequencing A project that using 5dpf AB control and sf3b4 / mutant for RNA sequencing       Model organism or animal sample from Danio rerio Mutant2   strain:sf3b4|dev stage:5dpf|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 RNA seq of zebrafish embryo S2 S2 RNA seq of 5dpf     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE BGISEQ BGISEQ-500   SRP414808   assembly:GRCz11 S2.AddRG.Reorder.Sort.bam bam 4600792600.0 23003963.0 S2.AddRG.Reorder.Sort.bam 0:100 1:100 A:1200126269;C:1095166595;G:1110394784;T:1195104952;N:0 100 100     1200126269 1095166595 1110394784 1195104952 0 SRX18849296 SRS16280581 SRA1565404 Dr. William TSE/ Kyushu University|Faculty of Agriculture Dr. William TSE/ Kyushu University 2 0.93762 0.94385 0.06417 0.06338 0.67288 0.67282 0.46354 0.46465 100 100 B B biological fallback assumption bgi bgi unknown random_priming unknown bulk unknown unknown   Japan 2022-12-26 Larval Larval Whole Organism All anatomical structures
72616 72616 SRR22891484 SRX18849295 SRS16280580 SRP414808 PRJNA915212 Danio rerio strain: 5dpf AB and sf3b4 / Raw sequence reads PRJNA915212 Whole Genome Sequencing A project that using 5dpf AB control and sf3b4 / mutant for RNA sequencing       Model organism or animal sample from Danio rerio Mutant1   strain:sf3b4|dev stage:5dpf|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 RNA seq of zebrafish embryo S1 S1 RNA seq of 5dpf     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE BGISEQ BGISEQ-500   SRP414808   assembly:GRCz11 S1.AddRG.Reorder.Sort.bam bam 4597426600.0 22987133.0 S1.AddRG.Reorder.Sort.bam 0:100 1:100 A:1198474483;C:1095576259;G:1111544092;T:1191831766;N:0 100 100     1198474483 1095576259 1111544092 1191831766 0 SRX18849295 SRS16280580 SRA1565404 Dr. William TSE/ Kyushu University|Faculty of Agriculture Dr. William TSE/ Kyushu University 2 0.93381 0.93956 0.06594 0.06432 0.67529 0.67225 0.46816 0.46785 100 100 B B biological fallback assumption bgi bgi unknown random_priming unknown bulk unknown unknown   Japan 2022-12-26 Larval Larval Whole Organism All anatomical structures
72617 72617 SRR22891485 SRX18849294 SRS16280579 SRP414808 PRJNA915212 Danio rerio strain: 5dpf AB and sf3b4 / Raw sequence reads PRJNA915212 Whole Genome Sequencing A project that using 5dpf AB control and sf3b4 / mutant for RNA sequencing       Model organism or animal sample from Danio rerio Control3   strain:AB|dev stage:5dpf|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 RNA seq of zebrafish embryo C3 C3 RNA seq of 5dpf     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE BGISEQ BGISEQ-500   SRP414808   assembly:GRCz11 C3.AddRG.Reorder.Sort.bam bam 4604458600.0 23022293.0 C3.AddRG.Reorder.Sort.bam 0:100 1:100 A:1212479855;C:1086425627;G:1078320217;T:1227232901;N:0 100 100     1212479855 1086425627 1078320217 1227232901 0 SRX18849294 SRS16280579 SRA1565404 Dr. William TSE/ Kyushu University|Faculty of Agriculture Dr. William TSE/ Kyushu University 2 0.9375 0.94189 0.06929 0.06838 0.68097 0.68032 0.46981 0.46746 100 100 B B biological fallback assumption bgi bgi unknown random_priming unknown bulk unknown unknown   Japan 2022-12-26 Larval Larval Whole Organism All anatomical structures
72618 72618 SRR22891486 SRX18849293 SRS16280578 SRP414808 PRJNA915212 Danio rerio strain: 5dpf AB and sf3b4 / Raw sequence reads PRJNA915212 Whole Genome Sequencing A project that using 5dpf AB control and sf3b4 / mutant for RNA sequencing       Model organism or animal sample from Danio rerio Control2   strain:AB|dev stage:5dpf|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 RNA seq of zebrafish embryo C2 C2 RNA seq of 5dpf     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE BGISEQ BGISEQ-500   SRP414808   assembly:GRCz11 C2.AddRG.Reorder.Sort.bam bam 4518373800.0 22591869.0 C2.AddRG.Reorder.Sort.bam 0:100 1:100 A:1177788565;C:1076096675;G:1084632400;T:1179856160;N:0 100 100     1177788565 1076096675 1084632400 1179856160 0 SRX18849293 SRS16280578 SRA1565404 Dr. William TSE/ Kyushu University|Faculty of Agriculture Dr. William TSE/ Kyushu University 2 0.93712 0.94281 0.05459 0.05451 0.67669 0.67543 0.46485 0.46607 100 100 B B biological fallback assumption bgi bgi unknown random_priming unknown bulk unknown unknown   Japan 2022-12-26 Larval Larval Whole Organism All anatomical structures
72619 72619 SRR22891487 SRX18849292 SRS16280577 SRP414808 PRJNA915212 Danio rerio strain: 5dpf AB and sf3b4 / Raw sequence reads PRJNA915212 Whole Genome Sequencing A project that using 5dpf AB control and sf3b4 / mutant for RNA sequencing       Model organism or animal sample from Danio rerio Control1   strain:AB|dev stage:5dpf|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 RNA seq of zebrafish embryo C1 C1 RNA seq of 5dpf     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE BGISEQ BGISEQ-500   SRP414808   assembly:GRCz11 C1.AddRG.Reorder.Sort.bam bam 4546744400.0 22733722.0 C1.AddRG.Reorder.Sort.bam 0:100 1:100 A:1170343546;C:1097144275;G:1111316933;T:1167939646;N:0 100 100     1170343546 1097144275 1111316933 1167939646 0 SRX18849292 SRS16280577 SRA1565404 Dr. William TSE/ Kyushu University|Faculty of Agriculture Dr. William TSE/ Kyushu University 2 0.94204 0.94786 0.05052 0.04964 0.68227 0.68097 0.46172 0.45485 100 100 B B biological fallback assumption bgi bgi unknown random_priming unknown bulk unknown unknown   Japan 2022-12-26 Larval Larval Whole Organism All anatomical structures

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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");;