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run_metadata

6 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "RANDOM" and tissue_curation = "Gut"

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devstage_curation_coarse 2

devstage_curation 2

tissue_curation_coarse 1

tissue_curation 1

technology 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • RANDOM · 6 ✖

experiment.library_layout 1

  • SINGLE · 6 ✖
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
32 32 DRR408242 DRX393848 DRS407006 DRP012035 PRJDB14274 Zebrafish Gut RNA seq. DRP012035 Transcriptome Analysis A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.     zebrafish wild type AB adult gut replicate 3 zebrafish adult gut replicate 3 SAMD00529462   sample name:zebrafish adult gut replicate 3|biological replicate:adult 3|strain:AB                 Illumina HiSeq 1500 sequencing of SAMD00529462 DRX393848 AR019 gut 6 adult 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012035 Illumina HiSeq 1500 sequencing of SAMD00529462       3546347364.0 28145614.0 DRR408242 0:126 1:0 A:919466631;C:829424335;G:818581155;T:978810217;N:65026 126 0     919466631 829424335 818581155 978810217 65026 DRX393848 DRS407006 DRA014885 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Japan 2024-09-20 Adult Adult Gut Digestive System
33 33 DRR408241 DRX393847 DRS407005 DRP012035 PRJDB14274 Zebrafish Gut RNA seq. DRP012035 Transcriptome Analysis A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.     zebrafish wild type AB adult gut replicate 2 zebrafish adult gut replicate 2 SAMD00529461   sample name:zebrafish adult gut replicate 2|biological replicate:adult 2|strain:AB                 Illumina HiSeq 1500 sequencing of SAMD00529461 DRX393847 AR006 gut 4 adult 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012035 Illumina HiSeq 1500 sequencing of SAMD00529461       3671973648.0 29142648.0 DRR408241 0:126 1:0 A:942167543;C:859431290;G:852661772;T:1017643011;N:70032 126 0     942167543 859431290 852661772 1017643011 70032 DRX393847 DRS407005 DRA014885 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Japan 2024-09-20 Adult Adult Gut Digestive System
34 34 DRR408240 DRX393846 DRS407004 DRP012035 PRJDB14274 Zebrafish Gut RNA seq. DRP012035 Transcriptome Analysis A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.     zebrafish wild type AB adult gut replicate 1 zebrafish adult gut replicate 1 SAMD00529460   sample name:zebrafish adult gut replicate 1|biological replicate:adult 1|strain:AB                 Illumina HiSeq 1500 sequencing of SAMD00529460 DRX393846 AR004 gut 2 adult 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012035 Illumina HiSeq 1500 sequencing of SAMD00529460       3480523704.0 27623204.0 DRR408240 0:126 1:0 A:898051986;C:827557593;G:816541244;T:938307607;N:65274 126 0     898051986 827557593 816541244 938307607 65274 DRX393846 DRS407004 DRA014885 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Japan 2024-09-20 Adult Adult Gut Digestive System
35 35 DRR408239 DRX393845 DRS407003 DRP012035 PRJDB14274 Zebrafish Gut RNA seq. DRP012035 Transcriptome Analysis A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.     zebrafish wild type AB larval gut replicate 3 zebrafish larval gut replicate 3 SAMD00529459   sample name:zebrafish larval gut replicate 3|biological replicate:larval 3|strain:AB                 Illumina HiSeq 1500 sequencing of SAMD00529459 DRX393845 AR012 gut 5 5 dpf 6 dpf larvae 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012035 Illumina HiSeq 1500 sequencing of SAMD00529459       3463982046.0 27491921.0 DRR408239 0:126 1:0 A:842552557;C:849757648;G:837664725;T:933942026;N:65090 126 0     842552557 849757648 837664725 933942026 65090 DRX393845 DRS407003 DRA014885 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Japan 2024-09-20 Larval Larval Gut Digestive System
36 36 DRR408238 DRX393844 DRS407002 DRP012035 PRJDB14274 Zebrafish Gut RNA seq. DRP012035 Transcriptome Analysis A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.     zebrafish wild type AB larval gut replicate 2 zebrafish larval gut replicate 2 SAMD00529458   sample name:zebrafish larval gut replicate 2|biological replicate:larval 2|strain:AB                 Illumina HiSeq 1500 sequencing of SAMD00529458 DRX393844 AR005 gut 3 5 dpf 6 dpf larvae 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012035 Illumina HiSeq 1500 sequencing of SAMD00529458       3782320416.0 30018416.0 DRR408238 0:126 1:0 A:930337206;C:920645770;G:906559955;T:1024704277;N:73208 126 0     930337206 920645770 906559955 1024704277 73208 DRX393844 DRS407002 DRA014885 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Japan 2024-09-20 Larval Larval Gut Digestive System
37 37 DRR408237 DRX393843 DRS407001 DRP012035 PRJDB14274 Zebrafish Gut RNA seq. DRP012035 Transcriptome Analysis A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.     zebrafish wild type AB larval gut replicate 1 zebrafish larval gut replicate 1 SAMD00529457   sample name:zebrafish larval gut replicate 1|biological replicate:larval 1|strain:AB                 Illumina HiSeq 1500 sequencing of SAMD00529457 DRX393843 AR002 gut 1 5 dpf 6 dpf larvae 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012035 Illumina HiSeq 1500 sequencing of SAMD00529457       3606885828.0 28626078.0 DRR408237 0:126 1:0 A:879148446;C:885673723;G:870330963;T:971663212;N:69484 126 0     879148446 885673723 870330963 971663212 69484 DRX393843 DRS407001 DRA014885 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Japan 2024-09-20 Larval Larval Gut Digestive 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");;