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run_metadata

8 rows where experiment.library_strategy = "RNA-Seq", technology = "unknown" and tissue_curation = "Swim Bladder"

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experiment.platform 2

experiment.library_selection 2

tissue_curation_coarse 1

tissue_curation 1

  • Swim Bladder · 8 ✖

technology 1

  • unknown · 8 ✖

experiment.library_strategy 1

  • RNA-Seq · 8 ✖

experiment.library_source 1

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
8066 8066 ERR035548 ERX013538 ERS017859 ERP000447 PRJEB2368 Sanger zebrafish sequencing E-MTAB-460 Other       Protocols: Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Zebrafish adult swim bladder SAMEA782574 Wellcome Sanger Institute ENA first public:2011 02 03|ENA last update:2018 03 08|External Id:SAMEA782574|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 02 03T12:40:41Z|INSDC last update:2018 03 08T15:25:22Z|INSDC status:public|StrainOrLine:Singapore|Submitter Id:E MTAB 460:Zebrafish adult swim bladder|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:swim bladder|sample name:E MTAB 460:Zebrafish adult swim bladder|sex:mixed                 Sanger zebrafish sequencing E MTAB 460 part2:5625 5 ZFswimbladder 2 RNA 1523495 Sanger zebrafish sequencing Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was enriched for polyA+ RNA by 2 rounds of polyA pull down with magnetic beads and included a DNase treatment between the 2 rounds. RNA was chemically fragmented LiCl precipitated reverse transcribed with random primers a second strand synthesized and made into a standard Illumina library with a fragment size of 250 to 300 bp. Experimental Factor: ORGANISM PART:swim bladder RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>2</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>85</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP000447 Illumina Genome Analyzer II paired end sequencing; Sanger zebrafish sequencing ENA FIRST PUBLIC:2011 06 14|ENA LAST UPDATE:2018 11 16 5625_5.srf srf 3631039360.0 22693996.0 E MTAB 460 part2:5625 5.srf 0:76 1:8 2:76 A:960241692;C:761151402;G:762172309;T:959064724;N:6857265 76 8 76   960241692 761151402 762172309 959064724 6857265 ERX013538 ERS017859 ERA033503 SC|Wellcome Trust Sanger Institute SC|Wellcome Trust Sanger Institute 2 0.86993 0.86373 0.16918 0.16735 0.68913 0.69384 0.50826 0.50673 76 76 B B biological fallback assumption illumina early_illumina unknown poly_a unknown bulk unknown unknown   United Kingdom 2011-02-03 Adult Adult Swim Bladder Swim Bladder
8068 8068 ERR023148 ERX009450 ERS017859 ERP000447 PRJEB2368 Sanger zebrafish sequencing E-MTAB-460 Other       Protocols: Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Zebrafish adult swim bladder SAMEA782574 Wellcome Sanger Institute ENA first public:2011 02 03|ENA last update:2018 03 08|External Id:SAMEA782574|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 02 03T12:40:41Z|INSDC last update:2018 03 08T15:25:22Z|INSDC status:public|StrainOrLine:Singapore|Submitter Id:E MTAB 460:Zebrafish adult swim bladder|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:swim bladder|sample name:E MTAB 460:Zebrafish adult swim bladder|sex:mixed                 Sanger zebrafish sequencing E MTAB 460:4191 5 RNA from Zebrafish adult swim bladder Sanger zebrafish sequencing Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Experimental Factor: ORGANISM PART:swim bladder RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP000447 Illumina Genome Analyzer II paired end sequencing; Sanger zebrafish sequencing ENA FIRST PUBLIC:2011 02 03|ENA LAST UPDATE:2018 11 16 4191_5.srf srf 4279981344.0 28157772.0 E MTAB 460:4191 5.srf 0:76 1:76 A:1465434155;C:660965580;G:667941564;T:1472658155;N:12981890 76 76     1465434155 660965580 667941564 1472658155 12981890 ERX009450 ERS017859 ERA015648 SC|Wellcome Trust Sanger Institute SC|Wellcome Trust Sanger Institute 2 0.83269 0.83071 0.36856 0.36801 0.79746 0.79677 0.49125 0.4911 76 76 B B biological fallback assumption illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2011-02-03 Adult Adult Swim Bladder Swim Bladder
8074 8074 ERR023143 ERX009444 ERS017859 ERP000447 PRJEB2368 Sanger zebrafish sequencing E-MTAB-460 Other       Protocols: Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Zebrafish adult swim bladder SAMEA782574 Wellcome Sanger Institute ENA first public:2011 02 03|ENA last update:2018 03 08|External Id:SAMEA782574|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 02 03T12:40:41Z|INSDC last update:2018 03 08T15:25:22Z|INSDC status:public|StrainOrLine:Singapore|Submitter Id:E MTAB 460:Zebrafish adult swim bladder|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:swim bladder|sample name:E MTAB 460:Zebrafish adult swim bladder|sex:mixed                 Sanger zebrafish sequencing E MTAB 460:3212 5 RNA from Zebrafish adult swim bladder Sanger zebrafish sequencing Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Experimental Factor: ORGANISM PART:swim bladder RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP000447 Illumina Genome Analyzer II paired end sequencing; Sanger zebrafish sequencing ENA FIRST PUBLIC:2011 02 03|ENA LAST UPDATE:2018 11 16 3212_5.srf srf 972304632.0 6396741.0 E MTAB 460:3212 5.srf 0:76 1:76 A:320388277;C:158735178;G:157312801;T:326747311;N:9121065 76 76     320388277 158735178 157312801 326747311 9121065 ERX009444 ERS017859 ERA015648 SC|Wellcome Trust Sanger Institute SC|Wellcome Trust Sanger Institute 2 0.84363 0.84242 0.3398 0.33885 0.79082 0.78987 0.48696 0.50187 76 76 B B biological fallback assumption illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2011-02-03 Adult Adult Swim Bladder Swim Bladder
55997 55997 SRR10895904 SRX7564575 SRS6001799 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 004   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Swim bladder|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100103858 L02 9 CL100103858 L02 9       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100103858_L02_527_2.fq.gz CL100103858_L02_527_1.fq.gz fastq fastq 9389292400.0 93892924.0 CL100103858 L02 527 1.fq.gz 0:100 1:100 A:2535177343;C:2107498353;G:2159172216;T:2574271698;N:13172790 100 100     2535177343 2107498353 2159172216 2574271698 13172790 SRX7564575 SRS6001799 SRA1026516 BGI|BGI-Research BGI 1 0.94054   0.10829   0.70818   0.51214   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Swim Bladder Swim Bladder
55998 55998 SRR10895905 SRX7564574 SRS6001799 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 004   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Swim bladder|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100103178 L02 9 CL100103178 L02 9       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100103178_L02_580_2.fq.gz CL100103178_L02_580_1.fq.gz fastq fastq 9451878800.0 94518788.0 CL100103178 L02 580 1.fq.gz 0:100 1:100 A:2482432185;C:2200816673;G:2254475373;T:2504225593;N:9928976 100 100     2482432185 2200816673 2254475373 2504225593 9928976 SRX7564574 SRS6001799 SRA1026516 BGI|BGI-Research BGI 1 0.91363   0.08854   0.67399   0.52315   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Swim Bladder Swim Bladder
55999 55999 SRR10895906 SRX7564573 SRS6001799 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 004   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Swim bladder|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100103178 L02 8 CL100103178 L02 8       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100103178_L02_579_1.fq.gz CL100103178_L02_579_2.fq.gz fastq fastq 6784370200.0 67843702.0 CL100103178 L02 579 1.fq.gz 0:100 1:100 A:1799307225;C:1565118646;G:1599826091;T:1813320759;N:6797479 100 100     1799307225 1565118646 1599826091 1813320759 6797479 SRX7564573 SRS6001799 SRA1026516 BGI|BGI-Research BGI 1 0.91866   0.10227   0.71928   0.50827   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Swim Bladder Swim Bladder
56000 56000 SRR10895907 SRX7564572 SRS6001799 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 004   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Swim bladder|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100103858 L02 8 CL100103858 L02 8       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100103858_L02_529_2.fq.gz CL100103858_L02_529_1.fq.gz fastq fastq 10614517200.0 106145172.0 CL100103858 L02 529 1.fq.gz 0:100 1:100 A:2821297968;C:2430515408;G:2486443963;T:2861653662;N:14606199 100 100     2821297968 2430515408 2486443963 2861653662 14606199 SRX7564572 SRS6001799 SRA1026516 BGI|BGI-Research BGI 1 0.94747   0.08863   0.64632   0.50637   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Swim Bladder Swim Bladder
56001 56001 SRR10895908 SRX7564571 SRS6001799 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 004   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Swim bladder|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100103858 L02 7 CL100103858 L02 7       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100103858_L02_526_2.fq.gz CL100103858_L02_526_1.fq.gz fastq fastq 8829000400.0 88290004.0 CL100103858 L02 526 1.fq.gz 0:100 1:100 A:2346419057;C:2025176439;G:2073455037;T:2371666164;N:12283703 100 100     2346419057 2025176439 2073455037 2371666164 12283703 SRX7564571 SRS6001799 SRA1026516 BGI|BGI-Research BGI 1 0.93744   0.08552   0.70918   0.49156   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Swim Bladder Swim Bladder

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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");;