run_metadata
6 rows where experiment.library_selection = "cDNA", experiment.platform = "ION_TORRENT" and tissue_curation = "Fin"
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| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 95 | 95 | DRR050167 | DRX045209 | DRS025834 | DRP003043 | PRJDB4416 | Transcriptome analysis in ES1 expressing rods of zebrafish | DRP003043 | Transcriptome Analysis | Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used. | Zebrafish rods expressing ES1 and EGFP | ES1 3 | SAMD00044057 | sample name:ES1 EGFP rod 003|strain:Tubingen long fin|cell type:rod | Ion Torrent PGM sequencing of SAMD00044057 | DRX045209 | 1 | 1 | 1 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ION_TORRENT | Ion Torrent PGM | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>105</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> | DRP003043 | Ion Torrent PGM sequencing of SAMD00044057 | 371748120.0 | 3469843.0 | DRR050167 | 0:107.14 | A:107190409;C:79475572;G:83520360;T:101561779;N:0 | 107 | 107190409 | 79475572 | 83520360 | 101561779 | 0 | DRX045209 | DRS025834 | DRA004229 | OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. | Osaka university | 1 | 0.81026 | 0.26715 | 0.86953 | 0.52321 | 51 | B | usable mapping rate | ion_torrent | ion_torrent | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Japan | 2016-03-09 | Undetermined | Undetermined | Fin | Surface Structure | |||||||||||||||||||||||||
| 96 | 96 | DRR050166 | DRX045208 | DRS025833 | DRP003043 | PRJDB4416 | Transcriptome analysis in ES1 expressing rods of zebrafish | DRP003043 | Transcriptome Analysis | Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used. | Zebrafish rods expressing ES1 and EGFP | ES1 2 | SAMD00044056 | sample name:ES1 EGFP rod 002|strain:Tubingen long fin|cell type:rod | Ion Torrent PGM sequencing of SAMD00044056 | DRX045208 | 1 | 1 | 1 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ION_TORRENT | Ion Torrent PGM | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>128</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> | DRP003043 | Ion Torrent PGM sequencing of SAMD00044056 | 425549011.0 | 3275261.0 | DRR050166 | 0:129.93 | A:126640704;C:86415371;G:90822163;T:121670773;N:0 | 129 | 126640704 | 86415371 | 90822163 | 121670773 | 0 | DRX045208 | DRS025833 | DRA004229 | OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. | Osaka university | 1 | 0.80223 | 0.31429 | 0.85861 | 0.5272 | 57 | B | usable mapping rate | ion_torrent | ion_torrent | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Japan | 2016-03-09 | Undetermined | Undetermined | Fin | Surface Structure | |||||||||||||||||||||||||
| 97 | 97 | DRR050165 | DRX045207 | DRS025832 | DRP003043 | PRJDB4416 | Transcriptome analysis in ES1 expressing rods of zebrafish | DRP003043 | Transcriptome Analysis | Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used. | Zebrafish rods expressing ES1 and EGFP | ES1 1 | SAMD00044055 | sample name:ES1 EGFP rod 001|strain:Tubingen long fin|cell type:rod | Ion Torrent PGM sequencing of SAMD00044055 | DRX045207 | 1 | 1 | 1 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ION_TORRENT | Ion Torrent PGM | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>147</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> | DRP003043 | Ion Torrent PGM sequencing of SAMD00044055 | 584599765.0 | 3941083.0 | DRR050165 | 0:148.33 | A:164329030;C:129885620;G:136727379;T:153657736;N:0 | 148 | 164329030 | 129885620 | 136727379 | 153657736 | 0 | DRX045207 | DRS025832 | DRA004229 | OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. | Osaka university | 1 | 0.83769 | 0.25395 | 0.83116 | 0.52784 | 185 | B | usable mapping rate | ion_torrent | ion_torrent | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Japan | 2016-03-09 | Undetermined | Undetermined | Fin | Surface Structure | |||||||||||||||||||||||||
| 98 | 98 | DRR050164 | DRX045206 | DRS025831 | DRP003043 | PRJDB4416 | Transcriptome analysis in ES1 expressing rods of zebrafish | DRP003043 | Transcriptome Analysis | Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used. | Zebrafish rods expressing EGFP | EGFP 3 | SAMD00044054 | sample name:EGFP rod 003|strain:Tubingen long fin|cell type:rod | Ion Torrent PGM sequencing of SAMD00044054 | DRX045206 | 1 | 1 | 1 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ION_TORRENT | Ion Torrent PGM | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>88</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> | DRP003043 | Ion Torrent PGM sequencing of SAMD00044054 | 343014114.0 | 3827762.0 | DRR050164 | 0:89.61 | A:99421434;C:73070267;G:77738821;T:92783592;N:0 | 89 | 99421434 | 73070267 | 77738821 | 92783592 | 0 | DRX045206 | DRS025831 | DRA004229 | OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. | Osaka university | 1 | 0.78953 | 0.25529 | 0.87367 | 0.52148 | 24 | B | usable mapping rate | ion_torrent | ion_torrent | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Japan | 2016-03-09 | Undetermined | Undetermined | Fin | Surface Structure | |||||||||||||||||||||||||
| 99 | 99 | DRR050163 | DRX045205 | DRS025830 | DRP003043 | PRJDB4416 | Transcriptome analysis in ES1 expressing rods of zebrafish | DRP003043 | Transcriptome Analysis | Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used. | Zebrafish rods expressing EGFP | EGFP 2 | SAMD00044053 | sample name:EGFP rod 002|strain:Tubingen long fin|cell type:rod | Ion Torrent PGM sequencing of SAMD00044053 | DRX045205 | 1 | 1 | 1 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ION_TORRENT | Ion Torrent PGM | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>137</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> | DRP003043 | Ion Torrent PGM sequencing of SAMD00044053 | 533069427.0 | 3824140.0 | DRR050163 | 0:139.40 | A:152608173;C:113928273;G:120051739;T:146481242;N:0 | 139 | 152608173 | 113928273 | 120051739 | 146481242 | 0 | DRX045205 | DRS025830 | DRA004229 | OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. | Osaka university | 1 | 0.80412 | 0.26768 | 0.85338 | 0.52255 | 245 | B | usable mapping rate | ion_torrent | ion_torrent | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Japan | 2016-03-09 | Undetermined | Undetermined | Fin | Surface Structure | |||||||||||||||||||||||||
| 100 | 100 | DRR050162 | DRX045204 | DRS025829 | DRP003043 | PRJDB4416 | Transcriptome analysis in ES1 expressing rods of zebrafish | DRP003043 | Transcriptome Analysis | Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used. | Zebrafish rods expressing EGFP | EGFP 1 | SAMD00044052 | sample name:EGFP rod 001|strain:Tubingen long fin|cell type:rod | Ion Torrent PGM sequencing of SAMD00044052 | DRX045204 | 1 | 1 | 1 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ION_TORRENT | Ion Torrent PGM | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>113</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> | DRP003043 | Ion Torrent PGM sequencing of SAMD00044052 | 478262965.0 | 4224064.0 | DRR050162 | 0:113.22 | A:136348264;C:104872341;G:113114502;T:123927858;N:0 | 113 | 136348264 | 104872341 | 113114502 | 123927858 | 0 | DRX045204 | DRS025829 | DRA004229 | OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. | Osaka university | 1 | 0.86947 | 0.29839 | 0.83317 | 0.51453 | 80 | B | usable mapping rate | ion_torrent | ion_torrent | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Japan | 2016-03-09 | Undetermined | Undetermined | Fin | Surface Structure |
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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");;