run_metadata
5 rows where devstage_curation = "Juvenile" and tissue_curation_coarse = "Respiratory System"
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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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 255 | 255 | DRR162486 | DRX153105 | DRS083166 | DRP004696 | PRJDB7713 | Age associated transcriptome analysis in 5 tissues of zebrafish | DRP004696 | Transcriptome Analysis | We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014. | gill sample from 2 mpf zebrafish replicate5 | SAMD00152434 | sample name:g02 5|age:2 month|biological replicate:5|tissue:gill | Illumina HiSeq 2000 paired end sequencing of SAMD00152434 | DRX153105 | 1 | 1 | Illumina TruSeq Stranded mRNA HT Kit | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | DRP004696 | Illumina HiSeq 2000 paired end sequencing of SAMD00152434 | 1270126600.0 | 6350633.0 | DRR162486 | 0:100 1:100 | A:342076596;C:293249973;G:295429735;T:339306175;N:64121 | 100 | 100 | 342076596 | 293249973 | 295429735 | 339306175 | 64121 | DRX153105 | DRS083166 | DRA007711 | UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology | Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo | 2 | 0.9321 | 0.91652 | 0.09414 | 0.09195 | 0.70084 | 0.70412 | 0.52077 | 0.51571 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Japan | 2018-12-24 | Juvenile | Juvenile | Gill | Respiratory System | |||||||||||||||||||
| 256 | 256 | DRR162485 | DRX153104 | DRS083165 | DRP004696 | PRJDB7713 | Age associated transcriptome analysis in 5 tissues of zebrafish | DRP004696 | Transcriptome Analysis | We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014. | gill sample from 2 mpf zebrafish replicate4 | SAMD00152433 | sample name:g02 4|age:2 month|biological replicate:4|tissue:gill | Illumina HiSeq 2000 paired end sequencing of SAMD00152433 | DRX153104 | 1 | 1 | Illumina TruSeq Stranded mRNA HT Kit | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | DRP004696 | Illumina HiSeq 2000 paired end sequencing of SAMD00152433 | 835205000.0 | 4176025.0 | DRR162485 | 0:100 1:100 | A:224993396;C:192858928;G:193779680;T:223531224;N:41772 | 100 | 100 | 224993396 | 192858928 | 193779680 | 223531224 | 41772 | DRX153104 | DRS083165 | DRA007711 | UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology | Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo | 2 | 0.9392 | 0.92364 | 0.08708 | 0.08554 | 0.70579 | 0.71017 | 0.53067 | 0.52045 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Japan | 2018-12-24 | Juvenile | Juvenile | Gill | Respiratory System | |||||||||||||||||||
| 257 | 257 | DRR162484 | DRX153103 | DRS083164 | DRP004696 | PRJDB7713 | Age associated transcriptome analysis in 5 tissues of zebrafish | DRP004696 | Transcriptome Analysis | We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014. | gill sample from 2 mpf zebrafish replicate3 | SAMD00152432 | sample name:g02 3|age:2 month|biological replicate:3|tissue:gill | Illumina HiSeq 2000 paired end sequencing of SAMD00152432 | DRX153103 | 1 | 1 | Illumina TruSeq Stranded mRNA HT Kit | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | DRP004696 | Illumina HiSeq 2000 paired end sequencing of SAMD00152432 | 1038999000.0 | 5194995.0 | DRR162484 | 0:100 1:100 | A:278673674;C:241111198;G:242737620;T:276422623;N:53885 | 100 | 100 | 278673674 | 241111198 | 242737620 | 276422623 | 53885 | DRX153103 | DRS083164 | DRA007711 | UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology | Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo | 2 | 0.92129 | 0.9116 | 0.08334 | 0.0814 | 0.71707 | 0.71821 | 0.5407 | 0.53611 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Japan | 2018-12-24 | Juvenile | Juvenile | Gill | Respiratory System | |||||||||||||||||||
| 258 | 258 | DRR162483 | DRX153102 | DRS083163 | DRP004696 | PRJDB7713 | Age associated transcriptome analysis in 5 tissues of zebrafish | DRP004696 | Transcriptome Analysis | We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014. | gill sample from 2 mpf zebrafish replicate2 | SAMD00152431 | sample name:g02 2|age:2 month|biological replicate:2|tissue:gill | Illumina HiSeq 2000 paired end sequencing of SAMD00152431 | DRX153102 | 1 | 1 | Illumina TruSeq Stranded mRNA HT Kit | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | DRP004696 | Illumina HiSeq 2000 paired end sequencing of SAMD00152431 | 632886400.0 | 3164432.0 | DRR162483 | 0:100 1:100 | A:169214113;C:147628963;G:147454557;T:168556741;N:32026 | 100 | 100 | 169214113 | 147628963 | 147454557 | 168556741 | 32026 | DRX153102 | DRS083163 | DRA007711 | UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology | Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo | 2 | 0.93019 | 0.91653 | 0.08504 | 0.08547 | 0.69367 | 0.70707 | 0.50674 | 0.50918 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Japan | 2018-12-24 | Juvenile | Juvenile | Gill | Respiratory System | |||||||||||||||||||
| 259 | 259 | DRR162482 | DRX153101 | DRS083162 | DRP004696 | PRJDB7713 | Age associated transcriptome analysis in 5 tissues of zebrafish | DRP004696 | Transcriptome Analysis | We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014. | gill sample from 2 mpf zebrafish replicate1 | SAMD00152430 | sample name:g02 1|age:2 month|biological replicate:1|tissue:gill | Illumina HiSeq 2000 paired end sequencing of SAMD00152430 | DRX153101 | 1 | 1 | Illumina TruSeq Stranded mRNA HT Kit | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | DRP004696 | Illumina HiSeq 2000 paired end sequencing of SAMD00152430 | 1323105600.0 | 6615528.0 | DRR162482 | 0:100 1:100 | A:355611103;C:306237205;G:307478272;T:353712733;N:66287 | 100 | 100 | 355611103 | 306237205 | 307478272 | 353712733 | 66287 | DRX153101 | DRS083162 | DRA007711 | UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology | Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo | 2 | 0.93808 | 0.92302 | 0.08542 | 0.08367 | 0.69477 | 0.69897 | 0.52278 | 0.50546 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Japan | 2018-12-24 | Juvenile | Juvenile | Gill | Respiratory 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");;