run_metadata
2 rows where experiment.library_strategy = "FL-cDNA" and tissue_curation = "Head"
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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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 8059 | 8059 | ERR022480 | ERX008923 | ERS000088 | ERP000400 | PRJEB2333 | Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer | E-MTAB-434 | Other | ZF female head sample1 | SAMEA708836 | Wellcome Sanger Institute | Alias:ZF female head sample1|Description:RNA extracted from female adult zebrafish head|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 02 26T10:44:13Z|INSDC last update:2018 03 08T15:24:37Z|INSDC status:public|SRA accession:ERS000088|Sample Name:ERS000088|Sex:female|Strain:Tuebingen|Title:Danio rerio | Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer | E MTAB 434:sequencing of Zebrafish adult female head | RNA from Zebrafish adult female head | Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer | Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. 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 resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 150 to 200 bp. | Experimental Factor: DEVELPOMENTAL STAGE:adult|Experimental Factor: ORGANISM PART:head | FL-cDNA | TRANSCRIPTOMIC | unspecified | PAIRED | ILLUMINA | Illumina Genome Analyzer II | ERP000400 | Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer | ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16 | 2719_5.srf | srf | 1622590272.0 | 15023984.0 | E MTAB 434:2719 5.srf | 0:54 1:54 | A:426435544;C:373743071;G:387589492;T:432086510;N:2735655 | 54 | 54 | 426435544 | 373743071 | 387589492 | 432086510 | 2735655 | ERX008923 | ERS000088 | ERA015179 | SC|Wellcome Trust Sanger Institute | SC|Wellcome Trust Sanger Institute | 2 | 0.94624 | 0.94338 | 0.17949 | 0.17965 | 0.66454 | 0.66872 | 0.51097 | 0.51377 | 54 | 54 | B | B | biological fallback assumption | illumina | early_illumina | unknown | poly_a | unknown | bulk | unknown | unknown | United Kingdom | 2010-02-26 | Adult | Adult | Head | Nervous System | ||||||||||||||||
| 8060 | 8060 | ERR022481 | ERX008923 | ERS000088 | ERP000400 | PRJEB2333 | Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer | E-MTAB-434 | Other | ZF female head sample1 | SAMEA708836 | Wellcome Sanger Institute | Alias:ZF female head sample1|Description:RNA extracted from female adult zebrafish head|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 02 26T10:44:13Z|INSDC last update:2018 03 08T15:24:37Z|INSDC status:public|SRA accession:ERS000088|Sample Name:ERS000088|Sex:female|Strain:Tuebingen|Title:Danio rerio | Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer | E MTAB 434:sequencing of Zebrafish adult female head | RNA from Zebrafish adult female head | Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer | Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. 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 resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 150 to 200 bp. | Experimental Factor: DEVELPOMENTAL STAGE:adult|Experimental Factor: ORGANISM PART:head | FL-cDNA | TRANSCRIPTOMIC | unspecified | PAIRED | ILLUMINA | Illumina Genome Analyzer II | ERP000400 | Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer | ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16 | 2719_6.srf | srf | 1693460736.0 | 15680192.0 | E MTAB 434:2719 6.srf | 0:54 1:54 | A:445666325;C:389360280;G:403789644;T:451529226;N:3115261 | 54 | 54 | 445666325 | 389360280 | 403789644 | 451529226 | 3115261 | ERX008923 | ERS000088 | ERA015179 | SC|Wellcome Trust Sanger Institute | SC|Wellcome Trust Sanger Institute | 2 | 0.94579 | 0.94429 | 0.17895 | 0.17923 | 0.66864 | 0.67164 | 0.51788 | 0.51083 | 54 | 54 | B | B | biological fallback assumption | illumina | early_illumina | unknown | poly_a | unknown | bulk | unknown | unknown | United Kingdom | 2010-02-26 | Adult | Adult | Head | Nervous 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");;