run_metadata
2 rows where devstage_curation = "Pharyngula" and experiment.library_selection = "RT-PCR"
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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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 49248 | 49248 | SRR7881079 | SRX4719723 | SRS3804945 | SRP162200 | PRJNA492186 | Danio rerio Genome sequencing | PRJNA492186 | Other | The transcriptome of zebrafish mutant and wt embryos. | wt | wt | strain:TU|age:30h|sex:not determined|tissue:whole body|phenotype:normal body|BioSampleModel:Model organism or animal | RNA Seq data of wt | RNA Seq data of wt | RNA Seq data of wt | For each sample mRNA was extracted from the whole body of one individual and the standard RNA Seq library was constructed and subjected to Illumina PE125 sequencing | RNA-Seq | TRANSCRIPTOMIC | RT-PCR | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP162200 | WT-blu_L5_I392.R1.clean.fastq.gz WT-blu_L5_I392.R2.clean.fastq.gz | fastq fastq | 3703694250.0 | 14814777.0 | WT blu L5 I392.R2.clean.fastq.gz | 0:125 1:125 | A:966446794;C:893928928;G:885838907;T:957360869;N:118752 | 125 | 125 | 966446794 | 893928928 | 885838907 | 957360869 | 118752 | SRX4719723 | SRS3804945 | SRA779493 | Ocean University of China|College of Marine Life Sciences | Ocean University of China | 2 | 0.97308 | 0.97256 | 0.07482 | 0.07588 | 0.70431 | 0.70595 | 0.49836 | 0.5007 | 125 | 125 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | other | unknown | bulk | unknown | unknown | China | 2018-09-20 | Pharyngula | Embryo | Trunk | Surface Structure | ||||||||||||||||||||
| 49249 | 49249 | SRR7881080 | SRX4719722 | SRS3804946 | SRP162200 | PRJNA492186 | Danio rerio Genome sequencing | PRJNA492186 | Other | The transcriptome of zebrafish mutant and wt embryos. | mutant | zmynd10 mutant | strain:TU|age:30h|sex:not determined|tissue:whole body|phenotype:curve body|BioSampleModel:Model organism or animal | RNA Seq data of zmynd10 mutant | RNA Seq data of zmynd10 mutant | RNA Seq data of zmynd10 mutant | For each sample mRNA was extracted from the whole body of one individual and the standard RNA Seq library was constructed and subjected to Illumina PE125 sequencing | RNA-Seq | TRANSCRIPTOMIC | RT-PCR | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP162200 | MT-blu_L5_I393.R1.clean.fastq.gz MT-blu_L5_I393.R2.clean.fastq.gz | fastq fastq | 4156063750.0 | 16624255.0 | MT blu L5 I393.R2.clean.fastq.gz | 0:125 1:125 | A:1084666899;C:1001943643;G:994799272;T:1074520227;N:133709 | 125 | 125 | 1084666899 | 1001943643 | 994799272 | 1074520227 | 133709 | SRX4719722 | SRS3804946 | SRA779493 | Ocean University of China|College of Marine Life Sciences | Ocean University of China | 2 | 0.97259 | 0.97221 | 0.07667 | 0.0775 | 0.70084 | 0.70199 | 0.4768 | 0.48903 | 125 | 125 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | other | unknown | bulk | unknown | unknown | China | 2018-09-20 | Pharyngula | Embryo | Trunk | 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");;