run_metadata
2 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "RT-PCR" and tissue_curation = "Trunk"
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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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 47611 | 47611 | SRR6671794 | SRX3648486 | SRS2913085 | SRP132190 | PRJNA432942 | Zebrafish genes regulated in response to Mucor circinelloides infection | PRJNA432942 | Other | Determination of the genes that can be important for the defense of the host to infection for Mucorales fungi using zebrafish and the fungus Mucor circinelloides as host and pathogen model respectively. Total RNA was sequenced RNA seq from abdominal organs of infected fish. | PBS2 | strain:AB|dev stage:Adult|sex:not determined|tissue:Abdomen|treatment:Control innoculated with PBS|BioSampleModel:Model organism or animal | RNA seq of Darnio rerio: uninffected | PBS2 | PBS2 | Total RNA isolated from uninfected abdominal tissue was used to generate the library using truseq kit | RNA-Seq | TRANSCRIPTOMIC | RT-PCR | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP132190 | PBS2_GCCAAT_L001_R1_001_BH8U70ADXX.filt.fastq.gz | fastq | 792892359.0 | 15546909.0 | PBS2 GCCAAT L001 R1 001 BH8U70ADXX.filt.fastq.gz | 0:51 | A:207417646;C:188867370;G:187996499;T:208448675;N:162169 | 51 | 207417646 | 188867370 | 187996499 | 208448675 | 162169 | SRX3648486 | SRS2913085 | SRA655550 | University of Murcia|Genetics and Microbiology | University of Murcia | 1 | 0.92826 | 0.02642 | 0.72815 | 0.45776 | 51 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Spain | 2018-09-28 | Adult | Adult | Trunk | Surface Structure | ||||||||||||||||||||||||||||
| 47612 | 47612 | SRR6671795 | SRX3648485 | SRS2913084 | SRP132190 | PRJNA432942 | Zebrafish genes regulated in response to Mucor circinelloides infection | PRJNA432942 | Other | Determination of the genes that can be important for the defense of the host to infection for Mucorales fungi using zebrafish and the fungus Mucor circinelloides as host and pathogen model respectively. Total RNA was sequenced RNA seq from abdominal organs of infected fish. | RDRZ | strain:AB|dev stage:Adult|sex:not determined|tissue:Abdomen|treatment:Infected with Mucor circinelloides spores|BioSampleModel:Model organism or animal | RNA seq of Darnio rerio: infected with Mucor circinelloides | RDRZ | RDRZ | Total RNA isolated from abdominal tissue infected with Mucor circinelloides was used to generate the library using truseq kit | RNA-Seq | TRANSCRIPTOMIC | RT-PCR | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP132190 | RDRZ_TGACCA_L001_R1_001_BH8U70ADXX.filt.fastq.gz | fastq | 741005418.0 | 14529518.0 | RDRZ TGACCA L001 R1 001 BH8U70ADXX.filt.fastq.gz | 0:51 | A:192330774;C:178252917;G:175501754;T:194766886;N:153087 | 51 | 192330774 | 178252917 | 175501754 | 194766886 | 153087 | SRX3648485 | SRS2913084 | SRA655550 | University of Murcia|Genetics and Microbiology | University of Murcia | 1 | 0.91685 | 0.03703 | 0.70873 | 0.49947 | 51 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Spain | 2018-09-28 | Adult | Adult | 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");;