run_metadata
2 rows where experiment.library_selection = "RANDOM PCR", experiment.library_source = "TRANSCRIPTOMIC" and experiment.library_strategy = "WGS"
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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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 60550 | 60550 | SRR12342828 | SRX8842536 | SRS7105601 | SRP274071 | PRJNA649399 | zebrafish 5 dpf sequencing | PRJNA649399 | Other | For a more comprehensive analysis for the role of oxr1a on zebrafish for protection against oxidative stress | WT CTRL | strain:no|isolate:without|breed:AB line|cultivar:1|ecotype:2|age:5 dpf|dev stage:larval|sex:male|tissue:whole fish|BioSampleModel:Model organism or animal | whole fish | 729729 | 729729 | AB line gene knockout | WGS | TRANSCRIPTOMIC | RANDOM PCR | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP274071 | WT_ctrl1 WT_ctrl2 | fastq fastq | 2795932250.0 | 11183729.0 | WT ctrl1.gz | 0:125 1:125 | A:714170507;C:687382036;G:684930011;T:709446720;N:2976 | 125 | 125 | 714170507 | 687382036 | 684930011 | 709446720 | 2976 | SRX8842536 | SRS7105601 | SRA1105186 | Southwest University|College of Animal Science and Technolgoy | Southwest University | 2 | 0.96284 | 0.9622 | 0.06398 | 0.06785 | 0.70276 | 0.70179 | 0.50363 | 0.50583 | 125 | 125 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2020-07-29 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||||||||||||
| 60823 | 60823 | SRR12494407 | SRX8985926 | SRS7239898 | SRP278434 | PRJNA658611 | zebrafish starvation stress | PRJNA658611 | Other | RNA Seq Analysis Reveals the Molecular Response Mechanisms in Zebrafish Larvae Undergoing Starvation During the Mouth opening Stage | sszf | strain:AB line|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:8 days|dev stage:larval fish|sex:not determined|tissue:not collected|BioSampleModel:Model organism or animal | Transcriptome analysis reveals the role of exogenous feeding in regulating antioxidant defenses during the mouth opening stage in zebrafish larvae | 821 | 821 | RNA sequencing | WGS | TRANSCRIPTOMIC | RANDOM PCR | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP278434 | Starved2-R2.R2.clean.fastq.gz Starved2-R1.R1.clean.fastq.gz Starved1-R2.R2.clean.fastq.gz Starved1-R1.R1.clean.fastq.gz Control2-R2.R2.clean.fastq.gz Control2-R1.R1.clean.fastq.gz Control1-R2.R2.clean.fastq.gz Control1-R1.R1.clean.fastq.gz | fastq fastq fastq fastq fastq fastq fastq fastq | 11815834250.0 | 47263337.0 | Control1 R1.R1.clean.fastq.gz | 0:125 1:125 | A:2985063485;C:2935671076;G:2921346976;T:2973732805;N:19908 | 125 | 125 | 2985063485 | 2935671076 | 2921346976 | 2973732805 | 19908 | SRX8985926 | SRS7239898 | SRA1115895 | Southwest University|College of Animal Science and Technolgoy | Southwest University | 2 | 0.9663 | 0.96526 | 0.05986 | 0.06116 | 0.70889 | 0.71108 | 0.50789 | 0.50441 | 125 | 125 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2020-08-21 | Larval | Larval | Undetermined | Undetermined |
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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");;