run_metadata
2 rows where experiment.library_selection = "RANDOM PCR", technology = "unknown" and tissue_curation = "Undetermined"
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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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 34127 | 34127 | SRR31359854 | SRX26733717 | SRS23223868 | SRP545360 | PRJNA1186345 | The pronephros/cloaca development difference between WT and gdf11 mutants at 24 hpf | PRJNA1186345 | Other | To identify specific genes or signaling pathways or genes with altered expression in pronephric ducts and cloaca in the absence of Gdf11 we analyzed transcriptomic changes using RNA deep sequencing on WT and gdf11 mutant embryos in Tgcdh17 dsRed background at 24 hpf. | LJW KV FKDL210002409 1a | strain:LJW KV FKDL210002409 1a|isolate:zebrafish|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|collection date:2024 02 18|geo loc name:China: Anhui Medical University Hefei|sex:not applicable|tissue:zebrafish|BioSampleModel:Model organism or animal | zebrafish mRNA sequencing | LJW KV FKDL210002409 1a | LJW KV FKDL210002409 1a | RNA seq | RNA-Seq | TRANSCRIPTOMIC | RANDOM PCR | PAIRED | ILLUMINA | Illumina HiSeq 1000 | SRP545360 | LJW-KV_FKDL210002409-1a_1.clean.fq.gz LJW-KV_FKDL210002409-1a_2.clean.fq.gz | fastq fastq | 8667883500.0 | 28892945.0 | LJW KV FKDL210002409 1a 1.clean.fq.gz | 0:150 1:150 | A:2771307253;C:1399313804;G:1767761135;T:2729383521;N:117787 | 150 | 150 | 2771307253 | 1399313804 | 1767761135 | 2729383521 | 117787 | SRX26733717 | SRS23223868 | SRA2015444 | Anhui Medical University|Basical Medicine | Anhui Medical University | B | B | biological fallback assumption | illumina | hiseq_era | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2024-11-15 | Undetermined | Embryo | Undetermined | Embryo Imprecise | ||||||||||||||||||||||||||||||||
| 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");;