run_metadata
3 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "CAGE" and tissue_curation_coarse = "All anatomical structures"
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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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 55270 | 55270 | SRR10215486 | SRX6935169 | SRS5465204 | SRP223930 | PRJNA575342 | CAGE /CappedRNA sequencig | PRJNA575342 | Other | CAGE and full length capped RNA sequencing for identification of transcription start TSS utilisation during Zebrafish Danio rerio embryonic development | S06 Prim5 | strain:AB|dev stage:Prim 5|sex:N/A|tissue:whole embryo|BioSampleModel:Model organism or animal | CAGE seq of Danio rerio whole embryo Prim 5 stage | Prim5 nAnTiCAGE | Prim5 nAnTiCAGE | nAnTiCAGE | RNA-Seq | TRANSCRIPTOMIC | CAGE | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP223930 | S06_Prim5_nAnTiCAGE_1.fastq.gz S06_Prim5_nAnTiCAGE_2.fastq.gz | fastq fastq | 2672456099.0 | 13565767.0 | S06 Prim5 nAnTiCAGE 1.fastq.gz | 0:97 1:100 | A:641958912;C:678208106;G:686299870;T:662301091;N:3688120 | 97 | 100 | 641958912 | 678208106 | 686299870 | 662301091 | 3688120 | SRX6935169 | SRS5465204 | SRA971223 | University of Birmingham|Cancer and Genomic Sciences | University of Birmingham | 2 | 0.94637 | 0.95975 | 0.15027 | 0.16177 | 0.74119 | 0.7441 | 0.50314 | 0.54386 | 97 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | cage | unknown | bulk | unknown | unknown | United Kingdom | 2019-10-02 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||
| 55271 | 55271 | SRR10215487 | SRX6935168 | SRS5465203 | SRP223930 | PRJNA575342 | CAGE /CappedRNA sequencig | PRJNA575342 | Other | CAGE and full length capped RNA sequencing for identification of transcription start TSS utilisation during Zebrafish Danio rerio embryonic development | S05 4 Somies | strain:AB|dev stage:4 5 somites|sex:N/A|tissue:whole embryo|BioSampleModel:Model organism or animal | CAGE seq of Danio rerio whole embryo 4 5 somites stage | 4Somites nAnTiCAGE | 4Somites nAnTiCAGE | nAnTiCAGE | RNA-Seq | TRANSCRIPTOMIC | CAGE | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP223930 | S05_4Somites_nAnTiCAGE_1.fastq.gz S05_4Somites_nAnTiCAGE_2.fastq.gz | fastq fastq | 1532850499.0 | 7780967.0 | S05 4Somites nAnTiCAGE 1.fastq.gz | 0:97 1:100 | A:368505591;C:387404999;G:393120996;T:381726796;N:2092117 | 97 | 100 | 368505591 | 387404999 | 393120996 | 381726796 | 2092117 | SRX6935168 | SRS5465203 | SRA971223 | University of Birmingham|Cancer and Genomic Sciences | University of Birmingham | 2 | 0.93818 | 0.96364 | 0.10425 | 0.1218 | 0.75116 | 0.74852 | 0.54456 | 0.54636 | 97 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | cage | unknown | bulk | unknown | unknown | United Kingdom | 2019-10-02 | Segmentation | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||
| 55275 | 55275 | SRR10215491 | SRX6935164 | SRS5465199 | SRP223930 | PRJNA575342 | CAGE /CappedRNA sequencig | PRJNA575342 | Other | CAGE and full length capped RNA sequencing for identification of transcription start TSS utilisation during Zebrafish Danio rerio embryonic development | S01 1Cell | strain:AB|dev stage:1cell|sex:N/A|tissue:whole embryo|BioSampleModel:Model organism or animal | CAGE seq of Danio rerio whole embryo 1 cell stage | 1Cell nAnTiCAGE | 1Cell nAnTiCAGE | nAnTiCAGE | RNA-Seq | TRANSCRIPTOMIC | CAGE | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP223930 | S01_1Cells_nAnTiCAGE_1.fastq.gz S01_1Cells_nAnTiCAGE_2.fastq.gz | fastq fastq | 1193891117.0 | 6060361.0 | S01 1Cells nAnTiCAGE 1.fastq.gz | 0:97 1:100 | A:286037352;C:298140071;G:310668851;T:297430066;N:1614777 | 97 | 100 | 286037352 | 298140071 | 310668851 | 297430066 | 1614777 | SRX6935164 | SRS5465199 | SRA971223 | University of Birmingham|Cancer and Genomic Sciences | University of Birmingham | 2 | 0.93733 | 0.97059 | 0.08219 | 0.07881 | 0.76682 | 0.75834 | 0.53879 | 0.54537 | 97 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | cage | unknown | bulk | unknown | unknown | United Kingdom | 2019-10-02 | Zygote | Embryo | Whole Organism | All anatomical structures |
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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");;