run_metadata
2 rows where devstage_curation = "Zygote" and experiment.library_strategy = "FL-cDNA"
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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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 75480 | 75480 | SRR24682235 | SRX20461638 | SRS17774509 | SRP438861 | PRJNA973729 | Danio rerio strain:AB Raw sequence reads | PRJNA973729 | Other | Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish. | 1 cell | strain:AB|dev stage:1cell|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal | full length transcriptome of Danio rerio: 1 cell | 1 cell | 1 cell | The RNA of each sample was reversely transcribed into cDNA using a SMARTer PCR cDNA Synthesis Kit. Prime STAR GXL DNA Polymerase Kit was used to PCR amplify the full length cDNA. The SMARTbell libraries were constructed with the SMARTbell template prep kit. Conduct damage repair and end repair. The stem loop sequencing adaptors were linked to both ends of the DNA fragment and used to remove the failed fragment using exonuclease. | FL-cDNA | TRANSCRIPTOMIC | cDNA | SINGLE | PACBIO_SMRT | Sequel | SRP438861 | assembly:GRCz11 | P02TYR22604096_1_r64053_20220510_083113_3_G01.ccs.bam | bam | 2275468478.0 | 775186.0 | P02TYR22604096 1 r64053 20220510 083113 3 G01.ccs.bam | 0:2935.38 | A:638155276;C:516035520;G:543447739;T:577829943;N:0 | 2935 | 638155276 | 516035520 | 543447739 | 577829943 | 0 | SRX20461638 | SRS17774509 | SRA1641718 | Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res | Institute of hydrobiology, chinese academy od sciences | 1 | 0.56682 | 0.00066 | 0.82994 | 0.48167 | 1465 | T | long read | pacbio | pacbio_modern | full_length | cdna_unspecified | smarter | bulk | unknown | unknown | China | 2023-05-21 | Zygote | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||||||||||||
| 75481 | 75481 | SRR24682236 | SRX20461637 | SRS17774508 | SRP438861 | PRJNA973729 | Danio rerio strain:AB Raw sequence reads | PRJNA973729 | Other | Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish. | unfertilized | strain:AB|dev stage:unfertilized|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal | full length transcriptome of Danio rerio: unfertilized | unfertilized | unfertilized | The RNA of each sample was reversely transcribed into cDNA using a SMARTer PCR cDNA Synthesis Kit. Prime STAR GXL DNA Polymerase Kit was used to PCR amplify the full length cDNA. The SMARTbell libraries were constructed with the SMARTbell template prep kit. Conduct damage repair and end repair. The stem loop sequencing adaptors were linked to both ends of the DNA fragment and used to remove the failed fragment using exonuclease. | FL-cDNA | TRANSCRIPTOMIC | cDNA | SINGLE | PACBIO_SMRT | Sequel | SRP438861 | assembly:GRCz11 | P02TYR22614794_1_r64053_20220510_083113_3_G01.ccs.bam | bam | 2243456468.0 | 884312.0 | P02TYR22614794 1 r64053 20220510 083113 3 G01.ccs.bam | 0:2536.95 | A:619660008;C:518127052;G:544711614;T:560957794;N:0 | 2536 | 619660008 | 518127052 | 544711614 | 560957794 | 0 | SRX20461637 | SRS17774508 | SRA1641718 | Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res | Institute of hydrobiology, chinese academy od sciences | 1 | 0.61172 | 0.00053 | 0.84859 | 0.47684 | 2357 | T | long read | pacbio | pacbio_modern | full_length | cdna_unspecified | smarter | bulk | unknown | unknown | China | 2023-05-21 | Zygote | Embryo | Embryo Imprecise | 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");;