run_metadata
4 rows where devstage_curation = "Pharyngula" 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 8056 | 8056 | ERR022486 | ERX008922 | ERS012705 | ERP000400 | PRJEB2333 | Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer | E-MTAB-434 | Other | E MTAB 308:Zebrafish embryo 1 dpf 2 | SAMEA898401 | Wellcome Sanger Institute | Age:1 days|Alias:E MTAB 308:Zebrafish embryo 1 dpf 2|Broker name:ArrayExpress|Description:Protocols: Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 08 19T15:57:35Z|INSDC last update:2018 03 08T15:25:04Z|INSDC status:public|InitialTimePoint:fertilization|OrganismPart:whole organism|SRA accession:ERS012705|Sample Name:ERS012705|Sex:unknown sex|StrainOrLine:Tuebingen|Title:Danio rerio | Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer | E MTAB 434:sequencing of Zebrafish embryo 1 dpf | RNA from Zebrafish embryo 1 dpf | Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer | Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 250 to 300 bp. | Experimental Factor: AGE:1 d|Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism | FL-cDNA | TRANSCRIPTOMIC | unspecified | PAIRED | ILLUMINA | Illumina Genome Analyzer II | ERP000400 | Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer | ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16 | 5141_3.srf | srf | 4788693120.0 | 31504560.0 | E MTAB 434:5141 3.srf | 0:76 1:76 | A:1329328273;C:1071568772;G:1063807333;T:1316891498;N:7097244 | 76 | 76 | 1329328273 | 1071568772 | 1063807333 | 1316891498 | 7097244 | ERX008922 | ERS012705 | ERA015179 | SC|Wellcome Trust Sanger Institute | SC|Wellcome Trust Sanger Institute | 2 | 0.95867 | 0.95691 | 0.14543 | 0.14805 | 0.69753 | 0.70078 | 0.46273 | 0.47662 | 76 | 76 | B | B | biological fallback assumption | illumina | early_illumina | unknown | poly_a | unknown | bulk | unknown | unknown | United Kingdom | 2010-08-19 | Pharyngula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 75474 | 75474 | SRR24682228 | SRX20461644 | SRS17774515 | SRP438861 | PRJNA973729 | Danio rerio strain:AB Raw sequence reads | PRJNA973729 | Other | Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish. | Prim 25 | strain:AB|dev stage:Prim 25|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal | full length transcriptome of Danio rerio: Prim 25 | Prim 25 | Prim 25 | 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 | P02TYR22604113_1_r64053_20220510_083113_4_H01.ccs.bam | bam | 1418704698.0 | 658058.0 | P02TYR22604113 1 r64053 20220510 083113 4 H01.ccs.bam | 0:2155.90 | A:417372714;C:300192249;G:323204197;T:377935538;N:0 | 2155 | 417372714 | 300192249 | 323204197 | 377935538 | 0 | SRX20461644 | SRS17774515 | SRA1641718 | Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res | Institute of hydrobiology, chinese academy od sciences | 1 | 0.62867 | 0.0097 | 0.79415 | 0.47483 | 3839 | T | long read | pacbio | pacbio_modern | full_length | cdna_unspecified | smarter | bulk | unknown | unknown | China | 2023-05-21 | Pharyngula | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||||||||||||
| 75475 | 75475 | SRR24682229 | SRX20461643 | SRS17774514 | SRP438861 | PRJNA973729 | Danio rerio strain:AB Raw sequence reads | PRJNA973729 | Other | Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish. | Prim 15 | strain:AB|dev stage:Prim 15|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal | full length transcriptome of Danio rerio: Prim 15 | Prim 15 | Prim 15 | 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 | P02TYR22604112_1_r64399e_20220512_090859_1_A02.ccs.bam | bam | 1383213564.0 | 564062.0 | P02TYR22604112 1 r64399e 20220512 090859 1 A02.ccs.bam | 0:2452.24 | A:403982699;C:294632569;G:316412345;T:368185951;N:0 | 2452 | 403982699 | 294632569 | 316412345 | 368185951 | 0 | SRX20461643 | SRS17774514 | SRA1641718 | Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res | Institute of hydrobiology, chinese academy od sciences | 1 | 0.5998 | 0.0069 | 0.79636 | 0.46586 | 2601 | T | long read | pacbio | pacbio_modern | full_length | cdna_unspecified | smarter | bulk | unknown | unknown | China | 2023-05-21 | Pharyngula | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||||||||||||
| 75476 | 75476 | SRR24682230 | SRX20461642 | SRS17774513 | SRP438861 | PRJNA973729 | Danio rerio strain:AB Raw sequence reads | PRJNA973729 | Other | Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish. | Prim 5 | strain:AB|dev stage:Prim 5|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal | full length transcriptome of Danio rerio: Prim 5 | Prim 5 | Prim 5 | 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 | P02TYR22604110_1_r64399e_20220512_090859_1_A02.ccs.bam | bam | 1245119132.0 | 541632.0 | P02TYR22604110 1 r64399e 20220512 090859 1 A02.ccs.bam | 0:2298.83 | A:367833391;C:262003404;G:283350026;T:331932311;N:0 | 2298 | 367833391 | 262003404 | 283350026 | 331932311 | 0 | SRX20461642 | SRS17774513 | SRA1641718 | Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res | Institute of hydrobiology, chinese academy od sciences | 1 | 0.62578 | 0.00824 | 0.79669 | 0.47095 | 636 | T | long read | pacbio | pacbio_modern | full_length | cdna_unspecified | smarter | bulk | unknown | unknown | China | 2023-05-21 | Pharyngula | 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");;