run_metadata
6 rows where experiment.platform = "COMPLETE_GENOMICS", technology = "unknown" 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 41782 | 41782 | SRR5162099 | SRX2480053 | SRS1910957 | SRP096313 | PRJNA360680 | S6K1 project raw sequence reads | PRJNA360680 | Other | PLC5shCtrl1 | breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:PLC5shCtrl1|BioSampleModel:Model organism or animal | PLC5shCtrl1 | PLC5shCtrl1 | PLC5shCtrl1 | Total RNA was isolated from the stable transfected cells shCtrl and shS6K1 from Hep3B and PLC5 cells using the mirVanaTM RNA isolation kit Applied Biosystems. The quality of RNA was assessed using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction. The RNA library was sequenced by the Beijing Genomics Institute Wuhan China. Single end reads 50 bp read length were sequenced on the BGISEQ 500RS sequencer. Qualified raw data were provided by the Beijing Genomics Institute in FASTQ format. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | COMPLETE_GENOMICS | Complete Genomics | SRP096313 | 1201388650.0 | 24027773.0 | CL100006841 L02 24 1.fq.gz | 0:50 | A:297299471;C:292335863;G:332701724;T:278571616;N:479976 | 50 | 297299471 | 292335863 | 332701724 | 278571616 | 479976 | SRX2480053 | SRS1910957 | SRA525651 | The Chinese University of Hong Kong|School of Life Sciences | The Chinese University of Hong Kong|School of Life Sciences | 1 | 0.00295 | 0.00039 | 0.99754 | 0.63223 | 50 | T | under 1.2% mapping rate | legacy | early | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2017-01-10 | Larval | Larval | Embryo Imprecise | All anatomical structures | |||||||||||||||||||||||||||||||
| 41783 | 41783 | SRR5162098 | SRX2480052 | SRS1910956 | SRP096313 | PRJNA360680 | S6K1 project raw sequence reads | PRJNA360680 | Other | Hep3BshS6K1 | breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:Hep3BshS6K1|BioSampleModel:Model organism or animal | Hep3BshS6K1 | Hep3BshS6K1 | Hep3BshS6K1 | Total RNA was isolated from the stable transfected cells shCtrl and shS6K1 from Hep3B and PLC5 cells using the mirVanaTM RNA isolation kit Applied Biosystems. The quality of RNA was assessed using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction. The RNA library was sequenced by the Beijing Genomics Institute Wuhan China. Single end reads 50 bp read length were sequenced on the BGISEQ 500RS sequencer. Qualified raw data were provided by the Beijing Genomics Institute in FASTQ format. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | COMPLETE_GENOMICS | Complete Genomics | SRP096313 | 1205347750.0 | 24106955.0 | CL100006841 L02 21 1.fq.gz | 0:50 | A:312935885;C:282462046;G:322914710;T:286516924;N:518185 | 50 | 312935885 | 282462046 | 322914710 | 286516924 | 518185 | SRX2480052 | SRS1910956 | SRA525651 | The Chinese University of Hong Kong|School of Life Sciences | The Chinese University of Hong Kong|School of Life Sciences | 1 | 0.00262 | 0.00033 | 0.99764 | 0.69195 | 50 | T | under 1.2% mapping rate | legacy | early | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2017-01-10 | Larval | Larval | Embryo Imprecise | All anatomical structures | |||||||||||||||||||||||||||||||
| 41784 | 41784 | SRR5162097 | SRX2480051 | SRS1910955 | SRP096313 | PRJNA360680 | S6K1 project raw sequence reads | PRJNA360680 | Other | PLC5shS6K1 | breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:PLC5shS6K1|BioSampleModel:Model organism or animal | PLC5shS6K1 | PLC5shS6K1 | PLC5shS6K1 | 1 | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | COMPLETE_GENOMICS | Complete Genomics | SRP096313 | 1205157400.0 | 24103148.0 | CL100006841 L02 25 1.fq.gz | 0:50 | A:305738728;C:286350102;G:329378158;T:283136091;N:554321 | 50 | 305738728 | 286350102 | 329378158 | 283136091 | 554321 | SRX2480051 | SRS1910955 | SRA525651 | The Chinese University of Hong Kong|School of Life Sciences | The Chinese University of Hong Kong|School of Life Sciences | 1 | 0.00275 | 0.00036 | 0.99801 | 0.66666 | 50 | T | under 1.2% mapping rate | legacy | early | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2017-01-10 | Larval | Larval | Embryo Imprecise | All anatomical structures | |||||||||||||||||||||||||||||||
| 41785 | 41785 | SRR5162096 | SRX2480050 | SRS1910954 | SRP096313 | PRJNA360680 | S6K1 project raw sequence reads | PRJNA360680 | Other | HepG2shS6K1 | breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:HepG2shS6K1|BioSampleModel:Model organism or animal | HepG2shS6K1 | HepG2shS6K1 | HepG2shS6K1 | Total RNA was isolated from the stable transfected cells shCtrl and shS6K1 from Hep3B and PLC5 cells using the mirVanaTM RNA isolation kit Applied Biosystems. The quality of RNA was assessed using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction. The RNA library was sequenced by the Beijing Genomics Institute Wuhan China. Single end reads 50 bp read length were sequenced on the BGISEQ 500RS sequencer. Qualified raw data were provided by the Beijing Genomics Institute in FASTQ format. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | COMPLETE_GENOMICS | Complete Genomics | SRP096313 | 1203548150.0 | 24070963.0 | CL100006841 L02 23 1.fq.gz | 0:50 | A:307598832;C:285812241;G:331356323;T:278082314;N:698440 | 50 | 307598832 | 285812241 | 331356323 | 278082314 | 698440 | SRX2480050 | SRS1910954 | SRA525651 | The Chinese University of Hong Kong|School of Life Sciences | The Chinese University of Hong Kong|School of Life Sciences | 1 | 0.00192 | 0.00012 | 0.99784 | 0.60818 | 50 | T | under 1.2% mapping rate | legacy | early | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2017-01-10 | Larval | Larval | Embryo Imprecise | All anatomical structures | |||||||||||||||||||||||||||||||
| 41786 | 41786 | SRR5162095 | SRX2480049 | SRS1910953 | SRP096313 | PRJNA360680 | S6K1 project raw sequence reads | PRJNA360680 | Other | Hep3BshCtrl1 | breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:Hep3BshCtrl1|BioSampleModel:Model organism or animal | Hep3BshCtrl1 | Hep3BshCtrl1 | Hep3BshCtrl1 | Total RNA was isolated from the stable transfected cells shCtrl and shS6K1 from Hep3B and PLC5 cells using the mirVanaTM RNA isolation kit Applied Biosystems. The quality of RNA was assessed using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction. The RNA library was sequenced by the Beijing Genomics Institute Wuhan China. Single end reads 50 bp read length were sequenced on the BGISEQ 500RS sequencer. Qualified raw data were provided by the Beijing Genomics Institute in FASTQ format. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | COMPLETE_GENOMICS | Complete Genomics | SRP096313 | 1201618100.0 | 24032362.0 | CL100006841 L02 20 1.fq.gz | 0:50 | A:301938424;C:291014141;G:326734280;T:281455564;N:475691 | 50 | 301938424 | 291014141 | 326734280 | 281455564 | 475691 | SRX2480049 | SRS1910953 | SRA525651 | The Chinese University of Hong Kong|School of Life Sciences | The Chinese University of Hong Kong|School of Life Sciences | 1 | 0.00522 | 0.00084 | 0.99722 | 0.61317 | 50 | T | under 1.2% mapping rate | legacy | early | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2017-01-10 | Larval | Larval | Embryo Imprecise | All anatomical structures | |||||||||||||||||||||||||||||||
| 41787 | 41787 | SRR5162094 | SRX2480048 | SRS1910952 | SRP096313 | PRJNA360680 | S6K1 project raw sequence reads | PRJNA360680 | Other | HepG2shCtrl1 | breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:HepG2shCtrl1|BioSampleModel:Model organism or animal | HepG2shCtrl1 | HepG2shCtrl1 | HepG2shCtrl1 | Total RNA was isolated from the stable transfected cells shCtrl and shS6K1 from Hep3B and PLC5 cells using the mirVanaTM RNA isolation kit Applied Biosystems. The quality of RNA was assessed using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction. The RNA library was sequenced by the Beijing Genomics Institute Wuhan China. Single end reads 50 bp read length were sequenced on the BGISEQ 500RS sequencer. Qualified raw data were provided by the Beijing Genomics Institute in FASTQ format. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | COMPLETE_GENOMICS | Complete Genomics | SRP096313 | 1205042850.0 | 24100857.0 | CL100006841 L02 22 1.fq.gz | 0:50 | A:310292006;C:282567913;G:329631833;T:282050651;N:500447 | 50 | 310292006 | 282567913 | 329631833 | 282050651 | 500447 | SRX2480048 | SRS1910952 | SRA525651 | The Chinese University of Hong Kong|School of Life Sciences | The Chinese University of Hong Kong|School of Life Sciences | 1 | 0.00164 | 0.00012 | 0.99784 | 0.62847 | 50 | T | under 1.2% mapping rate | legacy | early | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2017-01-10 | Larval | Larval | 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");;