run_metadata
3 rows where experiment.library_layout = "SINGLE", experiment.library_strategy = "OTHER" and experiment.platform = "OXFORD_NANOPORE"
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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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 10212 | 10212 | ERR6511331 | ERX6138167 | ERS7264190 | ERP131213 | PRJEB46978 | Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore sequencing | ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-12-08-2021-14:48:52:906-1159 | Other | Nano3P seq is a simple and robust method to accurately estimate transcript levels tail lengths and tail nucleotide composition information in full length individual reads with minimal library preparation biases both in the coding and non coding transcriptome. | ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28 | Zebrafish Nano3P seq of PolyA selected sample biological replicate 1 including 4 hpf RNA | Zebrafish PolyA 4 hpf | SAMEA9541420 | CENTER FOR GENOMIC REGULATION (CRG) | ENA FIRST PUBLIC:2023 12 28T01:07:23Z|ENA LAST UPDATE:2023 12 28T01:07:23Z|External Id:SAMEA9541420|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2023 12 28T01:07:23Z|INSDC last update:2023 12 28T01:07:23Z|INSDC status:public|Submitter Id:Zebrafish PolyA 4 hpf|common name:zebrafish|sample name:Zebrafish PolyA 4 hpf|scientific name:Danio rerio | MinION sequencing | ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 5 | cDNA8523612 | Nano3P seq | Nano3P seq | OTHER | TRANSCRIPTOMIC | unspecified | SINGLE | OXFORD_NANOPORE | MinION | ERP131213 | MinION sequencing | ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28 | zebrafish_polya_4hpf.tar.gz | nanopore | 330562220.0 | 233101.0 | ena RUN CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 5 | 0:1418.11 | A:86572446;C:74232962;G:69203462;T:100553350;N:0 | 1418 | 86572446 | 74232962 | 69203462 | 100553350 | 0 | ERX6138167 | ERS7264190 | ERA5757997 | CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive | CENTER FOR GENOMIC REGULATION (CRG) | 1 | 0.0 | 0.0 | 1.0 | 1536 | T | long read | ont | ont | full_length | poly_a | unknown | bulk | unknown | unknown | Spain | 2023-12-28 | Blastula | Embryo | Undetermined | Embryo Imprecise | ||||||||||||||||||||||
| 10213 | 10213 | ERR6511329 | ERX6138165 | ERS7264188 | ERP131213 | PRJEB46978 | Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore sequencing | ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-12-08-2021-14:48:52:906-1159 | Other | Nano3P seq is a simple and robust method to accurately estimate transcript levels tail lengths and tail nucleotide composition information in full length individual reads with minimal library preparation biases both in the coding and non coding transcriptome. | ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28 | Zebrafish Nano3P seq of Ribodepleted sample biological replicate 1 including 2 hpf 4 hpf 6 hpf RNAs | Zebrafish Ribodep Rep1 | SAMEA9541418 | CENTER FOR GENOMIC REGULATION (CRG) | ENA FIRST PUBLIC:2023 12 28T01:07:23Z|ENA LAST UPDATE:2023 12 28T01:07:23Z|External Id:SAMEA9541418|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2023 12 28T01:07:23Z|INSDC last update:2023 12 28T01:07:23Z|INSDC status:public|Submitter Id:Zebrafish Ribodep Rep1|common name:zebrafish|sample name:Zebrafish Ribodep Rep1|scientific name:Danio rerio | MinION sequencing | ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 3 | cDNA786327 | Nano3P seq | Nano3P seq | OTHER | TRANSCRIPTOMIC | unspecified | SINGLE | OXFORD_NANOPORE | MinION | ERP131213 | MinION sequencing | ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28 | zebrafish_ribodep_rep1.tar.gz | nanopore | 1745399583.0 | 1644167.0 | ena RUN CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 3 | 0:1061.57 | A:449704009;C:421915878;G:378879857;T:494899839;N:0 | 1061 | 449704009 | 421915878 | 378879857 | 494899839 | 0 | ERX6138165 | ERS7264188 | ERA5757997 | CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive | CENTER FOR GENOMIC REGULATION (CRG) | 1 | 0.01112 | 0.0 | 0.99997 | 1.0 | 546 | T | long read | ont | ont | full_length | rrna_depletion | unknown | bulk | unknown | unknown | Spain | 2023-12-28 | Multi-stage | Embryo | Undetermined | Embryo Imprecise | |||||||||||||||||||||
| 10215 | 10215 | ERR6511330 | ERX6138166 | ERS7264189 | ERP131213 | PRJEB46978 | Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore sequencing | ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-12-08-2021-14:48:52:906-1159 | Other | Nano3P seq is a simple and robust method to accurately estimate transcript levels tail lengths and tail nucleotide composition information in full length individual reads with minimal library preparation biases both in the coding and non coding transcriptome. | ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28 | Zebrafish Nano3P seq of Ribodepleted sample biological replicate 1 including 2 hpf 4 hpf 6 hpf RNAs | Zebrafish Ribodep Rep2 | SAMEA9541419 | CENTER FOR GENOMIC REGULATION (CRG) | ENA FIRST PUBLIC:2023 12 28T01:07:23Z|ENA LAST UPDATE:2023 12 28T01:07:23Z|External Id:SAMEA9541419|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2023 12 28T01:07:23Z|INSDC last update:2023 12 28T01:07:23Z|INSDC status:public|Submitter Id:Zebrafish Ribodep Rep2|common name:zebrafish|sample name:Zebrafish Ribodep Rep2|scientific name:Danio rerio | MinION sequencing | ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 4 | cDNA123791 | Nano3P seq | Nano3P seq | OTHER | TRANSCRIPTOMIC | unspecified | SINGLE | OXFORD_NANOPORE | MinION | ERP131213 | MinION sequencing | ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28 | zebrafish_ribodep_rep2.tar.gz | nanopore | 2038398139.0 | 1955617.0 | ena RUN CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 4 | 0:1042.33 | A:518369802;C:477535545;G:441294056;T:601198736;N:0 | 1042 | 518369802 | 477535545 | 441294056 | 601198736 | 0 | ERX6138166 | ERS7264189 | ERA5757997 | CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive | CENTER FOR GENOMIC REGULATION (CRG) | ont | ont | full_length | rrna_depletion | unknown | bulk | unknown | unknown | Spain | 2023-12-28 | Multi-stage | Embryo | Undetermined | Embryo Imprecise |
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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");;