run_metadata
5 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 10214 | 10214 | ERR6617900 | ERX6244443 | ERS7291130 | 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 | PolyA selected dRNA sequenced zebrafish 4hpf RNA | Zebrafish 4hpf dRNA | SAMEA9568396 | CENTER FOR GENOMIC REGULATION (CRG) | ENA FIRST PUBLIC:2023 12 28T01:07:30Z|ENA LAST UPDATE:2023 12 28T01:07:30Z|External Id:SAMEA9568396|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2023 12 28T01:07:30Z|INSDC last update:2023 12 28T01:07:30Z|INSDC status:public|Submitter Id:Zebrafish 4hpf dRNA1|common name:zebrafish|sample name:Zebrafish 4hpf dRNA1|scientific name:Danio rerio | MinION sequencing | ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 03 09 2021 14:33:13:450 1 | dRNA Zebrafish | Direct RNA Sequencing | Direct RNA Sequencing | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | OXFORD_NANOPORE | MinION | ERP131213 | MinION sequencing | ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28 | Zebrafish_4hpf_dRNA.fast5.tar.gz | nanopore | 772304625.0 | 897768.0 | ena RUN CENTER FOR GENOMIC REGULATION CRG 03 09 2021 14:33:13:450 1 | 0:860.25 | A:224977035;C:165273397;G:156659356;T:225394837;N:0 | 860 | 224977035 | 165273397 | 156659356 | 225394837 | 0 | ERX6244443 | ERS7291130 | ERA5995143 | CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive | CENTER FOR GENOMIC REGULATION (CRG) | 1 | 0.5 | 0.0 | 0.99997 | 1.0 | 962 | T | long read | ont | ont | full_length | poly_a | unknown | bulk | unknown | unknown | Spain | 2023-12-28 | Blastula | Embryo | Undetermined | Embryo Imprecise | |||||||||||||||||||||
| 11042 | 11042 | ERR9839781 | ERX9385638 | ERS12199238 | ERP138294 | PRJEB53494 | Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore cDNA sequencing | 94bf5509-4622-4d5f-b7c5-6a14bdfac340 | Other | RNA polyadenylation plays a central role in RNA maturation fate and stability. In response to developmental cues polyA tail lengths can vary affecting the translation efficiency and stability of mRNAs. Here we develop Nanopore three prime end capture sequencing Nano3P seq a novel method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance tail composition and tail length dynamics at per read resolution. By employing a template switching based sequencing protocol Nano3P seq can sequence any given RNA molecule from its three prime end regardless of its polyadenylation status without xxx need for PCR amplification or ligation of RNA adapters. We demonstrate that Nano3P seq captures a wide diversity of RNA biotypes providing quantitative estimates of RNA abundance and tail lengths in mRNA lncRNA sn/snoRNA scaRNA and rRNA molecules. We find that in addition to mRNA and lncRNA polyA tails can be identified in 16S mitochondrial rRNA in both mouse and zebrafish models. Moreover we show that mRNA tail lengths are dynamically regulated during vertebrate embryogenesis at an isoform specific level correlating with mRNA decay. Finally we identify non A bases within polyA tails of various lengths and reveal their distribution during vertebrate embryogenesis. Overall Nano3P seq is a simple and robust method for accurately estimating transcript levels tail lengths and tail composition heterogeneity in individual reads with minimal library preparation biases both in the coding and non coding transcriptome. | ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10 | Zebrafish Ribodepleted RNA 2hpf 4hpf 6hpf | Zebrafish Ribodepleted Rep3 | SAMEA110100413 | CENTER FOR GENOMIC REGULATION (CRG) | ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10|External Id:SAMEA110100413|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 10 10T00:20:53Z|INSDC last update:2022 10 10T00:20:53Z|INSDC status:public|Submitter Id:Zebrafish Ribodepleted Rep3|common name:zebrafish|sample name:Zebrafish Ribodepleted Rep3 | MinION sequencing | ena EXPERIMENT TAB 13 06 2022 16:07:52:807 817 | cDNA897892 ZFRDR3 | 1 | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | OXFORD_NANOPORE | MinION | ERP138294 | MinION sequencing | ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10 | cDNA897892_ZFRDR3.tar.gz | nanopore | 848659575.0 | 587586.0 | ena RUN TAB 13 06 2022 16:07:52:808 818 | 0:1444.32 | A:210205014;C:186527780;G:188214279;T:263712502;N:0 | 1444 | 210205014 | 186527780 | 188214279 | 263712502 | 0 | ERX9385638 | ERS12199238 | ERA15547404 | CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive | CENTER FOR GENOMIC REGULATION (CRG) | ont | ont | 3prime | poly_a | unknown | bulk | unknown | unknown | Spain | 2022-10-10 | Multi-stage | Embryo | Undetermined | Embryo Imprecise | ||||||||||||||||||||||||||||||
| 11043 | 11043 | ERR9839780 | ERX9385637 | ERS12199237 | ERP138294 | PRJEB53494 | Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore cDNA sequencing | 94bf5509-4622-4d5f-b7c5-6a14bdfac340 | Other | RNA polyadenylation plays a central role in RNA maturation fate and stability. In response to developmental cues polyA tail lengths can vary affecting the translation efficiency and stability of mRNAs. Here we develop Nanopore three prime end capture sequencing Nano3P seq a novel method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance tail composition and tail length dynamics at per read resolution. By employing a template switching based sequencing protocol Nano3P seq can sequence any given RNA molecule from its three prime end regardless of its polyadenylation status without xxx need for PCR amplification or ligation of RNA adapters. We demonstrate that Nano3P seq captures a wide diversity of RNA biotypes providing quantitative estimates of RNA abundance and tail lengths in mRNA lncRNA sn/snoRNA scaRNA and rRNA molecules. We find that in addition to mRNA and lncRNA polyA tails can be identified in 16S mitochondrial rRNA in both mouse and zebrafish models. Moreover we show that mRNA tail lengths are dynamically regulated during vertebrate embryogenesis at an isoform specific level correlating with mRNA decay. Finally we identify non A bases within polyA tails of various lengths and reveal their distribution during vertebrate embryogenesis. Overall Nano3P seq is a simple and robust method for accurately estimating transcript levels tail lengths and tail composition heterogeneity in individual reads with minimal library preparation biases both in the coding and non coding transcriptome. | ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10 | Zebrafish Ribodepleted RNA 2hpf 4hpf 6hpf | Zebrafish Ribodepleted Rep2 | SAMEA110100412 | CENTER FOR GENOMIC REGULATION (CRG) | ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10|External Id:SAMEA110100412|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 10 10T00:20:53Z|INSDC last update:2022 10 10T00:20:53Z|INSDC status:public|Submitter Id:Zebrafish Ribodepleted Rep2|common name:zebrafish|sample name:Zebrafish Ribodepleted Rep2 | MinION sequencing | ena EXPERIMENT TAB 13 06 2022 16:07:52:807 815 | cDNA123791 ZFRDR2 | 1 | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | OXFORD_NANOPORE | MinION | ERP138294 | MinION sequencing | ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10 | cDNA123791_ZFRDR2.tar.gz | nanopore | 2229275175.0 | 1955617.0 | ena RUN TAB 13 06 2022 16:07:52:807 816 | 0:1139.93 | A:533543922;C:498938137;G:515833119;T:680959997;N:0 | 1139 | 533543922 | 498938137 | 515833119 | 680959997 | 0 | ERX9385637 | ERS12199237 | ERA15547404 | CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive | CENTER FOR GENOMIC REGULATION (CRG) | ont | ont | 3prime | poly_a | unknown | bulk | unknown | unknown | Spain | 2022-10-10 | Multi-stage | Embryo | Undetermined | Embryo Imprecise | ||||||||||||||||||||||||||||||
| 11044 | 11044 | ERR9839779 | ERX9385636 | ERS12199236 | ERP138294 | PRJEB53494 | Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore cDNA sequencing | 94bf5509-4622-4d5f-b7c5-6a14bdfac340 | Other | RNA polyadenylation plays a central role in RNA maturation fate and stability. In response to developmental cues polyA tail lengths can vary affecting the translation efficiency and stability of mRNAs. Here we develop Nanopore three prime end capture sequencing Nano3P seq a novel method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance tail composition and tail length dynamics at per read resolution. By employing a template switching based sequencing protocol Nano3P seq can sequence any given RNA molecule from its three prime end regardless of its polyadenylation status without xxx need for PCR amplification or ligation of RNA adapters. We demonstrate that Nano3P seq captures a wide diversity of RNA biotypes providing quantitative estimates of RNA abundance and tail lengths in mRNA lncRNA sn/snoRNA scaRNA and rRNA molecules. We find that in addition to mRNA and lncRNA polyA tails can be identified in 16S mitochondrial rRNA in both mouse and zebrafish models. Moreover we show that mRNA tail lengths are dynamically regulated during vertebrate embryogenesis at an isoform specific level correlating with mRNA decay. Finally we identify non A bases within polyA tails of various lengths and reveal their distribution during vertebrate embryogenesis. Overall Nano3P seq is a simple and robust method for accurately estimating transcript levels tail lengths and tail composition heterogeneity in individual reads with minimal library preparation biases both in the coding and non coding transcriptome. | ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10 | Zebrafish Ribodepleted RNA 2hpf 4hpf 6hpf | Zebrafish Ribodepleted Rep1 | SAMEA110100411 | CENTER FOR GENOMIC REGULATION (CRG) | ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10|External Id:SAMEA110100411|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 10 10T00:20:53Z|INSDC last update:2022 10 10T00:20:53Z|INSDC status:public|Submitter Id:Zebrafish Ribodepleted Rep1|common name:zebrafish|sample name:Zebrafish Ribodepleted Rep1 | MinION sequencing | ena EXPERIMENT TAB 13 06 2022 16:07:52:807 813 | cDNA786327 ZFRDR1 | 1 | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | OXFORD_NANOPORE | MinION | ERP138294 | MinION sequencing | ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10 | cDNA786327_ZFRDR1.tar.gz | nanopore | 1900613556.0 | 1660167.0 | ena RUN TAB 13 06 2022 16:07:52:807 814 | 0:1144.83 | A:473050820;C:438054520;G:425169743;T:564338473;N:0 | 1144 | 473050820 | 438054520 | 425169743 | 564338473 | 0 | ERX9385636 | ERS12199236 | ERA15547404 | CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive | CENTER FOR GENOMIC REGULATION (CRG) | ont | ont | 3prime | poly_a | unknown | bulk | unknown | unknown | Spain | 2022-10-10 | Multi-stage | Embryo | Undetermined | Embryo Imprecise | ||||||||||||||||||||||||||||||
| 11045 | 11045 | ERR9839778 | ERX9385635 | ERS12199235 | ERP138294 | PRJEB53494 | Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore cDNA sequencing | 94bf5509-4622-4d5f-b7c5-6a14bdfac340 | Other | RNA polyadenylation plays a central role in RNA maturation fate and stability. In response to developmental cues polyA tail lengths can vary affecting the translation efficiency and stability of mRNAs. Here we develop Nanopore three prime end capture sequencing Nano3P seq a novel method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance tail composition and tail length dynamics at per read resolution. By employing a template switching based sequencing protocol Nano3P seq can sequence any given RNA molecule from its three prime end regardless of its polyadenylation status without xxx need for PCR amplification or ligation of RNA adapters. We demonstrate that Nano3P seq captures a wide diversity of RNA biotypes providing quantitative estimates of RNA abundance and tail lengths in mRNA lncRNA sn/snoRNA scaRNA and rRNA molecules. We find that in addition to mRNA and lncRNA polyA tails can be identified in 16S mitochondrial rRNA in both mouse and zebrafish models. Moreover we show that mRNA tail lengths are dynamically regulated during vertebrate embryogenesis at an isoform specific level correlating with mRNA decay. Finally we identify non A bases within polyA tails of various lengths and reveal their distribution during vertebrate embryogenesis. Overall Nano3P seq is a simple and robust method for accurately estimating transcript levels tail lengths and tail composition heterogeneity in individual reads with minimal library preparation biases both in the coding and non coding transcriptome. | ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10 | Zebrafish PolyA Selected RNA 4hpf | Zebrafish pA selected | SAMEA110100410 | CENTER FOR GENOMIC REGULATION (CRG) | ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10|External Id:SAMEA110100410|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 10 10T00:20:53Z|INSDC last update:2022 10 10T00:20:53Z|INSDC status:public|Submitter Id:Zebrafish pA selected|common name:zebrafish|sample name:Zebrafish pA selected | MinION sequencing | ena EXPERIMENT TAB 13 06 2022 16:07:52:807 811 | cDNA852361 ZFPA4R1 | 1 | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | OXFORD_NANOPORE | MinION | ERP138294 | MinION sequencing | ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10 | cDNA852361_ZFPA4R1.tar.gz | nanopore | 348224822.0 | 233101.0 | ena RUN TAB 13 06 2022 16:07:52:807 812 | 0:1493.88 | A:88963756;C:76104775;G:73909507;T:109246784;N:0 | 1493 | 88963756 | 76104775 | 73909507 | 109246784 | 0 | ERX9385635 | ERS12199235 | ERA15547404 | CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive | CENTER FOR GENOMIC REGULATION (CRG) | 1 | 0.34147 | 0.26829 | 0.99993 | 0.16666 | 1537 | T | long read | ont | ont | 3prime | poly_a | unknown | bulk | unknown | unknown | Spain | 2022-10-10 | Blastula | 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");;