{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Blastula\" and experiment.platform = \"OXFORD_NANOPORE\"", "rows": [[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", null, "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", null, null, null, null, null, null, null, null, "MinION sequencing", "ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 5", "cDNA8523612", "Nano3P seq", "Nano3P seq", null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "OXFORD_NANOPORE", "MinION", null, "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, null, null, null, 86572446, 74232962, 69203462, 100553350, 0, "ERX6138167", "ERS7264190", "ERA5757997", "CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive", "CENTER FOR GENOMIC REGULATION (CRG)", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 1536, null, "T", null, "long read", "ont", "ont", "full_length", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2023-12-28", "Blastula", "Embryo", "Undetermined", "Embryo Imprecise"], [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", null, "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", null, null, null, null, null, null, null, null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "OXFORD_NANOPORE", "MinION", null, "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, null, null, null, 224977035, 165273397, 156659356, 225394837, 0, "ERX6244443", "ERS7291130", "ERA5995143", "CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive", "CENTER FOR GENOMIC REGULATION (CRG)", 1, 0.5, null, 0.0, null, 0.99997, null, 1.0, null, 962, null, "T", null, "long read", "ont", "ont", "full_length", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2023-12-28", "Blastula", "Embryo", "Undetermined", "Embryo Imprecise"], [11041, "ERR9995536", "ERX9536682", "ERS12521224", "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", null, "dRNA seq of 4hpf Zebrafish embryos", "Zebrafish dRNA 4hpf", "SAMEA110422854", "CENTER FOR GENOMIC REGULATION (CRG)", "ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10|External Id:SAMEA110422854|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 10 10T00:21:01Z|INSDC last update:2022 10 10T00:21:01Z|INSDC status:public|Submitter Id:Zebrafish dRNA 4hpf|common name:zebrafish|sample name:Zebrafish dRNA 4hpf", null, null, null, null, null, null, null, null, "MinION sequencing", "ena EXPERIMENT TAB 27 07 2022 11:41:43:673 3", "Zebrafish dRNA 4hpf", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "OXFORD_NANOPORE", "MinION", null, "ERP138294", "MinION sequencing", "ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10|instrument model:PromethION", "PDBN042841_dRNA_4hpf.tar.gz", "nanopore", 772304625.0, 897768.0, "ena RUN TAB 27 07 2022 11:41:43:690 4", "0:860.25", "A:224977035;C:165273397;G:156659356;T:225394837;N:0", 860, null, null, null, 224977035, 165273397, 156659356, 225394837, 0, "ERX9536682", "ERS12521224", "ERA16500713", "CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive", "CENTER FOR GENOMIC REGULATION (CRG)", null, null, null, null, null, null, null, null, null, null, null, null, null, null, "ont", "ont", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2022-10-10", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "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", null, null, null, null, null, null, null, null, "MinION sequencing", "ena EXPERIMENT TAB 13 06 2022 16:07:52:807 811", "cDNA852361 ZFPA4R1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "OXFORD_NANOPORE", "MinION", null, "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, null, null, null, 88963756, 76104775, 73909507, 109246784, 0, "ERX9385635", "ERS12199235", "ERA15547404", "CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive", "CENTER FOR GENOMIC REGULATION (CRG)", 1, 0.34147, null, 0.26829, null, 0.99993, null, 0.16666, null, 1537, null, "T", null, "long read", "ont", "ont", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2022-10-10", "Blastula", "Embryo", "Undetermined", "Embryo Imprecise"]], "truncated": false, "filtered_table_rows_count": 4, "expanded_columns": [], "expandable_columns": [], "columns": ["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"], "primary_keys": [], "units": {}, "query": {"sql": "select 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 from run_metadata where \"devstage_curation\" = :p0 and \"experiment.platform\" = :p1 order by rowid limit 101", "params": {"p0": "Blastula", "p1": "OXFORD_NANOPORE"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Blastula&experiment.platform=OXFORD_NANOPORE", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Blastula&experiment.platform=OXFORD_NANOPORE&experiment.library_strategy=RNA-Seq", "selected": false}, {"value": "OTHER", "label": "OTHER", "count": 1, "toggle_url": 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"toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Blastula&experiment.platform=OXFORD_NANOPORE&experiment.library_selection=other", "selected": false}, {"value": "Oligo-dT", "label": "Oligo-dT", "count": 1, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Blastula&experiment.platform=OXFORD_NANOPORE&experiment.library_selection=Oligo-dT", "selected": false}, {"value": "unspecified", "label": "unspecified", "count": 1, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Blastula&experiment.platform=OXFORD_NANOPORE&experiment.library_selection=unspecified", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Blastula&experiment.platform=OXFORD_NANOPORE", "results": [{"value": "SINGLE", "label": "SINGLE", "count": 4, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Blastula&experiment.platform=OXFORD_NANOPORE&experiment.library_layout=SINGLE", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Blastula&experiment.platform=OXFORD_NANOPORE", "results": [{"value": "OXFORD_NANOPORE", "label": "OXFORD_NANOPORE", "count": 4, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Blastula", "selected": true}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Blastula&experiment.platform=OXFORD_NANOPORE", "results": [{"value": "Embryo", "label": "Embryo", "count": 4, "toggle_url": 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