{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", experiment.library_selection = \"CAGE\" and experiment.library_strategy = \"OTHER\"", "rows": [[9803, "ERR3909553", "ERX3918377", "ERS4309135", "ERP120006", "PRJEB36776", "CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red", "E-MTAB-8795", "Transcriptome Analysis", "The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics.", "ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 13", null, "Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. 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Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. 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To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics.", "ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 13", null, "Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. 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To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics.", "ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 13", null, "Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. 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To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics.", "ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 13", null, "Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. 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"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 \"experiment.library_layout\" = :p0 and \"experiment.library_selection\" = :p1 and \"experiment.library_strategy\" = :p2 order by rowid limit 101", "params": {"p0": "SINGLE", "p1": "CAGE", "p2": "OTHER"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=CAGE&experiment.library_strategy=OTHER", "results": [{"value": "OTHER", "label": "OTHER", "count": 26, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=CAGE", "selected": true}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=CAGE&experiment.library_strategy=OTHER", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 26, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=CAGE&experiment.library_strategy=OTHER&experiment.library_source=TRANSCRIPTOMIC", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=CAGE&experiment.library_strategy=OTHER", "results": [{"value": "CAGE", "label": "CAGE", "count": 26, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_strategy=OTHER", "selected": true}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=CAGE&experiment.library_strategy=OTHER", "results": [{"value": "SINGLE", "label": "SINGLE", "count": 26, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=CAGE&experiment.library_strategy=OTHER", "selected": true}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=CAGE&experiment.library_strategy=OTHER", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 26, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=CAGE&experiment.library_strategy=OTHER&experiment.platform=ILLUMINA", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=CAGE&experiment.library_strategy=OTHER", "results": [{"value": "Embryo", "label": "Embryo", "count": 26, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=CAGE&experiment.library_strategy=OTHER&devstage_curation_coarse=Embryo", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=CAGE&experiment.library_strategy=OTHER", "results": [{"value": "Segmentation", "label": "Segmentation", "count": 11, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=CAGE&experiment.library_strategy=OTHER&devstage_curation=Segmentation", "selected": false}, {"value": "Blastula", "label": "Blastula", "count": 5, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=CAGE&experiment.library_strategy=OTHER&devstage_curation=Blastula", "selected": false}, {"value": "Undetermined", "label": "Undetermined", "count": 5, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=CAGE&experiment.library_strategy=OTHER&devstage_curation=Undetermined", "selected": false}, {"value": "Gastrula", "label": "Gastrula", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=CAGE&experiment.library_strategy=OTHER&devstage_curation=Gastrula", "selected": false}, {"value": "Zygote", "label": "Zygote", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=CAGE&experiment.library_strategy=OTHER&devstage_curation=Zygote", "selected": false}, {"value": "Cleavage", "label": "Cleavage", "count": 1, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=CAGE&experiment.library_strategy=OTHER&devstage_curation=Cleavage", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=CAGE&experiment.library_strategy=OTHER", "results": [{"value": "All anatomical structures", "label": "All anatomical structures", "count": 23, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=CAGE&experiment.library_strategy=OTHER&tissue_curation_coarse=All+anatomical+structures", "selected": false}, {"value": "Reproductive System", "label": "Reproductive System", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=CAGE&experiment.library_strategy=OTHER&tissue_curation_coarse=Reproductive+System", "selected": false}, {"value": "Embryo Imprecise", "label": "Embryo Imprecise", "count": 1, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=CAGE&experiment.library_strategy=OTHER&tissue_curation_coarse=Embryo+Imprecise", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=CAGE&experiment.library_strategy=OTHER", "results": [{"value": "Embryo Imprecise", "label": "Embryo Imprecise", "count": 14, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=CAGE&experiment.library_strategy=OTHER&tissue_curation=Embryo+Imprecise", "selected": false}, {"value": "Whole Organism", "label": "Whole Organism", "count": 9, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=CAGE&experiment.library_strategy=OTHER&tissue_curation=Whole+Organism", "selected": false}, {"value": "Oocyte", "label": "Oocyte", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=CAGE&experiment.library_strategy=OTHER&tissue_curation=Oocyte", "selected": false}, {"value": "Undetermined", "label": "Undetermined", "count": 1, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=CAGE&experiment.library_strategy=OTHER&tissue_curation=Undetermined", "selected": false}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=CAGE&experiment.library_strategy=OTHER", "results": [{"value": "unknown", "label": "unknown", "count": 26, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=CAGE&experiment.library_strategy=OTHER&technology=unknown", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": null, "next_url": null, "private": false, "allow_execute_sql": true, "query_ms": 94.53139700053725}