{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"PCR\", experiment.library_strategy = \"RNA-Seq\" and tissue_curation_coarse = \"Multi-system\"", "rows": [[64970, "SRR14999363", "SRX11311655", "SRS9340853", "SRP324442", "PRJNA738523", "Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag", "GSE178343", "Other", "Here we describe successful implementation of CUT&RUN for profiling protein DNA interactions in zebrafish embryos. We apply modified a CUT&RUN method to generate high resolution maps of enrichment for H3K4me3  H3K27me3  H3K9me3  and RNA polymerase II during zebrafish gastrulation. Using this data  we identify a conserved subset of developmental genes that are enriched in both H3K4me3 and H3K27me3 during gastrulation  and we demonstrate the increased effectiveness of CUT&RUN for detecting protein enrichment at repetitive sequences with reduced mappability.  Our work demonstrates the power of combining CUT&RUN  with the strengths of the zebrafish system to better understand the changing embryonic chromatin landscape and its roles in shaping development. Overall design: CUT&RUN in 6hpf zebrafish embryos for H3K27me3  H3K4me3  H3K9me3  and pol II. 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We apply modified a CUT&RUN method to generate high resolution maps of enrichment for H3K4me3  H3K27me3  H3K9me3  and RNA polymerase II during zebrafish gastrulation. Using this data  we identify a conserved subset of developmental genes that are enriched in both H3K4me3 and H3K27me3 during gastrulation  and we demonstrate the increased effectiveness of CUT&RUN for detecting protein enrichment at repetitive sequences with reduced mappability.  Our work demonstrates the power of combining CUT&RUN  with the strengths of the zebrafish system to better understand the changing embryonic chromatin landscape and its roles in shaping development. Overall design: CUT&RUN in 6hpf zebrafish embryos for H3K27me3  H3K4me3  H3K9me3  and pol II. 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We apply modified a CUT&RUN method to generate high resolution maps of enrichment for H3K4me3  H3K27me3  H3K9me3  and RNA polymerase II during zebrafish gastrulation. Using this data  we identify a conserved subset of developmental genes that are enriched in both H3K4me3 and H3K27me3 during gastrulation  and we demonstrate the increased effectiveness of CUT&RUN for detecting protein enrichment at repetitive sequences with reduced mappability.  Our work demonstrates the power of combining CUT&RUN  with the strengths of the zebrafish system to better understand the changing embryonic chromatin landscape and its roles in shaping development. Overall design: CUT&RUN in 6hpf zebrafish embryos for H3K27me3  H3K4me3  H3K9me3  and pol II. 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We apply modified a CUT&RUN method to generate high resolution maps of enrichment for H3K4me3  H3K27me3  H3K9me3  and RNA polymerase II during zebrafish gastrulation. Using this data  we identify a conserved subset of developmental genes that are enriched in both H3K4me3 and H3K27me3 during gastrulation  and we demonstrate the increased effectiveness of CUT&RUN for detecting protein enrichment at repetitive sequences with reduced mappability.  Our work demonstrates the power of combining CUT&RUN  with the strengths of the zebrafish system to better understand the changing embryonic chromatin landscape and its roles in shaping development. Overall design: CUT&RUN in 6hpf zebrafish embryos for H3K27me3  H3K4me3  H3K9me3  and pol II. 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"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 \"experiment.library_selection\" = :p0 and \"experiment.library_strategy\" = :p1 and \"tissue_curation_coarse\" = :p2 order by rowid limit 101", "params": {"p0": "PCR", "p1": "RNA-Seq", "p2": "Multi-system"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=PCR&experiment.library_strategy=RNA-Seq&tissue_curation_coarse=Multi-system", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 9, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=PCR&tissue_curation_coarse=Multi-system", "selected": true}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=PCR&experiment.library_strategy=RNA-Seq&tissue_curation_coarse=Multi-system", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 9, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=PCR&experiment.library_strategy=RNA-Seq&tissue_curation_coarse=Multi-system&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_selection=PCR&experiment.library_strategy=RNA-Seq&tissue_curation_coarse=Multi-system", "results": [{"value": "PCR", "label": "PCR", "count": 9, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_strategy=RNA-Seq&tissue_curation_coarse=Multi-system", "selected": true}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=PCR&experiment.library_strategy=RNA-Seq&tissue_curation_coarse=Multi-system", "results": [{"value": "PAIRED", "label": "PAIRED", "count": 9, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=PCR&experiment.library_strategy=RNA-Seq&tissue_curation_coarse=Multi-system&experiment.library_layout=PAIRED", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=PCR&experiment.library_strategy=RNA-Seq&tissue_curation_coarse=Multi-system", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 9, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=PCR&experiment.library_strategy=RNA-Seq&tissue_curation_coarse=Multi-system&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_selection=PCR&experiment.library_strategy=RNA-Seq&tissue_curation_coarse=Multi-system", "results": [{"value": "Adult", "label": "Adult", "count": 9, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=PCR&experiment.library_strategy=RNA-Seq&tissue_curation_coarse=Multi-system&devstage_curation_coarse=Adult", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=PCR&experiment.library_strategy=RNA-Seq&tissue_curation_coarse=Multi-system", "results": [{"value": "Adult", "label": "Adult", "count": 9, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=PCR&experiment.library_strategy=RNA-Seq&tissue_curation_coarse=Multi-system&devstage_curation=Adult", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=PCR&experiment.library_strategy=RNA-Seq&tissue_curation_coarse=Multi-system", "results": [{"value": "Multi-system", "label": "Multi-system", "count": 9, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=PCR&experiment.library_strategy=RNA-Seq", "selected": true}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=PCR&experiment.library_strategy=RNA-Seq&tissue_curation_coarse=Multi-system", "results": [{"value": "Multi-tissue", "label": "Multi-tissue", "count": 9, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=PCR&experiment.library_strategy=RNA-Seq&tissue_curation_coarse=Multi-system&tissue_curation=Multi-tissue", "selected": false}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=PCR&experiment.library_strategy=RNA-Seq&tissue_curation_coarse=Multi-system", "results": [{"value": "unknown", "label": "unknown", "count": 9, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=PCR&experiment.library_strategy=RNA-Seq&tissue_curation_coarse=Multi-system&technology=unknown", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": null, "next_url": null, "private": false, "allow_execute_sql": true, "query_ms": 62.03862099937396}