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Another notable difference is that a filter is applied to remove reads with MAPQ scores below 30 prior to mcool file generation."}], "biosample_quantity_units": "cells", "@id": "/experiments-hi-c/4DNEX31J4Q7Y/", "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "dd1eac43-a52f-449a-8335-fb989b4ff836", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "in situ Hi-C on mESC line with Oct4-GFP with DpnII - 4DNEX31J4Q7Y", "external_references": [{"ref": "GEO:GSM2533820", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2533820"}], "experiment_sets": [{"uuid": "6acce021-98f2-4a33-a3dc-c0aa2145e0d4", "experimentset_type": "replicate", "display_title": "4DNESDXUWBD9", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "status": "released", "@id": "/experiment-set-replicates/4DNESDXUWBD9/", "accession": "4DNESDXUWBD9", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"display_title": "Bonev B et al. 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During neural differentiation, contacts between active TADs become less pronounced while inactive TADs interact more strongly. An extensive Polycomb network in stem cells is disrupted, while dynamic interactions between neural transcription factors appear in vivo. Finally, cell type-specific  enhancer-promoter contacts are established concomitant to gene expression. This work shows that multiple factors influence the dynamics of chromatin interactions in development.", "journal": "Cell", "authors": ["Bonev B", "Mendelson Cohen N", "Szabo Q", "Fritsch L", "Papadopoulos GL", "Lubling Y", "Xu X", "Lv X", "Hugnot JP", "Tanay A", "Cavalli G"], "short_attribution": "Bonev B et al. (2017)", "date_published": "2017-10-19", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"authors": ["Bonev B", "Mendelson Cohen N", "Szabo Q", "Fritsch L", "Papadopoulos GL", "Lubling Y", "Xu X", "Lv X", "Hugnot JP", "Tanay A", "Cavalli G"], "abstract": "Chromosome conformation capture technologies have revealed important insights into genome folding. Yet, how spatial genome architecture is related to gene expression and cell fate remains unclear. We comprehensively mapped 3D chromatin  organization during mouse neural differentiation in vitro and in vivo, generating the highest-resolution Hi-C maps available to date. We found that transcription is correlated with chromatin insulation and long-range interactions, but dCas9-mediated activation is insufficient for creating TAD boundaries de novo. Additionally, we discovered long-range contacts between gene bodies of exon-rich, active genes in all cell types. During neural differentiation, contacts between active TADs become less pronounced while inactive TADs interact more strongly. An extensive Polycomb network in stem cells is disrupted, while dynamic interactions between neural transcription factors appear in vivo. Finally, cell type-specific  enhancer-promoter contacts are established concomitant to gene expression. This work shows that multiple factors influence the dynamics of chromatin interactions in development.", "date_published": "2017-10-19", "display_title": "Bonev B et al. (2017) PMID:29053968", "uuid": "1c0ab106-2afe-4cda-bbbd-ceaea2627f37", "journal": "Cell", "ID": "PMID:29053968", "@id": "/publications/1c0ab106-2afe-4cda-bbbd-ceaea2627f37/", "short_attribution": "Bonev B et al. (2017)", "status": "current", "@type": ["Publication", "Item"], "title": "Multiscale 3D Genome Rewiring during Mouse Neural Development.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Enzyme", "value": "DpnII", "combined": "Enzyme: DpnII"}, "experiment_summary": "in situ Hi-C on mESC line with Oct4-GFP with DpnII", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSHFMTTNU/", "embedded_path": "biosample.badges", "item": {"messages": ["Biosample missing Cell Culture Details"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}]}, "validation-errors": []}