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"@id": "/file-formats/pairs/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2025-02-20T18:45:10.626731+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Giacomo Cavalli, UM", "experiment_type": "in situ Hi-C", "experiment_bucket": "HiC Processing Pipeline - v0.3.0", "assay_info": "DpnII", "dataset": "Hi-C on E14Tg2 cell line", "condition": "control - zfp608 gRNA without dCas9", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "ES-E14TG2a", "lab_name": "4DN DCIC, HMS"}}], "title": "HiC Processing Pipeline - v0.3.0", "description": "These are files generated using the updated Hi-C processing pipeline. They should be largely similar to those available in the Processed Files tab, which were generated with the previous version of the standard pipeline.  One potential difference of note is that the version of cooler used to generate the mcool file has a bug fix to prevent a pixel duplication issue which is observed in some files generated by the previous version of the pipeline.  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/4DNEXGGI1YTN/", "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "4c530b75-73c2-419d-8a98-5513f68eadb5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "in situ Hi-C on ES-E14TG2a with DpnII - 4DNEXGGI1YTN", "external_references": [{"ref": "GEO:GSM2716663", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2716663"}], "experiment_sets": [{"status": "released", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "accession": "4DNESXS1M9JR", "uuid": "532d75d8-e4a9-4258-83b2-bb86ac04f62d", "@id": "/experiment-set-replicates/4DNESXS1M9JR/", "experimentset_type": "replicate", "display_title": "4DNESXS1M9JR", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"short_attribution": "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.", "title": "Multiscale 3D Genome Rewiring during Mouse Neural Development.", "ID": "PMID:29053968", "@type": ["Publication", "Item"], "status": "current", "display_title": "Bonev B et al. (2017) PMID:29053968", "journal": "Cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"title": "Multiscale 3D Genome Rewiring during Mouse Neural Development.", "date_published": "2017-10-19", "display_title": "Bonev B et al. (2017) PMID:29053968", "short_attribution": "Bonev B et al. (2017)", "authors": ["Bonev B", "Mendelson Cohen N", "Szabo Q", "Fritsch L", "Papadopoulos GL", "Lubling Y", "Xu X", "Lv X", "Hugnot JP", "Tanay A", "Cavalli G"], "ID": "PMID:29053968", "@type": ["Publication", "Item"], "uuid": "1c0ab106-2afe-4cda-bbbd-ceaea2627f37", "@id": "/publications/1c0ab106-2afe-4cda-bbbd-ceaea2627f37/", "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.", "status": "current", "journal": "Cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Enzyme", "value": "DpnII", "combined": "Enzyme: DpnII"}, "experiment_summary": "in situ Hi-C on ES-E14TG2a with DpnII", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSZRRI5YZ/", "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": []}