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We will also optimize RICh-PET for the comprehensive mapping of chromatin interactions mediated by non-coding RNAs (Aim 1). The high-quality mapping data generated through these optimization efforts will be analyzed by a new computational platform (Three-Dimensional Nucleome Modeling Engine, or 3D-NOME) that makes use of hierarchical multi-scaling to model 3D genome structures (Aim 2, Data Analysis and Modeling component). We will also complement the 3D modeling with transcriptome, epigenome and SNP data associated with genetic diseases (GWAS) to provide functional annotation to structural units (Aim 2). We will continue by developing strategies to validate the nucleome geometry predicted by 3D-NOME both structurally, using new nuclear imaging technologies, and functionally, using cutting-edge genome- and epigenome-editing approaches, in both human cell lines and mouse models (Aim 3, Biological Validation Component). Finally, we will implement NPS to generate pilot 3D genome maps from a wide range of human cell lines and primary immune cells sorted from whole blood, to elucidate the spatiotemporal dynamics of human genome organization over major developmental and hematopoietic cell lineages, as well as among differentiating lymphocytes involved in the immune response (Aim 4, Data Generation Component). Together, these efforts will yield a powerful set of sophisticated, high-quality tools and mapping data for the larger research community, and will help establish the standards for future 3D/4D nucleome studies. 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"tooltip": "Percent of filtered reads (=47.45m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "8.279", "tooltip": "Percent of filtered reads (=4.81m)", "numberType": "percent"}]}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "pairs", "status": "released", "file_format": "pairs", "@id": "/file-formats/pairs/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Yijun Ruan, JAX", "experiment_type": "in situ ChIA-PET", "experiment_bucket": "HiC Processing Pipeline Results on ChIA-PET data", "assay_info": "CTCF protein", "dataset": "in situ ChIA-PET on WTC11", "condition": "CTCF", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "WTC-11 AAVS1-GFP C28", "lab_name": "4DN DCIC, HMS"}, "last_modified": {"date_modified": "2021-04-06T20:17:21.657910+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": 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The processing may not be optimal since the pipeline does not take into account DNA linkers used in ChIA-PET experiments."}], "biosample_quantity_units": "cells", "crosslinking_temperature": 20, "library_preparation_date": "2020-02-19", "fragment_size_selection_method": "gel", "@id": "/experiments-chiapet/4DNEXY93GZVY/", "@type": ["ExperimentChiapet", "Experiment", "Item"], "uuid": "ae84dbea-649f-4a4f-bfa9-9f36e4bf1ebf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "in situ ChIA-PET against CTCF protein on WTC-11 AAVS1-GFP C28 - 4DNEXY93GZVY", "external_references": [], "experiment_sets": [{"experimentset_type": "replicate", "uuid": "7e25fb30-7f96-4fd0-94f6-52508f065306", "accession": "4DNES8MZ76GP", "display_title": "4DNES8MZ76GP", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "@id": "/experiment-set-replicates/4DNES8MZ76GP/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "publications_of_exp": [], "experiment_categorizer": {"field": "Target", "value": "CTCF protein", "combined": "Target: CTCF protein"}, "experiment_summary": "in situ ChIA-PET against CTCF protein on WTC-11 AAVS1-GFP C28", "@context": "/terms/", "aggregated-items": {"badges": []}, "validation-errors": []}