{"lab": {"uuid": "eb9725d9-44bb-4e4b-a5ad-e152fb3a06eb", "display_title": "Xiaowei Zhuang, HARVARD", "status": "current", "correspondence": [{"contact_email": "emh1YW5nQGNoZW1pc3RyeS5oYXJ2YXJkLmVkdQ==", "@id": "/users/acfc5a08-19ff-47ef-9261-75e6134dc0fe/", "display_title": "Xiaowei Zhuang"}], "title": "Xiaowei Zhuang, HARVARD", "@type": ["Lab", "Item"], "@id": "/labs/xiaowei-zhuang-lab/", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.eb9725d9-44bb-4e4b-a5ad-e152fb3a06eb"]}}, "award": {"name": "1UM1HG011585-01", "center_title": "CDIMV - Ren", "uuid": "ee89349a-1d43-4048-9142-bc750f0f3b32", "status": "current", "description": "CDIMV: The transcriptional regulatory sequences communicate with each other dynamically in the 3D nuclear space to direct cell type specific gene expression. Currently, a major barrier to understanding the transcriptional regulatory programs is the lack of tools, models and maps to explore the chromatin architecture in diverse cell types and physiological contexts. We will address this pressing need by deploying transformative technologies to study the chromatin architecture in mammalian cells at an unprecedented resolution and scale. Specifically, we will generate navigable, cell-type-specific reference maps of chromatin architecture in the mouse, macaque and human brains by integrating high resolution and high throughput imaging and orthogonal single-cell-based genomic methods. We will also dissect the role of chromatin architecture in gene regulation through a set of controlled perturbation experiments in the mouse ES cells (ESC) and ESC-derived neural progenitor cells (NPC). We will develop structural models of chromatin organization with advanced polymer physics and statistical learning methods, and validate their predictive power in embryonic stem cells and in ex vivo brain slices. Finally, we will make the reference maps, analytical tools, visualization methods and structural models available to the broader community. The proposed research project will dramatically transform our ability to analyze the 4D Nucleome of complex tissues, and produce the much-needed maps, tools and models for understanding the gene regulatory programs encoded in the linear genome sequences.", "@type": ["Award", "Item"], "@id": "/awards/1UM1HG011585-01/", "project": "4DN", "display_title": "CENTER FOR INTEGRATED MULTI-MODAL AND MULTI-SCALE NUCLEOME RESEARCH", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "pi": {"error": "no view permissions"}}, "labels": ["Cy3"], "status": "released", "target": [{"@id": "/bio-features/1a7f48ac-a39e-4570-88dd-d3c948774b53/", "organism_name": "human", "display_title": "transcript", "uuid": "1a7f48ac-a39e-4570-88dd-d3c948774b53", "@type": ["BioFeature", "Item"], "status": "released", "feature_type": {"uuid": "e8f56a24-20ce-4e7c-9e8d-a4f409398574", "preferred_name": "transcript", "@id": "/ontology-terms/SO:0000673/", "term_url": "http://purl.obolibrary.org/obo/SO_0000673", "@type": ["OntologyTerm", "Item"], "term_id": "SO:0000673", "term_name": "transcript", "status": "released", "display_title": "transcript", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "aliases": ["xiaowei-zhuang-lab:rna-merfish-cy3"], "description": "RNA-MERFISH in Cy3 (together with Alexa 750 and Alexa 647) to detect nascent RNA transcripts of  1137 gene overlapping with 1,041 genomic loci targeted by DNA MERFISH", "date_created": "2024-10-17T14:36:32.070842+00:00", "other_probes": ["oligo probe library", "readout oligo library"], "submitted_by": {"error": "no view permissions"}, "labeled_probe": "imaging oligos", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-10-18T22:35:31.206284+00:00"}, "imaging_rounds": "1-18", "public_release": "2024-10-18", "schema_version": "2", "project_release": "2024-10-18", "type_labeled_probe": "DNA primer", "override_display_title": "RNA-MERFISH to detect 1137 genes overlapping 1041 genomic loci (targeted by DNA MERFISH) by Cy3-labeled imaging oligos", "@id": "/imaging-paths/fcd47739-3121-40ae-a77a-102e620c17d7/", "@type": ["ImagingPath", "Item"], "uuid": "fcd47739-3121-40ae-a77a-102e620c17d7", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "RNA-MERFISH to detect 1137 genes overlapping 1041 genomic loci (targeted by DNA MERFISH) by Cy3-labeled imaging oligos", "external_references": [], "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}