{"lab": {"correspondence": [{"contact_email": "emh1YW5nQGNoZW1pc3RyeS5oYXJ2YXJkLmVkdQ==", "@id": "/users/acfc5a08-19ff-47ef-9261-75e6134dc0fe/", "display_title": "Xiaowei Zhuang"}], "@id": "/labs/xiaowei-zhuang-lab/", "@type": ["Lab", "Item"], "status": "current", "uuid": "eb9725d9-44bb-4e4b-a5ad-e152fb3a06eb", "display_title": "Xiaowei Zhuang, HARVARD", "title": "Xiaowei Zhuang, HARVARD", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.eb9725d9-44bb-4e4b-a5ad-e152fb3a06eb"]}}, "award": {"uuid": "ee89349a-1d43-4048-9142-bc750f0f3b32", "@type": ["Award", "Item"], "display_title": "CENTER FOR INTEGRATED MULTI-MODAL AND MULTI-SCALE NUCLEOME RESEARCH", "status": "current", "center_title": "CDIMV - Ren", "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.", "@id": "/awards/1UM1HG011585-01/", "name": "1UM1HG011585-01", "project": "4DN", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["xiaowei-zhuang-lab:genome_wide_brain_ct_mecp2"], "accession": "4DNESPE924IP", "condition": "Mouse primary motor cortex - mecp2 KO", "description": "Genome-wide chromatin imaging by DNA-MERFISH of 2000 loci in mouse primary motor cortex of Mecp2 heteozygous knock-out mice, together with RNA-MERFISH of 240 gene transcripts", "date_created": "2023-11-15T20:41:25.577675+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "Chromatin tracing in mouse primary motor cortex", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-06-26T19:12:33.541214+00:00"}, "public_release": "2023-11-27", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"accession": "4DNEXYXXV9AQ", "display_title": "multiplexed FISH on primary motor cortex - 4DNEXYXXV9AQ", "uuid": "82f15e77-cea6-4a67-af31-2a4b03f5cb80", "status": "released", "@id": "/experiments-mic/4DNEXYXXV9AQ/", "@type": ["ExperimentMic", "Experiment", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 1, "replicate_exp": {"accession": "4DNEXDSE1987", "display_title": "multiplexed FISH on primary motor cortex - 4DNEXDSE1987", "uuid": "32b53129-8f25-4df6-82a4-a5e8cc010a51", "status": "released", "@id": "/experiments-mic/4DNEXDSE1987/", "@type": ["ExperimentMic", "Experiment", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 3, "tec_rep_no": 1, "replicate_exp": {"accession": "4DNEXRBK6HWZ", "display_title": "multiplexed FISH on primary motor cortex - 4DNEXRBK6HWZ", "uuid": "52964056-822d-43a0-b1e5-ecc1d7f43b20", "status": "released", "@id": "/experiments-mic/4DNEXRBK6HWZ/", "@type": ["ExperimentMic", "Experiment", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 4, "tec_rep_no": 1, "replicate_exp": {"accession": "4DNEXH6CINOZ", "display_title": "multiplexed FISH on primary motor cortex - 4DNEXH6CINOZ", "uuid": "171bbf21-a162-45da-b08f-f1cdee46d5cd", "status": "released", "@id": "/experiments-mic/4DNEXH6CINOZ/", "@type": ["ExperimentMic", "Experiment", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_headers": [{"lab": {"display_title": "4DN DCIC, HMS", "status": "current", "@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "Processed files in this dataset are provided in the 4DN standard FISH-Omics Format - Chromatin Tracing (FOF-CT).\n\nThis is a collection of tabular files, consisting of several tables.\nThe DNA-spot/trace core table is organized around individual DNA bright Spots that are spatially linked together in a three-dimensional (3D) polymeric Trace.\nAdditional optional tables can complement this information and vary according to the specific dataset. \n\nThe full documentation is available here: https://fish-omics-format.readthedocs.io/", "name": "fof-ct.note", "award": {"status": "current", "@id": "/awards/2U01CA200059-06/", "@type": ["Award", "Item"], "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Note on FOF-CT file format", "status": "released", "aliases": ["4dn-dcic-lab:fof_ct_note"], "options": {"filetype": "md", "collapsible": true, "default_open": false}, "date_created": "2022-03-07T18:23:27.469177+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-03-08T14:28:37.893086+00:00"}, "schema_version": "2", "@id": "/static-sections/a09a2833-b56b-4e81-8eff-bb8ae6aaa596/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "a09a2833-b56b-4e81-8eff-bb8ae6aaa596", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.e4a22298-1da4-4e59-8a65-9e661f47fb48"]}, "display_title": "Note on FOF-CT file format", "external_references": [], "content": "Processed files in this dataset are provided in the 4DN standard FISH-Omics Format - Chromatin Tracing (FOF-CT).\n\nThis is a collection of tabular files, consisting of several tables.\nThe DNA-spot/trace core table is organized around individual DNA bright Spots that are spatially linked together in a three-dimensional (3D) polymeric Trace.\nAdditional optional tables can complement this information and vary according to the specific dataset. \n\nThe full documentation is available here: https://fish-omics-format.readthedocs.io/", "filetype": "md", "content_as_html": "

Processed files in this dataset are provided in the 4DN standard FISH-Omics Format - Chromatin Tracing (FOF-CT).

\n

This is a collection of tabular files, consisting of several tables.\nThe DNA-spot/trace core table is organized around individual DNA bright Spots that are spatially linked together in a three-dimensional (3D) polymeric Trace.\nAdditional optional tables can complement this information and vary according to the specific dataset.

\n

The full documentation is available here: https://fish-omics-format.readthedocs.io/

"}, {"lab": {"display_title": "4DN DCIC, HMS", "status": "current", "@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "The original FOF-CT Core files (4DNFIY7ULW4E, 4DNFIDJJZFYF, 4DNFIM453D3J, 4DNFIN99DPHD) have been replaced with the current version to correct the 'XYZ_unit' header from 'nm' to 'micron'.", "name": "Replaced_processed_files_4DNESPE924IP", "award": {"status": "current", "@id": "/awards/2U01CA200059-06/", "@type": ["Award", "Item"], "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "FOF-CT Core files replaced ", "status": "released", "aliases": ["4dn-dcic-lab:replaced_processed_files"], "options": {"filetype": "md", "collapsible": false, "default_open": true, "convert_ext_links": true}, "date_created": "2025-05-14T14:50:30.828973+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-05-14T14:56:41.134715+00:00"}, "schema_version": "2", "@id": "/static-sections/6a4d7413-17c8-4ffd-a1fb-af9e7f89513c/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "6a4d7413-17c8-4ffd-a1fb-af9e7f89513c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.6f9809b1-b9b4-4f2f-8e6d-0762bce320ef"]}, "display_title": "FOF-CT Core files replaced ", "external_references": [], "content": "The original FOF-CT Core files (4DNFIY7ULW4E, 4DNFIDJJZFYF, 4DNFIM453D3J, 4DNFIN99DPHD) have been replaced with the current version to correct the 'XYZ_unit' header from 'nm' to 'micron'.", "filetype": "md", "content_as_html": "

The original FOF-CT Core files (4DNFIY7ULW4E, 4DNFIDJJZFYF, 4DNFIM453D3J, 4DNFIN99DPHD) have been replaced with the current version to correct the 'XYZ_unit' header from 'nm' to 'micron'.

"}, {"lab": {"display_title": "4DN DCIC, HMS", "status": "current", "@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "The experiments associated with this study are derived from either [d8f51a9c-1e1a-4a6c-9432-ddf7de64e836](https://data.4dnucleome.org/microscope-configurations/d8f51a9c-1e1a-4a6c-9432-ddf7de64e836) or [f0172a96-2bf5-4e6a-938d-f205c6e728c9](https://data.4dnucleome.org/microscope-configurations/f0172a96-2bf5-4e6a-938d-f205c6e728c9) microscopes ", "name": "microscope_note_2", "award": {"status": "current", "@id": "/awards/2U01CA200059-06/", "@type": ["Award", "Item"], "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Microscope configuration", "status": "released", "aliases": ["4dn-dcic-lab:microscope_note_2"], "options": {"filetype": "md", "collapsible": true, "default_open": true, "convert_ext_links": true}, "date_created": "2025-06-26T19:09:32.639966+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-06-26T19:09:32.641770+00:00"}, "schema_version": "2", "@id": "/static-sections/f8cb1d7e-1ff9-4534-8ab4-6837f04b259f/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "f8cb1d7e-1ff9-4534-8ab4-6837f04b259f", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.6f9809b1-b9b4-4f2f-8e6d-0762bce320ef"]}, "display_title": "Microscope configuration", "external_references": [], "content": "The experiments associated with this study are derived from either [d8f51a9c-1e1a-4a6c-9432-ddf7de64e836](https://data.4dnucleome.org/microscope-configurations/d8f51a9c-1e1a-4a6c-9432-ddf7de64e836) or [f0172a96-2bf5-4e6a-938d-f205c6e728c9](https://data.4dnucleome.org/microscope-configurations/f0172a96-2bf5-4e6a-938d-f205c6e728c9) microscopes ", "filetype": "md", "content_as_html": "

The experiments associated with this study are derived from either d8f51a9c-1e1a-4a6c-9432-ddf7de64e836 or f0172a96-2bf5-4e6a-938d-f205c6e728c9 microscopes

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These cell type-dependent variations in nuclear architecture and chromatin organization exhibit strong correlations with both the total transcriptional activity of the cell and transcriptional regulation of cell type-specific marker genes. Moreover, we found that the methylated DNA binding protein MeCP2 promotes active-inactive chromatin segregation and regulates transcription in a nuclear radial position-dependent manner that is highly correlated with its function in modulating active-inactive chromatin compartmentalization.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"date_published": "2025-02-28", "ID": "PMID:40009678", "@type": ["Publication", "Item"], "display_title": "Liu S et al. (2025) PMID:40009678", "abstract": "3D organization of the genome plays a critical role in regulating gene expression. How 3D-genome organization differs among different cell types and relates to cell type-dependent transcriptional regulation remains unclear. Here, we used genome-scale DNA and RNA imaging to investigate 3D-genome organization in transcriptionally distinct cell types in the mouse cerebral cortex. We uncovered a wide spectrum of differences in the nuclear architecture and 3D-genome organization among different cell types, ranging from the size of the cell nucleus to higher-order chromosome structures and radial positioning of chromatin loci within the nucleus. These cell type-dependent variations in nuclear architecture and chromatin organization exhibit strong correlations with both the total transcriptional activity of the cell and transcriptional regulation of cell type-specific marker genes. 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