{"lab": {"uuid": "fe7249ca-3622-469a-ad9d-e5a85441bf52", "@id": "/labs/ahilya-sawh-lab/", "correspondence": [{"contact_email": "YWhpbHlhLnNhd2hAZ21haWwuY29t", "@id": "/users/a3b6e5d9-34ea-4997-a4cb-e4204c90bac5/", "display_title": "Ahilya Sawh"}], "status": "current", "title": "Ahilya Sawh Lab", "@type": ["Lab", "Item"], "display_title": "Ahilya Sawh Lab", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.fe7249ca-3622-469a-ad9d-e5a85441bf52"]}}, "award": {"center": "External", "center_title": "External", "name": "external-award", "description": "Funding source is from outside 4DN.", "project": "External", "display_title": "EXTERNAL AWARD", "status": "current", "@id": "/awards/external-award/", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "badges": [{"badge": {"display_title": "Replicate Numbers", "@id": "/badges/replicate-numbers/", "warning": "Replicate Numbers", "uuid": "24a64a84-3c33-4d76-aaf2-e5ef45eff347", "badge_icon": "/static/img/badges/replicates-orange-circle.svg", "description": "Issues with replicate numbers", "@type": ["Badge", "Item"], "status": "released", "badge_classification": "Warning", "title": "Replicate Numbers", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "messages": ["Replicate set contains only a single biological replicate"]}], "status": "released", "aliases": ["external-lab:expset_multiplexed_fish_c_elegans_chrV_WT"], "accession": "4DNES4LQ2W7R", "condition": "ChrV - 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PHASE II", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Microscope configuration - Sawh AN et al. 2020", "status": "released", "aliases": ["4dn-dcic-lab:microscope_note_sawh_2020"], "options": {"filetype": "md", "collapsible": true, "default_open": true, "convert_ext_links": true}, "date_created": "2025-06-24T17:30:00.509451+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-06-24T17:30:00.511322+00:00"}, "schema_version": "2", "@id": "/static-sections/dcb7e11d-9ae2-4134-a222-b354ee219ed2/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "dcb7e11d-9ae2-4134-a222-b354ee219ed2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.6f9809b1-b9b4-4f2f-8e6d-0762bce320ef"]}, "display_title": "Microscope configuration - Sawh AN et al. 2020", "external_references": [], "content": "The experiments associated with this study are derived from either [e9aeab8a-8c8f-4e8d-b673-20c6c53dc447](https://data.4dnucleome.org/microscope-configurations/e9aeab8a-8c8f-4e8d-b673-20c6c53dc447) or [b904ca5d-fcac-4a7d-b703-dc98adedabf5](https://data.4dnucleome.org/microscope-configurations/b904ca5d-fcac-4a7d-b703-dc98adedabf5) microscopes.", "filetype": "md", "content_as_html": "<div class=\"markdown-container\"><p>The experiments associated with this study are derived from either <a href=\"https://data.4dnucleome.org/microscope-configurations/e9aeab8a-8c8f-4e8d-b673-20c6c53dc447\" rel=\"noopener noreferrer\" target=\"_blank\">e9aeab8a-8c8f-4e8d-b673-20c6c53dc447</a> or <a href=\"https://data.4dnucleome.org/microscope-configurations/b904ca5d-fcac-4a7d-b703-dc98adedabf5\" rel=\"noopener noreferrer\" target=\"_blank\">b904ca5d-fcac-4a7d-b703-dc98adedabf5</a> microscopes.</p></div>"}, {"lab": {"@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "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 - 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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": "<div class=\"markdown-container\"><p>Processed files in this dataset are provided in the 4DN standard FISH-Omics Format - Chromatin Tracing (FOF-CT).</p>\n<p>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. </p>\n<p>The full documentation is available here: https://fish-omics-format.readthedocs.io/</p></div>"}], "project_release": "2025-04-21", "contributing_labs": [{"uuid": "9827adc7-c9a9-44ae-a689-c83e09fee179", "status": "current", "correspondence": [{"contact_email": "c3VzYW4ubWFuZ29AdW5pYmFzLmNo", "@id": "/users/8b7b64e6-0e32-4635-8d23-568b29ddda6a/", "display_title": "Susan Mango"}], "@id": "/labs/susan-mango-lab/", "display_title": "Susan Mango", "@type": ["Lab", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.9827adc7-c9a9-44ae-a689-c83e09fee179"]}}], "experiments_in_set": [{"@id": "/experiments-mic/4DNEXPGC27XJ/", "status": "released", "@type": ["ExperimentMic", "Experiment", "Item"], "uuid": "8b7ee062-9856-4c6f-9cce-7b07a598f2c2", "accession": "4DNEXPGC27XJ", "display_title": "multiplexed FISH on multicellular organism - 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Wild type", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "multicellular organism", "lab_name": "Ahilya Sawh Lab"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_type": {"assay_classification": "Fluorescence Localization", "uuid": "bcdda46a-489d-4d22-be80-c9c21552c915", "assay_subclass_short": "FISH", "experiment_category": "Microscopy", "display_title": "multiplexed FISH", "other_tags": ["Single Cell"], "status": "released", "@id": "/experiment-types/multiplexed-fish/", "assay_subclassification": "Chromatin Tracing", "@type": ["ExperimentType", "Item"], "title": "multiplexed FISH", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "experiment_categorizer": {"field": "Target", "value": "22 TADs on ChrV (roundworm)", "combined": "Target: 22 TADs on ChrV (roundworm)"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2025-04-21T17:18:28.184202+00:00"}}], "experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNES4LQ2W7R/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "28e1604b-44f3-49fd-b581-9abf59bee996", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNES4LQ2W7R", "external_references": [], "produced_in_pub": {"title": "Lamina-Dependent Stretching and Unconventional Chromosome Compartments in Early  C. elegans Embryos.", "display_title": "Sawh AN et al. (2020) PMID:32105612", "status": "current", "@type": ["Publication", "Item"], "abstract": "Current models suggest that chromosome domains segregate into either an active  (A) or inactive (B) compartment. B-compartment chromatin is physically separated  from the A compartment and compacted by the nuclear lamina. To examine these  models in the developmental context of C. elegans embryogenesis, we undertook  chromosome tracing to map the trajectories of entire autosomes. Early embryonic  chromosomes organized into an unconventional barbell-like configuration, with two  densely folded B compartments separated by a central A compartment. Upon  gastrulation, this conformation matured into conventional A/B compartments. We  used unsupervised clustering to uncover subpopulations with differing folding  properties and variable positioning of compartment boundaries. These  conformations relied on tethering to the lamina to stretch the chromosome;  detachment from the lamina compacted, and allowed intermingling between, A/B  compartments. These findings reveal the diverse conformations of early embryonic  chromosomes and uncover a previously unappreciated role for the lamina in  systemic chromosome stretching.", "url": "https://www.ncbi.nlm.nih.gov/pubmed/32105612", "@id": "/publications/996fc79a-65e1-4527-9e7b-0c4b8b9d7511/", "authors": ["Sawh AN", "Shafer MER", "Su JH", "Zhuang X", "Wang S", "Mango SE"], "ID": "PMID:32105612", "uuid": "996fc79a-65e1-4527-9e7b-0c4b8b9d7511", "journal": "Molecular cell", "date_published": "2020-04-02", "short_attribution": "Sawh AN et al. (2020)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"status": "current", "abstract": "Current models suggest that chromosome domains segregate into either an active  (A) or inactive (B) compartment. B-compartment chromatin is physically separated  from the A compartment and compacted by the nuclear lamina. To examine these  models in the developmental context of C. elegans embryogenesis, we undertook  chromosome tracing to map the trajectories of entire autosomes. Early embryonic  chromosomes organized into an unconventional barbell-like configuration, with two  densely folded B compartments separated by a central A compartment. Upon  gastrulation, this conformation matured into conventional A/B compartments. We  used unsupervised clustering to uncover subpopulations with differing folding  properties and variable positioning of compartment boundaries. These  conformations relied on tethering to the lamina to stretch the chromosome;  detachment from the lamina compacted, and allowed intermingling between, A/B  compartments. These findings reveal the diverse conformations of early embryonic  chromosomes and uncover a previously unappreciated role for the lamina in  systemic chromosome stretching.", "display_title": "Sawh AN et al. 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