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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": {"display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "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": [{"@id": "/labs/susan-mango-lab/", "status": "current", "display_title": "Susan Mango", "correspondence": [{"contact_email": "c3VzYW4ubWFuZ29AdW5pYmFzLmNo", "@id": "/users/8b7b64e6-0e32-4635-8d23-568b29ddda6a/", "display_title": "Susan Mango"}], "@type": ["Lab", "Item"], "uuid": "9827adc7-c9a9-44ae-a689-c83e09fee179", "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": [{"@type": ["ExperimentMic", "Experiment", "Item"], "@id": "/experiments-mic/4DNEXBODJ1L2/", "status": "released", "display_title": "multiplexed FISH on multicellular organism - 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central region, Wild type", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "multicellular organism", "lab_name": "Ahilya Sawh Lab"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_type": {"assay_subclassification": "Chromatin Tracing", "@id": "/experiment-types/multiplexed-fish/", "assay_subclass_short": "FISH", "other_tags": ["Single Cell"], "title": "multiplexed FISH", "status": "released", "display_title": "multiplexed FISH", "experiment_category": "Microscopy", "assay_classification": "Fluorescence Localization", "@type": ["ExperimentType", "Item"], "uuid": "bcdda46a-489d-4d22-be80-c9c21552c915", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"value": "3 TADs on ChrV (central region) (roundworm)", "field": "Target", "combined": "Target: 3 TADs on ChrV (central region) (roundworm)"}, "last_modified": {"date_modified": "2025-04-21T17:18:26.927255+00:00"}}], "experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNESCSUHS2E/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "3959e6f9-523f-4030-8c02-8b2f47739a43", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNESCSUHS2E", "external_references": [], "produced_in_pub": {"display_title": "Sawh AN et al. (2020) PMID:32105612", "title": "Lamina-Dependent Stretching and Unconventional Chromosome Compartments in Early  C. elegans Embryos.", "uuid": "996fc79a-65e1-4527-9e7b-0c4b8b9d7511", "@id": "/publications/996fc79a-65e1-4527-9e7b-0c4b8b9d7511/", "ID": "PMID:32105612", "@type": ["Publication", "Item"], "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.", "url": "https://www.ncbi.nlm.nih.gov/pubmed/32105612", "journal": "Molecular cell", "authors": ["Sawh AN", "Shafer MER", "Su JH", "Zhuang X", "Wang S", "Mango SE"], "short_attribution": "Sawh AN et al. (2020)", "date_published": "2020-04-02", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"status": "current", "title": "Lamina-Dependent Stretching and Unconventional Chromosome Compartments in Early  C. elegans Embryos.", "journal": "Molecular cell", "uuid": "996fc79a-65e1-4527-9e7b-0c4b8b9d7511", "authors": ["Sawh AN", "Shafer MER", "Su JH", "Zhuang X", "Wang S", "Mango SE"], "@type": ["Publication", "Item"], "@id": "/publications/996fc79a-65e1-4527-9e7b-0c4b8b9d7511/", "display_title": "Sawh AN et al. (2020) PMID:32105612", "date_published": "2020-04-02", "ID": "PMID:32105612", "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.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 1, "imaging_paths": [{"path": {"labeled_probe": "DAPI", "display_title": "DAPI", "@type": ["ImagingPath", "Item"], "@id": "/imaging-paths/fa8df2a3-c490-4d4c-b575-1bb6ee4598e1/", "uuid": "fa8df2a3-c490-4d4c-b575-1bb6ee4598e1", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "channel": "ch00"}, {"path": {"labeled_probe": "fiducial beads", "display_title": "fiducial beads", "@type": ["ImagingPath", "Item"], "@id": "/imaging-paths/4b5b2e62-7bb1-4c70-bdab-b281688b87c4/", "uuid": "4b5b2e62-7bb1-4c70-bdab-b281688b87c4", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "channel": "ch01"}, {"path": {"labeled_probe": "imaging oligos", "display_title": "3 TADs on ChrV (central region) imaged using ATTO 561 imaging probes", "@type": ["ImagingPath", "Item"], "override_display_title": "3 TADs on ChrV (central region) imaged using ATTO 561 imaging probes", "imaging_rounds": "1-20", "@id": "/imaging-paths/37e6f9b4-71d7-4929-98e8-388c71e2f39e/", "uuid": "37e6f9b4-71d7-4929-98e8-388c71e2f39e", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "target": [{"@type": ["BioFeature", "Item"], "organism_name": "roundworm", "display_title": "3 TADs on ChrV (central region) (roundworm)", "uuid": "9e500152-10cc-4418-9a73-16ec4489cdcb", "@id": "/bio-features/9e500152-10cc-4418-9a73-16ec4489cdcb/", "status": "released", "preferred_label": "3 TADs on ChrV (central region)", "feature_type": {"@id": "/ontology-terms/SO:0000001/", "status": "released", "term_name": "region", "preferred_name": "region", "display_title": "region", "term_id": "SO:0000001", "@type": ["OntologyTerm", "Item"], "term_url": "http://purl.obolibrary.org/obo/SO_0000001", "uuid": "41b7a2c5-f2d9-46b4-a49d-51502fe61bb3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "channel": "ch02"}, {"path": {"labeled_probe": "imaging oligos", "display_title": "3 TADs on ChrV (central region) imaged using Alexa Fluor 647 imaging probes", "@type": ["ImagingPath", "Item"], "override_display_title": "3 TADs on ChrV (central region) imaged using Alexa Fluor 647 imaging probes", "imaging_rounds": "1-20", "@id": "/imaging-paths/97721f5e-4338-4b26-8e68-f64e7d893368/", "uuid": "97721f5e-4338-4b26-8e68-f64e7d893368", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "target": [{"@type": ["BioFeature", "Item"], "organism_name": "roundworm", "display_title": "3 TADs on ChrV (central region) (roundworm)", "uuid": "9e500152-10cc-4418-9a73-16ec4489cdcb", "@id": "/bio-features/9e500152-10cc-4418-9a73-16ec4489cdcb/", "status": "released", "preferred_label": "3 TADs on ChrV (central region)", "feature_type": {"@id": "/ontology-terms/SO:0000001/", "status": "released", "term_name": "region", "preferred_name": "region", "display_title": "region", "term_id": "SO:0000001", "@type": ["OntologyTerm", "Item"], "term_url": "http://purl.obolibrary.org/obo/SO_0000001", "uuid": "41b7a2c5-f2d9-46b4-a49d-51502fe61bb3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "channel": "ch03"}], "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/experiment-set-replicates/4DNESCSUHS2E/", "embedded_path": "badges", "item": {"messages": ["Replicate set contains only a single biological replicate"], "badge": {"commendation": null, "warning": "Replicate Numbers", "uuid": "24a64a84-3c33-4d76-aaf2-e5ef45eff347", "@id": "/badges/replicate-numbers/", "badge_icon": "/static/img/badges/replicates-orange-circle.svg", "description": "Issues with replicate numbers"}}}]}, "validation-errors": []}