{"lab": {"title": "Robert Coleman, EINSTEIN", "@type": ["Lab", "Item"], "status": "current", "correspondence": [{"contact_email": "cm9iZXJ0LmNvbGVtYW4yQGVpbnN0ZWluLnl1LmVkdQ==", "@id": "/users/ac1542b9-f3de-491f-9f2d-f9f0be5c0f56/", "display_title": "Robert Coleman"}], "display_title": "Robert Coleman, EINSTEIN", "@id": "/labs/robert-coleman-lab/", "uuid": "3b4ae9a9-e440-4918-8923-38bec007a650", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3b4ae9a9-e440-4918-8923-38bec007a650"]}}, "award": {"center_title": "IT - Singer", "display_title": "TOOLS FOR IMAGING THE FUNCTIONAL GENOME IN LIVING CELLS AND TISSUES", "description": "IT: This goal of this proposal is to develop imaging tools capable of imaging the functional genome by mapping the three dimensional binding sites and clustering of transcription factors and histone modifiers. We will use single molecule particle tracking within the entire nucleus of the cell in real time. Initially this will be done in culture ES cells, and ultimately in living animals. There will be three locations involved: Albert Einstein College of Medicine, the University of California at Berkeley and the Janelia Research Campus of the HHMI, where the Transcription Imaging Consortium integrates the efforts of the investigators of this proposal. The reagents will be developed at Einstein and Berkeley and the microscope technology that has been developed and used predominantly at Janelia, will inform further modifications in building similar microscopes at Berkeley and Einstein. Genes of interest will be marked to image promoter-enhancer interactions in cells, tissues and organisms with high resolution. The microscopes employed and developed for these applications will be the multifocal microscope, the lattice light sheet microscope, the adaptive optics microscope and the high-speed three-color super registration microscope. Importantly, we will evaluate the levels of phototoxicity for the imaging protocols on each microscope and develop approaches to minimize it. Microscopes developed will be made available to the Nucleome community at the Einstein and Berkeley sites and at Janelia through a resource sharing facility, the Advanced Imaging Center, supported by the HHMI and the Moore Foundation with the explicit purpose of disseminating the use of the technology. No funds are requested for the Janelia component of this proposal. All funds will be for development of microscopes and reagents that will be at Berkeley and Einstein.", "uuid": "e7adc531-c594-4f3e-a432-252dd5b5748d", "status": "current", "name": "1U01EB021236-01", "@id": "/awards/1U01EB021236-01/", "project": "4DN", "@type": ["Award", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["robert-coleman-lab:Halo_BAF180_Bddel_H3.3_SNAP"], "accession": "4DNES2DS2N1U", "condition": "Halo tagged BAF180-BDdel and transient H3.3-SNAP", "description": "SPT experiments on U2OS Cells stably expressing Halo-BAF180-BDdel and transiently expressing H3.3-SNAP", "date_created": "2019-04-19T18:32:17.054350+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "SPT on U2OS cells", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-08-04T22:58:56.374264+00:00"}, "public_release": "2019-08-04", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-mic/4DNEXBBPMBG7/", "@type": ["ExperimentMic", "Experiment", "Item"], "display_title": "SPT on U2OS - 4DNEXBBPMBG7", "uuid": "3710b781-e54d-4f12-a7dd-c4b69c999b17", "status": "released", "accession": "4DNEXBBPMBG7", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-mic/4DNEX62DIRZ3/", "@type": ["ExperimentMic", "Experiment", "Item"], "display_title": "SPT on U2OS - 4DNEX62DIRZ3", "uuid": "9d93f541-3818-4148-9ee1-24a00eb597ec", "status": "released", "accession": "4DNEX62DIRZ3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 3, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-mic/4DNEXHGX2FME/", "@type": ["ExperimentMic", "Experiment", "Item"], "display_title": "SPT on U2OS - 4DNEXHGX2FME", "uuid": "926b4a9f-7c3b-4ced-8100-4a63d64bb17a", "status": "released", "accession": "4DNEXHGX2FME", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 3, "tec_rep_no": 2, "replicate_exp": {"@id": "/experiments-mic/4DNEXK4I5L6I/", "@type": ["ExperimentMic", "Experiment", "Item"], "display_title": "SPT on U2OS - 4DNEXK4I5L6I", "uuid": "01b54724-67fb-42c2-8c68-2418294ce765", "status": "released", "accession": "4DNEXK4I5L6I", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 4, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-mic/4DNEXV7MK7NO/", "@type": ["ExperimentMic", "Experiment", "Item"], "display_title": "SPT on U2OS - 4DNEXV7MK7NO", "uuid": "e1147198-dc8d-4829-ae28-66eea000eea3", "status": "released", "accession": "4DNEXV7MK7NO", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 4, "tec_rep_no": 2, "replicate_exp": {"@id": "/experiments-mic/4DNEX4CQ235L/", "@type": ["ExperimentMic", "Experiment", "Item"], "display_title": "SPT on U2OS - 4DNEX4CQ235L", "uuid": "38d51ea6-3b11-4cf7-8f4f-2143bd2c8136", "status": "released", "accession": "4DNEX4CQ235L", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_headers": [{"lab": {"display_title": "4DN DCIC, HMS", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "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": "**SPT**\n\nSingle particle tracking (SPT) is a method to track the position\n of a single molecule over time in live cells. Advances in \nmicroscopy and molecular biology techniques have enabled a \nbroad range of applications.\n\nThe protocol involves preparing the target molecule to be \nidentifiable under the microscope, tracking its position over \ntime and analyzing its trajectory. Generally, the preparation \nof the molecule of interest is performed by genetically \nmodifying it with tags followed by the binding of reporter \nmolecules such as fluorescent dyes. However, depending on the \nmolecule of interest, the goal of the experiment and the type \nof microscope used, different techniques are also implemented.\n Following the preparation of the molecule, a high-resolution \nmicroscope is used to take snapshots of the position of the \nmolecule at different intervals of time. Tracking a single \nmolecule in a live cell is a demanding task, requiring both \nsensitivity and accuracy. Tailored to the application, this \ncan be achieved by specialized microscopy techniques like TIRF\n or PALM. Analysis of the resulting images results in a file \nthat describes the trajectory of the molecule.\n\n4DN processed files are in a format that includes the ID of a \ntrajectory, the time interval, and the coordinates of the \nposition. Further analysis of the trajectory of the molecule \nis necessary to gain biological insight. \n", "name": "item-page-headers.ExperimentType.spt", "award": {"@id": "/awards/1U01CA200059-01/", "@type": ["Award", "Item"], "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Assay Description", "status": "released", "aliases": ["4dn-dcic-lab:experiment_infobox_spt"], "options": {"filetype": "md", "collapsible": false, "default_open": false}, "date_created": "2018-09-07T15:49:58.130720+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-08-04T22:53:31.013900+00:00"}, "schema_version": "2", "@id": "/static-sections/6a313162-e70c-4fbe-93c5-bc78f5faf0c7/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "6a313162-e70c-4fbe-93c5-bc78f5faf0c7", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.56c9c683-bb11-471b-b590-c656f7dc03c1"]}, "display_title": "Assay Description", "external_references": [], "content": "**SPT**\n\nSingle particle tracking (SPT) is a method to track the position\n of a single molecule over time in live cells. Advances in \nmicroscopy and molecular biology techniques have enabled a \nbroad range of applications.\n\nThe protocol involves preparing the target molecule to be \nidentifiable under the microscope, tracking its position over \ntime and analyzing its trajectory. Generally, the preparation \nof the molecule of interest is performed by genetically \nmodifying it with tags followed by the binding of reporter \nmolecules such as fluorescent dyes. However, depending on the \nmolecule of interest, the goal of the experiment and the type \nof microscope used, different techniques are also implemented.\n Following the preparation of the molecule, a high-resolution \nmicroscope is used to take snapshots of the position of the \nmolecule at different intervals of time. Tracking a single \nmolecule in a live cell is a demanding task, requiring both \nsensitivity and accuracy. Tailored to the application, this \ncan be achieved by specialized microscopy techniques like TIRF\n or PALM. Analysis of the resulting images results in a file \nthat describes the trajectory of the molecule.\n\n4DN processed files are in a format that includes the ID of a \ntrajectory, the time interval, and the coordinates of the \nposition. Further analysis of the trajectory of the molecule \nis necessary to gain biological insight. \n", "filetype": "md", "content_as_html": "<div class=\"markdown-container\"><p><strong>SPT</strong></p>\n<p>Single particle tracking (SPT) is a method to track the position\n of a single molecule over time in live cells. Advances in \nmicroscopy and molecular biology techniques have enabled a \nbroad range of applications.</p>\n<p>The protocol involves preparing the target molecule to be \nidentifiable under the microscope, tracking its position over \ntime and analyzing its trajectory. Generally, the preparation \nof the molecule of interest is performed by genetically \nmodifying it with tags followed by the binding of reporter \nmolecules such as fluorescent dyes. However, depending on the \nmolecule of interest, the goal of the experiment and the type \nof microscope used, different techniques are also implemented.\n Following the preparation of the molecule, a high-resolution \nmicroscope is used to take snapshots of the position of the \nmolecule at different intervals of time. Tracking a single \nmolecule in a live cell is a demanding task, requiring both \nsensitivity and accuracy. Tailored to the application, this \ncan be achieved by specialized microscopy techniques like TIRF\n or PALM. Analysis of the resulting images results in a file \nthat describes the trajectory of the molecule.</p>\n<p>4DN processed files are in a format that includes the ID of a \ntrajectory, the time interval, and the coordinates of the \nposition. Further analysis of the trajectory of the molecule \nis necessary to gain biological insight. </p></div>"}], "project_release": "2019-08-04", "experiments_in_set": [{"@type": ["ExperimentMic", "Experiment", "Item"], "status": "released", "accession": "4DNEXBBPMBG7", "uuid": "3710b781-e54d-4f12-a7dd-c4b69c999b17", "@id": "/experiments-mic/4DNEXBBPMBG7/", "display_title": "SPT on U2OS - 4DNEXBBPMBG7", "processed_files": [{"file_type_detailed": "spt results (spt)", "genome_assembly": "GRCh38", "md5sum": "460322052420cb3cead1d45fc6596727", "display_title": "4DNFILDFAYNV.spt", "@type": ["FileProcessed", "File", "Item"], "file_size": 634041, "href": "/files-processed/4DNFILDFAYNV/@@download/4DNFILDFAYNV.spt", "@id": "/files-processed/4DNFILDFAYNV/", "upload_key": "825540b9-47c1-4a63-843b-25c053a0903b/4DNFILDFAYNV.spt", "file_type": "spt results", "status": "released", "file_format": {"@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-55f0-94f446118b2c", "@id": "/file-formats/spt/", 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Removal of PBAF's bromodomains stabilizes H3.3 binding within chromatin indicating that bromodomains may play a  direct role in remodeling of the nucleosome. Our data suggests that PBAF's dynamic bromodomain mediated engagement of a nucleosome may reflect the chromatin remodeling potential of differentially bound chromatin states.", "url": "https://www.ncbi.nlm.nih.gov/pubmed/35364106", "short_attribution": "Kenworthy CA et al. 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Our live-cell single molecule fluorescence microscopy study reveals chromatin hubs throughout the nucleus where PBAF rapidly cycles on and off the genome. Deletion of PBAF's bromodomains impairs targeting and stable engagement of chromatin in hubs. Dual color imaging reveals that PBAF targets both euchromatic and heterochromatic hubs with distinct genome binding kinetic profiles that mimic chromatin stability. Removal of PBAF's bromodomains stabilizes H3.3 binding within chromatin indicating that bromodomains may play a  direct role in remodeling of the nucleosome. 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