{"lab": {"@type": ["Lab", "Item"], "uuid": "c41d6cdb-de46-439c-9823-10efd30f11e5", "display_title": "Xavier Darzacq, BERKELEY", "correspondence": [{"contact_email": "ZGFyemFjcUBiZXJrZWxleS5lZHU=", "@id": "/users/5983564d-2432-412b-b7eb-ef98308c2692/", "display_title": "Xavier Darzacq"}], "status": "current", "@id": "/labs/xavier-darzacq-lab/", "title": "Xavier Darzacq, BERKELEY", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c41d6cdb-de46-439c-9823-10efd30f11e5"]}}, "award": {"display_title": "TOOLS FOR IMAGING THE FUNCTIONAL GENOME IN LIVING CELLS AND TISSUES", "center_title": "IT - Singer", "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.", "@type": ["Award", "Item"], "@id": "/awards/1U01EB021236-01/", "uuid": "e7adc531-c594-4f3e-a432-252dd5b5748d", "project": "4DN", "status": "current", "name": "1U01EB021236-01", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["xavier-darzacq-lab:spot_on_set_u2os_halo_3nls_spt12_cond2_2ms_100Hz_PAJF549"], "accession": "4DNESV3SE5O6", "condition": "2 ms pulse on U2OS Halo-3xNLS at 100Hz", "description": "spaSPT with 2 ms excitation pulse on U2OS Halo-3xNLS with PAJF549 at 100Hz frame rate, with 4 biological replicates, around 20 cells", "date_created": "2018-07-20T20:58:26.491762+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "SPT on U2OS cells for Spot-On analysis", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-10-04T18:19:42.073125+00:00"}, "public_release": "2018-07-27", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"uuid": "3b1f889e-6f12-4087-9d53-5aabe057888e", "@type": ["ExperimentMic", "Experiment", "Item"], "status": "released", "accession": "4DNEX4YIVD5H", "display_title": "SPT on U2OS - 4DNEX4YIVD5H", "@id": "/experiments-mic/4DNEX4YIVD5H/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 1, "replicate_exp": {"uuid": "d46696f2-0add-43bd-a3e5-5c01793d2c36", "@type": ["ExperimentMic", "Experiment", "Item"], "status": "released", "accession": "4DNEXB45ZM24", "display_title": "SPT on U2OS - 4DNEXB45ZM24", "@id": "/experiments-mic/4DNEXB45ZM24/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 3, "tec_rep_no": 1, "replicate_exp": {"uuid": "e35e2ce6-359b-4211-84c5-104cee7fb07f", "@type": ["ExperimentMic", "Experiment", "Item"], "status": "released", "accession": "4DNEXT1533EC", "display_title": "SPT on U2OS - 4DNEXT1533EC", "@id": "/experiments-mic/4DNEXT1533EC/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 4, "tec_rep_no": 1, "replicate_exp": {"uuid": "5a3a737d-dabf-4d3e-b4f4-8a5fee2892a1", "@type": ["ExperimentMic", "Experiment", "Item"], "status": "released", "accession": "4DNEX8SO1FDG", "display_title": "SPT on U2OS - 4DNEX8SO1FDG", "@id": "/experiments-mic/4DNEX8SO1FDG/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_headers": [{"lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "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": "**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. 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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. 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