{"lab": {"title": "Xavier Darzacq, BERKELEY", "@type": ["Lab", "Item"], "status": "current", "correspondence": [{"contact_email": "ZGFyemFjcUBiZXJrZWxleS5lZHU=", "@id": "/users/5983564d-2432-412b-b7eb-ef98308c2692/", "display_title": "Xavier Darzacq"}], "display_title": "Xavier Darzacq, BERKELEY", "@id": "/labs/xavier-darzacq-lab/", "uuid": "c41d6cdb-de46-439c-9823-10efd30f11e5", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c41d6cdb-de46-439c-9823-10efd30f11e5"]}}, "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": ["xavier-darzacq-lab:spot_on_set_jm8n4T2_spt07_cond2_2ms_100Hz_PAJF646"], "accession": "4DNESYSZEQD2", "condition": "2 ms pulse on JM8N4 mESC Halo-Sox2 at 100Hz", "description": "spaSPT with 2 ms excitation pulse on JM8N4 mESC Halo-Sox2 with PAJF646 at 100Hz frame rate, with 4 biological replicates, around 20 cells", "date_created": "2018-07-20T20:57:48.060378+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "SPT on JM8N4 cells for Spot-On analysis", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-10-04T18:19:11.141103+00:00"}, "public_release": "2018-07-27", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-mic/4DNEX1RZKGBT/", "@type": ["ExperimentMic", "Experiment", "Item"], "display_title": "SPT on JM8.N4 (Tier 2) - 4DNEX1RZKGBT", "uuid": "cefbb14e-c560-4688-ba33-99ae8b51ca69", "status": "released", "accession": "4DNEX1RZKGBT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-mic/4DNEXS3LGE4L/", "@type": ["ExperimentMic", "Experiment", "Item"], "display_title": "SPT on JM8.N4 (Tier 2) - 4DNEXS3LGE4L", "uuid": "50b8adb5-ee58-4368-be3d-4e4cf6e2242c", "status": "released", "accession": "4DNEXS3LGE4L", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 3, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-mic/4DNEXA12AYGE/", "@type": ["ExperimentMic", "Experiment", "Item"], "display_title": "SPT on JM8.N4 (Tier 2) - 4DNEXA12AYGE", "uuid": "23350b50-0038-4298-baa8-ae2961e03031", "status": "released", "accession": "4DNEXA12AYGE", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 4, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-mic/4DNEX6UTLBK1/", "@type": ["ExperimentMic", "Experiment", "Item"], "display_title": "SPT on JM8.N4 (Tier 2) - 4DNEX6UTLBK1", "uuid": "96524f31-965c-478c-ab3c-8f9582845d71", "status": "released", "accession": "4DNEX6UTLBK1", "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. 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We validate Spot-On using experimentally realistic simulations and show that Spot-On outperforms other methods. We then apply Spot-On to spaSPT  data from live mammalian cells spanning a wide range of nuclear dynamics and demonstrate that Spot-On consistently and robustly infers subpopulation fractions and diffusion constants.", "url": "https://www.ncbi.nlm.nih.gov/pubmed/29300163", "short_attribution": "Hansen AS et al. (2018)", "ID": "doi:10.7554/eLife.33125", "date_published": "2018-01-04", "authors": ["Hansen AS", "Woringer M", "Grimm JB", "Lavis LD", "Tjian R", "Darzacq X"], "title": "Robust model-based analysis of single-particle tracking experiments with Spot-On.", "@type": ["Publication", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"authors": ["Hansen AS", "Woringer M", "Grimm JB", "Lavis LD", "Tjian R", "Darzacq X"], "@type": ["Publication", "Item"], "abstract": "Single-particle tracking (SPT) has become an important method to bridge biochemistry and cell biology since it allows direct observation of protein binding and diffusion dynamics in live cells. However, accurately inferring information from SPT studies is challenging due to biases in both data analysis and experimental design. To address analysis bias, we introduce 'Spot-On', an intuitive web-interface. Spot-On implements a kinetic modeling framework that accounts for known biases, including molecules moving out-of-focus, and robustly  infers diffusion constants and subpopulations from pooled single-molecule trajectories. To minimize inherent experimental biases, we implement and validate stroboscopic photo-activation SPT (spaSPT), which minimizes motion-blur bias and  tracking errors. We validate Spot-On using experimentally realistic simulations and show that Spot-On outperforms other methods. We then apply Spot-On to spaSPT  data from live mammalian cells spanning a wide range of nuclear dynamics and demonstrate that Spot-On consistently and robustly infers subpopulation fractions and diffusion constants.", "title": "Robust model-based analysis of single-particle tracking experiments with Spot-On.", "date_published": "2018-01-04", "uuid": "83e74398-ac79-4372-91d3-250e7390d636", "status": "current", "display_title": "Hansen AS et al. (2018) doi:10.7554/eLife.33125", "ID": "doi:10.7554/eLife.33125", "@id": "/publications/83e74398-ac79-4372-91d3-250e7390d636/", "journal": "eLife", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 4, "imaging_paths": [{"path": {"@id": "/imaging-paths/2a07967e-6a4c-4cb8-82f3-143e78f04cc4/", "display_title": "Sox2 mouse protein with HaloTag targeted by PAJF646-labeled Halo Tag", "status": "released", "labeled_probe": "Halo Tag", "@type": ["ImagingPath", "Item"], "uuid": "2a07967e-6a4c-4cb8-82f3-143e78f04cc4", "target": [{"status": "released", "@id": "/bio-features/d6e98cf9-4630-4d35-8706-628f286cf891/", "uuid": "d6e98cf9-4630-4d35-8706-628f286cf891", "feature_mods": [{"mod_type": "HaloTag"}], "@type": ["BioFeature", "Item"], "display_title": "Sox2 mouse protein with HaloTag", "organism_name": "mouse", "relevant_genes": [{"status": "released", "@type": ["Gene", "Item"], "preferred_symbol": "Sox2", "geneid": "20674", "uuid": "db4fa807-b3aa-4cf5-84da-3c0bb4d4c857", "display_title": "Sox2", "@id": "/genes/20674/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "feature_type": {"term_id": "SO:0000104", "term_name": "polypeptide", "uuid": "91f427e6-5246-4992-8123-b4f8fa9eef01", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "protein", "preferred_name": "protein", "@id": "/ontology-terms/SO:0000104/", "term_url": "http://purl.obolibrary.org/obo/SO_0000104", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "channel": "ch00"}], "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSV1CJKBL/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["Biosample missing culture_harvest_date", "Biosample missing doubling_number", "Biosample missing passage_number", "Biosample missing culture_duration", "Biosample missing morphology_image", "Biosample is a stem cell line with unknown passage number missing karyotype"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}, {"parent": "/biosamples/4DNBSHAWH8VP/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["Biosample missing culture_harvest_date", "Biosample missing doubling_number", "Biosample missing passage_number", "Biosample missing culture_duration", "Biosample missing morphology_image", "Biosample is a stem cell line with unknown passage number missing karyotype"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}, {"parent": "/biosamples/4DNBSIOAFVHB/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["Biosample missing culture_harvest_date", "Biosample missing doubling_number", "Biosample missing passage_number", "Biosample missing culture_duration", "Biosample missing morphology_image", "Biosample is a stem cell line with unknown passage number missing karyotype"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}, {"parent": "/biosamples/4DNBSSOXLHCL/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["Biosample missing culture_harvest_date", "Biosample missing doubling_number", "Biosample missing passage_number", "Biosample missing culture_duration", "Biosample missing morphology_image", "Biosample is a stem cell line with unknown passage number missing karyotype"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}]}, "validation-errors": []}