{"lab": {"title": "Xavier Darzacq, BERKELEY", "status": "current", "@type": ["Lab", "Item"], "uuid": "c41d6cdb-de46-439c-9823-10efd30f11e5", "display_title": "Xavier Darzacq, BERKELEY", "@id": "/labs/xavier-darzacq-lab/", "correspondence": [{"contact_email": "ZGFyemFjcUBiZXJrZWxleS5lZHU=", "@id": "/users/5983564d-2432-412b-b7eb-ef98308c2692/", "display_title": "Xavier Darzacq"}], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c41d6cdb-de46-439c-9823-10efd30f11e5"]}}, "award": {"uuid": "e7adc531-c594-4f3e-a432-252dd5b5748d", "project": "4DN", "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.", "status": "current", "@type": ["Award", "Item"], "center_title": "IT - Singer", "name": "1U01EB021236-01", "@id": "/awards/1U01EB021236-01/", "display_title": "TOOLS FOR IMAGING THE FUNCTIONAL GENOME IN LIVING CELLS AND TISSUES", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["xavier-darzacq-lab:spot_on_exp_jm8n4T2_spt14_cond2_7ms_100Hz_PAJF549_1"], "protocol": {"@id": "/protocols/7fcb821f-7906-4a82-ad6f-c26ce77c80b0/", "status": "released", "display_title": "SpotOn_4DN_spaSPT_protocol.pdf", "uuid": "7fcb821f-7906-4a82-ad6f-c26ce77c80b0", "@type": ["Protocol", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNEX7ZRL16Q", "biosample": {"status": "released", "@id": "/biosamples/4DNBSV1CJKBL/", "display_title": "4DNBSV1CJKBL", "accession": "4DNBSV1CJKBL", "@type": ["Biosample", "Item"], "biosample_type": "stem cells", "biosource_summary": "JM8.N4 (Tier 2)", "uuid": "b25ca545-d118-4124-b5c2-3ea10b761039", "treatments_summary": "None", "modifications_summary": "Crispr generation of HALO-tagged Sox2", "biosource": [{"lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "url": "https://www.komp.org/pdf.php?cloneID=8669", "award": {"uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "@type": ["Award", "Item"], "status": "current", "@id": "/awards/1U01CA200059-01/", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"term_id": "CL:0000034", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000034/", "display_title": "stem cell", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "preferred_name": "stem cell", "synonyms": ["animal stem cell"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["dcic:jm8n4T2", "4dn-dcic-lab:jm8n4T2"], "accession": "4DNSRHAXQ8PG", "cell_line": {"slim_terms": [{"display_title": "cell line", "@id": "/ontology-terms/CLO:0000031/", "status": "released", "@type": ["OntologyTerm", "Item"], "uuid": "f9483d7e-4731-47d1-b8e0-1aac05ba2b49", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/ontology-terms/4DN:0000250/", "uuid": "bcfb5e65-b6b5-40a7-834d-9fb5a4d016bd", "term_name": "JM8.N4", "term_id": "4DN:0000250", "@type": ["OntologyTerm", "Item"], "display_title": "JM8.N4", "preferred_name": "JM8.N4", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"status": "released", "uuid": "456c4d51-710b-4bcf-9df6-1e06c810a3b6", "@id": "/individuals-mouse/4DNINMJOZAAE/", "display_title": "4DNINMJOZAAE", "@type": ["IndividualMouse", "Individual", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "references": [], "description": "The JM8.N4 ES subline is derived from the JM8 parental line which were derived from C57BL/6N mice.", "date_created": "2017-07-28T16:33:53.795108+00:00", "submitted_by": {"error": "no view permissions"}, "SOP_cell_line": {"uuid": "06248bc3-40ad-4f0a-9348-835e4a33d543", "@id": "/protocols/06248bc3-40ad-4f0a-9348-835e4a33d543/", "status": "released", "display_title": "4DN_JM8N4_SOP_170727.pdf", "@type": ["Protocol", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-09-19T19:54:44.625320+00:00"}, "modifications": [], "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 2", "public_release": "2017-07-28T16:33:53.795108+00:00", "schema_version": "2", "project_release": "2017-07-28T16:33:53.795108+00:00", "biosource_vendor": {"display_title": "Darzacq lab", "status": "released", "@type": ["Vendor", "Item"], "uuid": "a7c57a02-856a-4d5e-b33b-13ee8ccaec63", "@id": "/vendors/darzacq-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "alternate_accessions": [], "@id": "/biosources/4DNSRHAXQ8PG/", "@type": ["Biosource", "Item"], "uuid": "771e0bad-9d7c-4b8b-9f9f-a95d05f19519", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "JM8.N4 (Tier 2) - 4DNSRHAXQ8PG", "external_references": [], "biosource_name": "JM8.N4 (Tier 2)", "biosource_category": ["Tier 2", "Mouse stem cell"], "organism": {"display_title": "M. musculus", "name": "mouse", "@id": "/organisms/10090/", "@type": ["Organism", "Item"], "status": "released", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "badges": [{"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": {"@id": "/badges/biosample-metadata-incomplete/", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "status": "released", "display_title": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-icon.svg", "title": "Biosample Metadata Incomplete", "warning": "Biosample Metadata Incomplete", "badge_classification": "Warning", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "modifications": [{"display_title": "Crispr generation of HALO-tagged Sox2", "modification_type": "Crispr", "@id": "/modifications/d448b665-36a5-4215-ac8a-1bec636ad52a/", "@type": ["Modification", "Item"], "genomic_change": "insertion", "status": "released", "uuid": "d448b665-36a5-4215-ac8a-1bec636ad52a", "description": "FLAG-Halo-Sox2 clone C3. Homozygous endogenous N-terminal tagging of Sox2. Full details at: https://elifesciences.org/articles/22280", "override_modification_name": "Crispr generation of HALO-tagged Sox2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "treatments": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "sop_mapping": {"has_sop": "No"}, "date_created": "2018-07-20T20:42:59.272850+00:00", "submitted_by": {"error": "no view permissions"}, "imaging_paths": [{"path": {"display_title": "Sox2 mouse protein with HaloTag targeted by PAJF549-labeled Halo Tag", "status": "released", "@type": ["ImagingPath", "Item"], "labeled_probe": "Halo Tag", "@id": "/imaging-paths/595acd55-9075-4a1d-a0d5-842d6c3199e6/", "uuid": "595acd55-9075-4a1d-a0d5-842d6c3199e6", "target": [{"@type": ["BioFeature", "Item"], "display_title": "Sox2 mouse protein with HaloTag", "organism_name": "mouse", "uuid": "d6e98cf9-4630-4d35-8706-628f286cf891", "status": "released", "@id": "/bio-features/d6e98cf9-4630-4d35-8706-628f286cf891/", "feature_mods": [{"mod_type": "HaloTag"}], "relevant_genes": [{"preferred_symbol": "Sox2", "@type": ["Gene", "Item"], "status": "released", "@id": "/genes/20674/", "geneid": "20674", "display_title": "Sox2", "uuid": "db4fa807-b3aa-4cf5-84da-3c0bb4d4c857", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "feature_type": {"term_url": "http://purl.obolibrary.org/obo/SO_0000104", "display_title": "protein", "@id": "/ontology-terms/SO:0000104/", "status": "released", "term_name": "polypeptide", "@type": ["OntologyTerm", "Item"], "term_id": "SO:0000104", "uuid": "91f427e6-5246-4992-8123-b4f8fa9eef01", "preferred_name": "protein", "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"}], "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2020-10-26T15:03:04.023305+00:00"}, "public_release": "2018-07-27", "schema_version": "3", "experiment_type": {"display_title": "SPT", "title": "SPT", "@type": ["ExperimentType", "Item"], "uuid": "d654c884-fc4f-4d53-818c-fc06fc33dfb3", "experiment_category": "Microscopy", "status": "released", "assay_subclass_short": "SPT", "@id": "/experiment-types/spt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "project_release": "2018-07-27", "microscopy_technique": "Highly Inclined Laminated Optical Sheet", "microscope_settings_master": {"@id": "/microscope-settings-a2/f67c89db-f701-44e5-8081-abdc7a489aab/", "uuid": "f67c89db-f701-44e5-8081-abdc7a489aab", "display_title": "MicroscopeSettingA2 from 2018-07-20", "status": "released", "@type": ["MicroscopeSettingA2", "MicroscopeSetting", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@id": "/experiments-mic/4DNEX7ZRL16Q/", "@type": ["ExperimentMic", "Experiment", "Item"], "uuid": "9318069c-663b-4263-b7ed-2cf9d759b96b", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "SPT on JM8.N4 (Tier 2) - 4DNEX7ZRL16Q", "external_references": [], "experiment_sets": [{"experimentset_type": "replicate", "status": "released", "@id": "/experiment-set-replicates/4DNES59H5198/", "accession": "4DNES59H5198", "uuid": "ae543a12-d1f9-4691-add7-e458fbfee682", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "display_title": "4DNES59H5198", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"authors": ["Hansen AS", "Woringer M", "Grimm JB", "Lavis LD", "Tjian R", "Darzacq X"], "short_attribution": "Hansen AS et al. (2018)", "status": "current", "uuid": "83e74398-ac79-4372-91d3-250e7390d636", "@type": ["Publication", "Item"], "ID": "doi:10.7554/eLife.33125", "display_title": "Hansen AS et al. (2018) doi:10.7554/eLife.33125", "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.", "journal": "eLife", "@id": "/publications/83e74398-ac79-4372-91d3-250e7390d636/", "date_published": "2018-01-04", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"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.", "@type": ["Publication", "Item"], "ID": "doi:10.7554/eLife.33125", "authors": ["Hansen AS", "Woringer M", "Grimm JB", "Lavis LD", "Tjian R", "Darzacq X"], "@id": "/publications/83e74398-ac79-4372-91d3-250e7390d636/", "short_attribution": "Hansen AS et al. (2018)", "display_title": "Hansen AS et al. (2018) doi:10.7554/eLife.33125", "title": "Robust model-based analysis of single-particle tracking experiments with Spot-On.", "status": "current", "uuid": "83e74398-ac79-4372-91d3-250e7390d636", "date_published": "2018-01-04", "journal": "eLife", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Target", "value": "Sox2 mouse protein with HaloTag", "combined": "Target: Sox2 mouse protein with HaloTag"}, "experiment_summary": "SPT on JM8.N4 (Tier 2)", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSV1CJKBL/", "embedded_path": "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": []}