{"lab": {"status": "current", "title": "Robert Coleman, EINSTEIN", "uuid": "3b4ae9a9-e440-4918-8923-38bec007a650", "correspondence": [{"contact_email": "cm9iZXJ0LmNvbGVtYW4yQGVpbnN0ZWluLnl1LmVkdQ==", "@id": "/users/ac1542b9-f3de-491f-9f2d-f9f0be5c0f56/", "display_title": "Robert Coleman"}], "@type": ["Lab", "Item"], "@id": "/labs/robert-coleman-lab/", "display_title": "Robert Coleman, EINSTEIN", "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", "uuid": "e7adc531-c594-4f3e-a432-252dd5b5748d", "project": "4DN", "@type": ["Award", "Item"], "@id": "/awards/1U01EB021236-01/", "name": "1U01EB021236-01", "status": "current", "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.", "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"]}}, "md5sum": "520a8786953b6e6614a00ad4a9a3940b", "status": "released", "aliases": ["robert-coleman-lab:Halo_BAF180BDdel_SAHA_B8_T2_proc_file_1"], "filename": "Halo_BAF180BDdel_SAHA_B8_T2_proc_file_1.txt", "accession": "4DNFIKPRZB7C", "file_size": 2035178, "file_type": "spt results", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "spt", "uuid": "d13d06cf-218e-4f61-55f0-94f446118b2c", "status": "released", "@id": "/file-formats/spt/", "file_format": "spt", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "date_created": "2019-06-06T16:19:23.179303+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-07-22T18:43:02.579243+00:00"}, "content_md5sum": "520a8786953b6e6614a00ad4a9a3940b", "public_release": "2019-11-26", "schema_version": "3", "genome_assembly": "GRCh38", "project_release": "2019-11-26", "file_classification": "processed file", "@id": "/files-processed/4DNFIKPRZB7C/", "@type": ["FileProcessed", "File", "Item"], "uuid": "ce41eb3f-bf0b-4232-b3c4-e621e4754e5e", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFIKPRZB7C.spt", "external_references": [], "experiments": [{"uuid": "d6078963-bbbf-4473-80ac-497a85e24aa5", "@type": ["ExperimentMic", "Experiment", "Item"], "@id": "/experiments-mic/4DNEXW4C9BFZ/", "status": "released", "display_title": "SPT on U2OS - 4DNEXW4C9BFZ", "accession": "4DNEXW4C9BFZ", "biosample": {"display_title": "4DNBSEAVT21I", "status": "released", "@id": "/biosamples/4DNBSEAVT21I/", "biosource_summary": "U2OS", "@type": ["Biosample", "Item"], "uuid": "3efc3932-c45f-42f4-9671-d4b0b3f67e35", "accession": "4DNBSEAVT21I", "treatments_summary": "pFRT-Halo-BAF180-Bddel plasmid DNA treatment (2 \u03bcg/mL, 48h at 37\u00b0C) and SAHA treatment (2.5 \u03bcM, 24.0h at 37.0\u00b0C)", "modifications_summary": "None", "biosource": [{"status": "released", "@id": "/biosources/4DNSRXN5YHHZ/", "@type": ["Biosource", "Item"], "cell_line_tier": "Unclassified", "display_title": "U2OS - 4DNSRXN5YHHZ", "biosource_type": "immortalized cell line", "uuid": "7256801c-9c6e-4563-a97a-a295fccf5f07", "cell_line": {"term_id": "EFO:0002869", "status": "released", "uuid": "a72dc763-e53a-4429-9137-64ba424c0d41", "@type": ["OntologyTerm", "Item"], "preferred_name": "U2OS", "display_title": "U2OS", "@id": "/ontology-terms/EFO:0002869/", "term_name": "U2OS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "status": "released", "display_title": "H. sapiens", "scientific_name": "Homo sapiens", "@id": "/organisms/9606/", "name": "human", "@type": ["Organism", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"uuid": "01b91fc0-6552-4a09-ad79-c7766cd4cfea", "preferred_name": "bone tissue", "term_name": "bone tissue", "display_title": "bone tissue", "@id": "/ontology-terms/UBERON:0002481/", "term_id": "UBERON:0002481", "status": "released", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"protected_data": false, "status": "released", "uuid": "b7d5e27d-e831-4f99-a72f-426f95422e3f", "@type": ["IndividualHuman", "Individual", "Item"], "@id": "/individuals-human/4DNINPN9UG9G/", "display_title": "4DNINPN9UG9G", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "cell_culture_details": [{"@type": ["BiosampleCellCulture", "Item"], "status": "released", "display_title": "BiosampleCellCulture from 2019-04-19", "in_vitro_differentiated": "No", "@id": "/biosample-cell-cultures/6287da71-4f0b-450c-8747-ad916d191213/", "uuid": "6287da71-4f0b-450c-8747-ad916d191213", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_type": {"title": "SPT", "status": "released", "uuid": "d654c884-fc4f-4d53-818c-fc06fc33dfb3", "@type": ["ExperimentType", "Item"], "display_title": "SPT", "@id": "/experiment-types/spt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_sets": [{"experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNESCE4GQDC/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "accession": "4DNESCE4GQDC", "display_title": "4DNESCE4GQDC", "status": "released", "uuid": "e3398e91-81e1-4d36-a58d-71a068403fda", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "last_modified": {"date_modified": "2021-12-03T08:46:30.023731+00:00"}}], "file_type_detailed": "spt results (spt)", "track_and_facet_info": {"experimental_lab": "Robert Coleman, EINSTEIN", "experiment_type": "SPT", "experiment_bucket": "processed file", "assay_info": "PBRM1 protein-6 bromo domains deleted", "dataset": "SPT on U2OS cells", "condition": "Transient Expressing Halo Tagged BAF180-BDdel with SAHA treatment", "replicate_info": "Biorep 8, Techrep 2", "biosource_name": "U2OS", "lab_name": "Robert Coleman, EINSTEIN"}, "title": "4DNFIKPRZB7C", "href": "/files-processed/4DNFIKPRZB7C/@@download/4DNFIKPRZB7C.spt", "upload_key": "ce41eb3f-bf0b-4232-b3c4-e621e4754e5e/4DNFIKPRZB7C.spt", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/ce41eb3f-bf0b-4232-b3c4-e621e4754e5e/4DNFIKPRZB7C.spt", "tsv_notes": "", "workflow_run_inputs": [{"@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "uuid": "1cce62fe-3a25-4439-8e0c-1847cfa31b10", "display_title": "md5 0.2.6 run 2019-08-13 19:09:03.396883", "status": "released", "@id": "/workflow-runs-awsem/1cce62fe-3a25-4439-8e0c-1847cfa31b10/", "output_files": [{"workflow_argument_name": "report"}], "workflow": {"@type": ["Workflow", "Item"], "title": "md5 0.2.6", "@id": "/workflows/4DNWF2HFF82B/", "uuid": "c77a117b-9a58-477e-aaa5-291a109a99f6", "display_title": "md5 0.2.6 - 4DNWF2HFF82B", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "input_files": [{"workflow_argument_name": "input_file", "value": {"accession": "4DNFIKPRZB7C", "uuid": "ce41eb3f-bf0b-4232-b3c4-e621e4754e5e", "@id": "/files-processed/4DNFIKPRZB7C/", "@type": ["FileProcessed", "File", "Item"], "status": "released", "filename": "Halo_BAF180BDdel_SAHA_B8_T2_proc_file_1.txt", "display_title": "4DNFIKPRZB7C.spt", "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f446118b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/spt/", "file_format": "spt", "display_title": "spt", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "workflow_run_outputs": [], "experiment_sets": [], "source_experiment_sets": [{"uuid": "e3398e91-81e1-4d36-a58d-71a068403fda", "display_title": "4DNESCE4GQDC", "status": "released", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "@id": "/experiment-set-replicates/4DNESCE4GQDC/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@context": "/terms/", "aggregated-items": {"last_modified": [{"parent": "/experiments-mic/4DNEXW4C9BFZ/", "embedded_path": "experiments.last_modified", "item": {"date_modified": "2021-12-03T08:46:30.023731+00:00"}}, {"parent": "/files-processed/4DNFIKPRZB7C/", "embedded_path": "last_modified", "item": {"date_modified": "2021-07-22T18:43:02.579243+00:00"}}]}, "validation-errors": []}