{"lab": {"uuid": "e30d3cc6-74fc-4c59-92e0-656cfea3c9a8", "title": "David Baddeley, YALE", "@id": "/labs/david-baddeley-lab/", "@type": ["Lab", "Item"], "display_title": "David Baddeley, YALE", "status": "current", "correspondence": [{"contact_email": "ZGF2aWQuYmFkZGVsZXlAeWFsZS5lZHU=", "@id": "/users/82332a78-7709-431b-b063-25ec65d82a90/", "display_title": "David Baddeley"}], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.e30d3cc6-74fc-4c59-92e0-656cfea3c9a8"]}}, "award": {"project": "4DN", "display_title": "AN INTEGRATED IMAGING SYSTEM FOR HIGH-THROUGHPUT NANOSCOPY OF THE 4D NUCLEOME", "uuid": "83702425-25f4-413b-9826-7257e2732506", "center_title": "IT - Bewersdorf", "name": "1U01EB021232-01", "@type": ["Award", "Item"], "description": "IT: The complex of DNA, protein, and RNA known as chromatin is the substrate for essential cellular processes such as gene transcription, regulation, replication, and repair. Unravelling its structure and dynamics is therefore essential f we are to understand the mechanics of these processes and their effects in development and disease. Chromatin is, however, a difficult target to study: it is found in a crowded environment within the nucleus, is structurally organized on multiple length scales, is variable within and between nuclei, and is highly dynamic. Capturing this information requires instrumentation which can (i) measure on multiple length scales, from the whole cell down to tens of nm, (ii) follow chromatin dynamics in living cells, and (iii) acquire and quantify thousands of images in a manageable time frame to overcome the intrinsic variability and provide a statistical description of chromatin behavior. Such an instrument does not yet exist, with existing instrumentation being limited in resolution, dynamic speed, and throughput. We propose an innovative multi-disciplinary approach that combines developments in optics, data processing and modeling to realize an integrated system for automated high-throughput super- resolution imaging and dense single-molecule tracking in the cell nucleus. Our Specific Aims are: 1) Develop an automated multicolor 3D single-molecule switching (SMS) nanoscope for dynamic imaging and particle-tracking in the nucleus, 2) Develop data processing tools for high-throughput 3D- SMS nanoscopy of 100-1,000 cells/h, 3) Develop chromatin modeling tools that take advantage of the unprecedented level of detail and statistical depth of the 4D data provided by high-throughput particle- tracking and SMS nanoscopy, and 4) test the performance and refine our technical developments by applying them to a diverse set of representative and important questions in the field of chromatin architecture, including the mobility and dynamics of transcription factors and nucleosomes, and the processes of synaptonemal assembly and telomere recombination. The proposal represents a fundamental departure from the traditional view of the nanoscopy image generation procedure as a hands-on process heavily involving an expert user to an automated, high- throughput method with focus on quantification and efficiency. By making nanoscopy studies of tens of thousands of cells feasible, we anticipate that our instrument will enable, for the first time, the spatiotemporal dynamics of the nucleome to be quantitatively investigated down to the single nucleosome level.", "@id": "/awards/1U01EB021232-01/", "status": "current", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "badges": [{"badge": {"display_title": "Replicate Numbers", "@type": ["Badge", "Item"], "description": "Issues with replicate numbers", "@id": "/badges/replicate-numbers/", "badge_classification": "Warning", "title": "Replicate Numbers", "warning": "Replicate Numbers", "badge_icon": "/static/img/badges/replicates-orange-circle.svg", "status": "released", "uuid": "24a64a84-3c33-4d76-aaf2-e5ef45eff347", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "messages": ["Replicate set contains only a single biological replicate"]}], "status": "released", "aliases": ["joerg-bewersdorf-lab:HTSMS-u2os-DNAmito"], "accession": "4DNESMWANQOC", "condition": "DNA/mitochondria in U2OS", "description": "Validation experiment of fast 3D, two-color single-molecule switching nanoscopy on relatively thin targets. This sample targets one structure (mitochondrial nucleoids) which is expected to be inside of the organelle targeted by the other probe (mitochondrial outer membrane).", "date_created": "2019-08-05T15:32:55.387866+00:00", "sample_image": {"display_title": "Thumbnail for 4DNFIU7ODDMZ", "@type": ["Image", "Item"], "uuid": "d689c3b1-04b6-4aa6-baec-40cd5bdec52b", "caption": "Sample rendered image of mitochondrial nucleoids - TOMM20 (red) and DNA (green)", "@id": "/images/d689c3b1-04b6-4aa6-baec-40cd5bdec52b/", "status": "released", "attachment": {"href": "@@download/attachment/4DNFIU7ODDMZ.jpeg", "md5sum": "d2bcfdfa6509fbbfe26988473e830563", "height": 1809, "type": "image/jpeg", "download": "4DNFIU7ODDMZ.jpeg", "width": 1779}, "microscopy_file": {"accession": "4DNFIU7ODDMZ", "display_title": "4DNFIU7ODDMZ.ome.tiff", "@id": "/files-microscopy/4DNFIU7ODDMZ/", "@type": ["FileMicroscopy", "File", "Item"], "omerolink": "https://omero.hms.harvard.edu/pathviewer/viewer/untiled/975141", "status": "released", "uuid": "33bb6ddc-cc57-4fec-af1b-5e4eb9f5148c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "submitted_by": {"error": "no view permissions"}, "dataset_label": "SMSN (Barentine et al 2019 bioRxiv)", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-11-15T18:24:02.892887+00:00"}, "public_release": "2019-11-15", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"display_title": "Immunofluorescence on U2OS (Tier 2) - 4DNEXHV5ZRHE", "@id": "/experiments-mic/4DNEXHV5ZRHE/", "accession": "4DNEXHV5ZRHE", "@type": ["ExperimentMic", "Experiment", "Item"], "status": "released", "uuid": "2870df23-4c40-4c93-9500-c01c6d39d658", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_headers": [{"lab": {"status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "Localization files for the HT-SMSN dataset are in an hdf5 \nformat, generated by PYME (Python Microscopy Environment). \nEven without PYME or other specialized software packages, \nthese can be opened in python using the h5py library. \n\nDescription of file format and included data can be found [here](\n/documents/933f2977-05f4-43c7-9eeb-7994290ff56a/@@download/attachment/ht-smsn-h5.pdf).\n\nSome sample commands for looking at h5 file contents can be \nfound [here](/publications/7d9fad19-54c4-419e-8d99-8157f5c1904b/#processed_data).", "name": "ht-smsn.h5-header", "award": {"uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "status": "current", "@type": ["Award", "Item"], "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "@id": "/awards/1U01CA200059-01/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Note on Localization h5 Processed Files", "status": "released", "aliases": ["4dn-dcic-lab:h5-note"], "options": {"filetype": "md", "collapsible": true, "default_open": false}, "date_created": "2019-11-14T21:00:30.923825+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-11-15T18:24:04.832990+00:00"}, "schema_version": "2", "@id": "/static-sections/037ffbe7-bc11-47aa-99eb-b9759ced1fa3/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "037ffbe7-bc11-47aa-99eb-b9759ced1fa3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.e2324f87-0625-4bbc-803b-d47677aebe08"]}, "display_title": "Note on Localization h5 Processed Files", "external_references": [], "content": "Localization files for the HT-SMSN dataset are in an hdf5 \nformat, generated by PYME (Python Microscopy Environment). \nEven without PYME or other specialized software packages, \nthese can be opened in python using the h5py library. \n\nDescription of file format and included data can be found [here](\n/documents/933f2977-05f4-43c7-9eeb-7994290ff56a/@@download/attachment/ht-smsn-h5.pdf).\n\nSome sample commands for looking at h5 file contents can be \nfound [here](/publications/7d9fad19-54c4-419e-8d99-8157f5c1904b/#processed_data).", "filetype": "md", "content_as_html": "<div class=\"markdown-container\"><p>Localization files for the HT-SMSN dataset are in an hdf5 \nformat, generated by PYME (Python Microscopy Environment). \nEven without PYME or other specialized software packages, \nthese can be opened in python using the h5py library. </p>\n<p>Description of file format and included data can be found <a href=\"/documents/933f2977-05f4-43c7-9eeb-7994290ff56a/@@download/attachment/ht-smsn-h5.pdf\">here</a>.</p>\n<p>Some sample commands for looking at h5 file contents can be \nfound <a href=\"/publications/7d9fad19-54c4-419e-8d99-8157f5c1904b/#processed_data\">here</a>.</p></div>"}], "project_release": "2019-11-15", "contributing_labs": [{"uuid": "37c44536-e572-49ab-85bb-d8a86875e0b7", "@type": ["Lab", "Item"], "status": "current", "correspondence": [{"contact_email": "am9lcmcuYmV3ZXJzZG9yZkB5YWxlLmVkdQ==", "@id": "/users/9e620077-dc63-46bd-9dce-44bd016df029/", "display_title": "Joerg Bewersdorf"}], "@id": "/labs/joerg-bewersdorf-lab/", "display_title": "Joerg Bewersdorf, YALE", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.37c44536-e572-49ab-85bb-d8a86875e0b7"]}}], "experiments_in_set": [{"@id": "/experiments-mic/4DNEXHV5ZRHE/", "status": "released", "@type": ["ExperimentMic", "Experiment", "Item"], "accession": "4DNEXHV5ZRHE", "display_title": "Immunofluorescence on U2OS (Tier 2) - 4DNEXHV5ZRHE", "files": [{"@type": ["FileMicroscopy", "File", "Item"], "file_type_detailed": "time-series (hdf5)", "href": "/files-microscopy/4DNFIXJ7ZWPY/@@download/4DNFIXJ7ZWPY.hdf5", "file_size": 907781648, "file_type": "time-series", "file_classification": "raw file", "display_title": "4DNFIXJ7ZWPY.hdf5", "status": "released", "uuid": "d85e7323-72c7-48dd-97fc-0d9c5e4ff051", "upload_key": "d85e7323-72c7-48dd-97fc-0d9c5e4ff051/4DNFIXJ7ZWPY.hdf5", "accession": "4DNFIXJ7ZWPY", "md5sum": "63a354a509916a2d700975aa2c2b69a9", "@id": "/files-microscopy/4DNFIXJ7ZWPY/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/d85e7323-72c7-48dd-97fc-0d9c5e4ff051/4DNFIXJ7ZWPY.hdf5", "lab": {"@type": ["Lab", "Item"], "status": "current", "display_title": "David Baddeley, YALE", "@id": "/labs/david-baddeley-lab/", "name": "david-baddeley-lab", "uuid": "e30d3cc6-74fc-4c59-92e0-656cfea3c9a8", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.e30d3cc6-74fc-4c59-92e0-656cfea3c9a8"]}}, "related_files": [{"relationship_type": "parent of", "file": {"file_type": "z-stack", "@type": ["FileMicroscopy", "File", "Item"], "file_type_detailed": "z-stack (ome.tiff)", "status": "released", "accession": "4DNFIU7ODDMZ", "display_title": "4DNFIU7ODDMZ.ome.tiff", "uuid": "33bb6ddc-cc57-4fec-af1b-5e4eb9f5148c", "@id": "/files-microscopy/4DNFIU7ODDMZ/", "file_format": {"uuid": "d13d06cf-218e-4f61-22f0-91f226248b2c", "display_title": "ome.tiff", "@type": ["FileFormat", "Item"], "file_format": "ome.tiff", "status": "released", "@id": "/file-formats/ome.tiff/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "contributing_labs": [{"status": "current", "name": "joerg-bewersdorf-lab", "@id": "/labs/joerg-bewersdorf-lab/", "display_title": "Joerg Bewersdorf, YALE", "@type": ["Lab", "Item"], "uuid": "37c44536-e572-49ab-85bb-d8a86875e0b7", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.37c44536-e572-49ab-85bb-d8a86875e0b7"]}}], "file_format": {"file_format": "hdf5", "@id": "/file-formats/hdf5/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "hdf5", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Baddeley, YALE", "experiment_type": "Immunofluorescence", "experiment_bucket": "raw file", "assay_info": "TOMM20 protein, Chromosomes", "dataset": "SMSN (Barentine et al 2019 bioRxiv)", "condition": "DNA/mitochondria in U2OS", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "U2OS (Tier 2)", "lab_name": "David Baddeley, YALE"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["FileMicroscopy", "File", "Item"], "file_type_detailed": "z-stack (ome.tiff)", "href": "/files-microscopy/4DNFIU7ODDMZ/@@download/4DNFIU7ODDMZ.ome.tiff", "file_size": 2291418267, "file_type": "z-stack", "file_classification": "visualization", "display_title": "4DNFIU7ODDMZ.ome.tiff", "status": "released", "uuid": "33bb6ddc-cc57-4fec-af1b-5e4eb9f5148c", "upload_key": "33bb6ddc-cc57-4fec-af1b-5e4eb9f5148c/4DNFIU7ODDMZ.ome.tiff", "accession": "4DNFIU7ODDMZ", "md5sum": "6bc7134a8e397850cc78b5f83cbb8e73", "@id": "/files-microscopy/4DNFIU7ODDMZ/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/33bb6ddc-cc57-4fec-af1b-5e4eb9f5148c/4DNFIU7ODDMZ.ome.tiff", "lab": {"@type": ["Lab", "Item"], "status": "current", "display_title": "David Baddeley, YALE", "@id": "/labs/david-baddeley-lab/", "name": "david-baddeley-lab", "uuid": "e30d3cc6-74fc-4c59-92e0-656cfea3c9a8", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.e30d3cc6-74fc-4c59-92e0-656cfea3c9a8"]}}, "related_files": [{"relationship_type": "derived from", "file": {"file_type": "time-series", "@type": ["FileMicroscopy", "File", "Item"], "file_type_detailed": "time-series (hdf5)", "status": "released", "accession": "4DNFIXJ7ZWPY", "display_title": "4DNFIXJ7ZWPY.hdf5", "uuid": "d85e7323-72c7-48dd-97fc-0d9c5e4ff051", "@id": "/files-microscopy/4DNFIXJ7ZWPY/", "file_format": {"uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce1", "display_title": "hdf5", "@type": ["FileFormat", "Item"], "file_format": "hdf5", "status": "released", "@id": "/file-formats/hdf5/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "contributing_labs": [{"status": "current", "name": "joerg-bewersdorf-lab", "@id": "/labs/joerg-bewersdorf-lab/", "display_title": "Joerg Bewersdorf, YALE", "@type": ["Lab", "Item"], "uuid": "37c44536-e572-49ab-85bb-d8a86875e0b7", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.37c44536-e572-49ab-85bb-d8a86875e0b7"]}}], "file_format": {"file_format": "ome.tiff", "@id": "/file-formats/ome.tiff/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "ome.tiff", "uuid": "d13d06cf-218e-4f61-22f0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Baddeley, YALE", "experiment_type": "Immunofluorescence", "experiment_bucket": "raw file", "assay_info": "TOMM20 protein, Chromosomes", "dataset": "SMSN (Barentine et al 2019 bioRxiv)", "condition": "DNA/mitochondria in U2OS", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "U2OS (Tier 2)", "lab_name": "David Baddeley, YALE"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "uuid": "2870df23-4c40-4c93-9500-c01c6d39d658", "processed_files": [{"file_type": "localizations", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/f8b20bfd-967e-4bd1-a45a-5b276ac2cae3/4DNFIMCSA8UD.hdf5", "file_size": 6764821, "uuid": "f8b20bfd-967e-4bd1-a45a-5b276ac2cae3", "upload_key": "f8b20bfd-967e-4bd1-a45a-5b276ac2cae3/4DNFIMCSA8UD.hdf5", "file_classification": "processed file", "file_format": {"@id": "/file-formats/hdf5/", "display_title": "hdf5", "status": "released", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce1", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "display_title": "4DNFIMCSA8UD.hdf5", "file_type_detailed": "localizations (hdf5)", "md5sum": "624b3ca5e9d75cd51dc049a900ee0963", "href": "/files-processed/4DNFIMCSA8UD/@@download/4DNFIMCSA8UD.hdf5", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "genome_assembly": "GRCh38", "@id": "/files-processed/4DNFIMCSA8UD/", "status": "released", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIMCSA8UD", "contributing_labs": [{"name": "joerg-bewersdorf-lab", "uuid": "37c44536-e572-49ab-85bb-d8a86875e0b7", "@type": ["Lab", "Item"], "display_title": "Joerg Bewersdorf, YALE", "@id": "/labs/joerg-bewersdorf-lab/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.37c44536-e572-49ab-85bb-d8a86875e0b7"]}}], "last_modified": {"date_modified": "2021-12-16T08:30:06.096180+00:00"}, "lab": {"@id": "/labs/david-baddeley-lab/", "name": "david-baddeley-lab", "display_title": "David Baddeley, YALE", "uuid": "e30d3cc6-74fc-4c59-92e0-656cfea3c9a8", "@type": ["Lab", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.e30d3cc6-74fc-4c59-92e0-656cfea3c9a8"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "David Baddeley, YALE", "experiment_type": "Immunofluorescence", "experiment_bucket": "processed file", "assay_info": "TOMM20 protein, Chromosomes", "dataset": "SMSN (Barentine et al 2019 bioRxiv)", "condition": "DNA/mitochondria in U2OS", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "U2OS (Tier 2)", "lab_name": "David Baddeley, YALE"}, "external_references": []}], "biosample": {"biosample_category": ["Tier 2"], "biosource_summary": "U2OS (Tier 2)", "biosample_type": "immortalized cells", "@id": "/biosamples/4DNBSA3NSYOL/", "status": "released", "display_title": "4DNBSA3NSYOL", "uuid": "12d768f6-5c2e-43ed-8c08-f8e6f0880e17", "treatments_summary": "None", "@type": ["Biosample", "Item"], "accession": 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