{"lab": {"title": "Chao-Ting Wu, HARVARD", "@type": ["Lab", "Item"], "status": "current", "correspondence": [{"contact_email": "dHd1QGdlbmV0aWNzLm1lZC5oYXJ2YXJkLmVkdQ==", "@id": "/users/af7beabd-7452-4b15-bc84-3ba5f72521d5/", "display_title": "Chao-Ting Wu"}], "display_title": "Chao-Ting Wu, HARVARD", "@id": "/labs/chao-ting-wu-lab/", "uuid": "8932f234-660e-4fad-b0a3-342dcc799438", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8932f234-660e-4fad-b0a3-342dcc799438"]}}, "award": {"center_title": "External", "center": "External", "display_title": "EXTERNAL AWARD", "description": "Funding source is from outside 4DN.", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "status": "current", "name": "external-award", "@id": "/awards/external-award/", "project": "External", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["chao-ting-wu-lab:oligostorm"], "accession": "4DNESQN4JCAS", "condition": "8 Mb walks on chr19", "documents": [{"display_title": "Understanding Vutara Particles.csv File.pdf", "status": "released", "@id": "/documents/107a9f91-f97b-4581-a52e-c46e4072473e/", "@type": ["Document", "Item"], "uuid": "107a9f91-f97b-4581-a52e-c46e4072473e", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "description": "Super-resolution imaging of 8 Mb of chromosome 19 by OligoSTORM in human fibroblasts. 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GM23248 - 4DNEXAFPKJFF", "uuid": "570a3a0f-70e2-4973-a957-688d8df64401", "status": "released", "accession": "4DNEXAFPKJFF", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 3, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-mic/4DNEXPSOC1ZK/", "@type": ["ExperimentMic", "Experiment", "Item"], "display_title": "multiplexed FISH on GM23248 - 4DNEXPSOC1ZK", "uuid": "86aed8f2-a637-4aae-8bfa-a81aa1f86c33", "status": "released", "accession": "4DNEXPSOC1ZK", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 4, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-mic/4DNEXPRBBX2L/", "@type": ["ExperimentMic", "Experiment", "Item"], "display_title": "multiplexed FISH on GM23248 - 4DNEXPRBBX2L", "uuid": "2d0a342f-a111-4497-a87a-aed468c28179", "status": "released", "accession": "4DNEXPRBBX2L", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 5, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-mic/4DNEX9EF563X/", "@type": ["ExperimentMic", "Experiment", "Item"], "display_title": "multiplexed FISH on GM23248 - 4DNEX9EF563X", "uuid": "bff623c7-bf9e-4d45-af7f-f1cf9352e9e2", "status": "released", "accession": "4DNEX9EF563X", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 6, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-mic/4DNEX3K9EZJ4/", "@type": ["ExperimentMic", "Experiment", "Item"], "display_title": "multiplexed FISH on GM23248 - 4DNEX3K9EZJ4", "uuid": "eb6a253f-21cf-4141-9a8d-003f9872506d", "status": "released", "accession": "4DNEX3K9EZJ4", "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": "Particle localizations for the OligoSTORM dataset from Nir et al. 2018 are in csv format, as produced by the Vutara SRX software from Bruker.\nA detailed description of all the columns is provided in [this extract](/documents/107a9f91-f97b-4581-a52e-c46e4072473e/@@download/attachment/Understanding%20Vutara%20Particles.csv%20File.pdf) from the software manual.", "name": "oligostorm.particles-format", "award": {"@id": "/awards/2U01CA200059-06/", "@type": ["Award", "Item"], "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Note on file format for particle localization from Vutara", "status": "released", "aliases": ["4dn-dcic-lab:note_particles_csv_vutara_format"], "options": {"filetype": "md", "collapsible": true, "default_open": true}, "date_created": "2021-07-15T18:46:48.069572+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-07-15T18:47:13.573746+00:00"}, "schema_version": "2", "@id": "/static-sections/8ecacdd9-3ad5-4a0b-b4df-a2a6fb4e4f64/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "8ecacdd9-3ad5-4a0b-b4df-a2a6fb4e4f64", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.e4a22298-1da4-4e59-8a65-9e661f47fb48"]}, "display_title": "Note on file format for particle localization from Vutara", "external_references": [], "content": "Particle localizations for the OligoSTORM dataset from Nir et al. 2018 are in csv format, as produced by the Vutara SRX software from Bruker.\nA detailed description of all the columns is provided in [this 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Imaging through the depths of entire nuclei, we capture pairs of homologous regions in diploid cells, obtaining evidence that maternal and paternal homologous regions can be differentially organized. Finally, using restraint-based modeling to integrate imaging and Hi-C data, we implement a method-integrative modeling of genomic regions (IMGR)-to increase the genomic resolution of our traces to 10 kb.", "url": "https://www.ncbi.nlm.nih.gov/pubmed/30586358", "short_attribution": "Nir G et al. 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