{"lab": {"title": "Steve Henikoff, FREDHUTCH", "uuid": "3a41e042-a9f3-4205-a28a-4c20ba2edda2", "correspondence": [{"contact_email": "c3RldmVoQGZoY3JjLm9yZw==", "@id": "/users/bed386a9-7ee0-4ac0-ab50-741018edf928/", "display_title": "Steve Henikoff"}], "@type": ["Lab", "Item"], "display_title": "Steve Henikoff, FREDHUTCH", "status": "current", "@id": "/labs/steve-henikoff-lab/", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3a41e042-a9f3-4205-a28a-4c20ba2edda2"]}}, "award": {"@id": "/awards/TCPA-2017-04/", "uuid": "4ddcac2d-72b6-40a7-ac68-67efba21a0d0", "status": "current", "project": "4DN", "description": "TCPA: The 4D Nucleome project focuses on describing the 3D organization within the nucleus, with \nthe ultimate goal of understanding this organization in mechanistic terms. Our project uses novel methods for epigenomic profiling that detect 3D contact sites without cross-linking and with much higher resolution than current technologies. We recently introduced a novel strategy for chromatin profiling called CUT&RUN (Cleavage Under Targets & Release Using Nuclease), in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the supernatant for paired-end DNA sequencing. The method yields precise transcription factor (TF) profiles, yet is simple to perform and is inherently robust, with extremely low backgrounds requiring ~1/10 th the sequencing depth of chromatin immunoprecipitation (ChIP). CUT&RUN binding and cleavage occurs in situ, allowing for both quantitative high-resolution chromatin mapping and probing of the 3D chromatin environment. Together with our new native ChIP-seq protocol, we distinguish direct \u201canchor\u201d sites of a \nchromatin-bound protein from contacting sites without fixation, a kind of inference has not been possible with current methods of interrogating 3D chromatin architecture. We have two Aims: First, we will annotate the genome at high density for CTCF and cohesin sites, distinguishing between anchor and contact sites in 4D Nucleome cell lines. Second, we will continue development of a new replacement technology for 3D contact mapping, using CUT&RUN as a \u201cfront-end\u201d for proximity ligation (CUT&PASTE \u2013 Cleave Under Targets & Polish And Splice Touching Ends), building on our novel sci-HiC protocol for high-resolution TF-specific 3D interaction mapping. By annotating more contact sites in genomes and assigning the directionality of contacts, we move towards a mechanistic model of how topology within the nucleus is organized. Participation in the 4DN program would provide the opportunity to compare and integrate our CUT&RUN/PASTE datasets with 4DN datasets on common cell lines and differentiating tissues, ideally positioning consortium investigators to adopt our alternative strategy for their own 4DN efforts.", "center_title": "TCPA - Henikoff", "display_title": "TETHERED NUCLEASE STRATEGIES FOR IN SITU MAPPING OF 3D NUCLEAR ORGANIZATION", "@type": ["Award", "Item"], "name": "TCPA-2017-04", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "replaced", "aliases": ["henikoff_lab:cutnrun_K562_K4m2_3min_repset"], "accession": "4DNESWC8XDNG", "condition": "3 min digest", "description": "Replicates of CUT&RUN on K562 cells using H3K4me2 (Upstate 07-030) with a digestion time of 3min", "date_created": "2018-02-23T08:44:16.273514+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "H3K4me2 - K562", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-06-28T15:17:56.296149+00:00"}, "public_release": "2019-06-27", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"uuid": "01d4b4d5-5311-41d8-bba6-8fba492a61f0", "@type": ["ExperimentSeq", "Experiment", "Item"], "status": "released", "@id": "/experiments-seq/4DNEXZUFAK2G/", "display_title": "CUT&RUN against H3K4me2 on K562 (Tier 2) - 4DNEXZUFAK2G", "accession": "4DNEXZUFAK2G", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 1, "replicate_exp": {"uuid": "5ad96506-c56a-4c40-83e5-0a7922baf569", "@type": ["ExperimentSeq", "Experiment", "Item"], "status": "released", "@id": "/experiments-seq/4DNEXERG7TH2/", "display_title": "CUT&RUN against H3K4me2 on K562 (Tier 2) - 4DNEXERG7TH2", "accession": "4DNEXERG7TH2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 3, "tec_rep_no": 1, "replicate_exp": {"uuid": "94251812-f524-4344-8754-db24a041ca2d", "@type": ["ExperimentSeq", "Experiment", "Item"], "status": "released", "@id": "/experiments-seq/4DNEX1YDKYUO/", "display_title": "CUT&RUN against H3K4me2 on K562 (Tier 2) - 4DNEX1YDKYUO", "accession": "4DNEX1YDKYUO", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 4, "tec_rep_no": 1, "replicate_exp": {"uuid": "98f6680b-ca56-43b9-8c71-d5f9ca5a5126", "@type": ["ExperimentSeq", "Experiment", "Item"], "status": "released", "@id": "/experiments-seq/4DNEXWWYU2FY/", "display_title": "CUT&RUN against H3K4me2 on K562 (Tier 2) - 4DNEXWWYU2FY", "accession": "4DNEXWWYU2FY", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_content": [{"content": {"content": "This experiment set was replaced by [4DNES5KUU6OY](https://data.4dnucleome.org/experiment-set-replicates/4DNES5KUU6OY/) because existing sets from the same line and using the same antibody that differed only in reaction time (a variable determined to not qualitatively affect the results) were merged into a single replicate set. In addition, new biological replicates were added.", "options": {"filetype": "md", "title_icon": "info", "collapsible": false, "default_open": true}, "lab": {"display_title": "Steve Henikoff, FREDHUTCH", "@id": "/labs/steve-henikoff-lab/", "uuid": "3a41e042-a9f3-4205-a28a-4c20ba2edda2", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3a41e042-a9f3-4205-a28a-4c20ba2edda2"]}}, "@type": ["StaticSection", "UserContent", "Item"], "title": "Note: Replaced Item - 4DNESWC8XDNG", "uuid": "6b7e0158-7766-4b4f-9d32-cfdd30edb5e2", "name": "static-header.replaced_item_4DNESWC8XDNG", "status": "released", "display_title": "Note: Replaced Item - 4DNESWC8XDNG", "filetype": "md", "award": {"uuid": "4ddcac2d-72b6-40a7-ac68-67efba21a0d0", "status": "current", "@id": "/awards/TCPA-2017-04/", "display_title": "TETHERED NUCLEASE STRATEGIES FOR IN SITU MAPPING OF 3D NUCLEAR ORGANIZATION", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@id": "/static-sections/6b7e0158-7766-4b4f-9d32-cfdd30edb5e2/", "content_as_html": "<div class=\"markdown-container\"><p>This experiment set was replaced by <a href=\"https://data.4dnucleome.org/experiment-set-replicates/4DNES5KUU6OY/\" rel=\"noopener noreferrer\" target=\"_blank\">4DNES5KUU6OY</a> because existing sets from the same line and using the same antibody that differed only in reaction time (a variable determined to not qualitatively affect the results) were merged into a single replicate set. In addition, new biological replicates were added.</p></div>", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267227777"]}}, "location": "header"}], "static_headers": [{"lab": {"display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "\n**Data Use Guidelines:** This is a data set generated by the \n4DN Network and made freely available to the scientific \ncommunity. If you are intending to use these data for a \npublication, we ask that you please contact the data \ngenerating lab to discuss possible coordinated publication. \nIn your manuscript, please cite the 4DN White Paper \n([doi:10.1038/nature23884](https://doi.org/10.1038/nature23884)) \nand the 4DN Data Portal paper \n([doi:10.1038/s41467-022-29697-4](https://doi.org/10.1038/s41467-022-29697-4)), \nand please acknowledge the 4DN lab which generated the data. Please direct any questions to the [Data Coordination and Integration Center](mailto:support@4dnucleome.org).", "name": "item-page-headers.ExperimentSet.data-usage-guidelines", "award": {"uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "@id": "/awards/1U01CA200059-01/", "status": "current", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Data Usage Guidelines", "status": "released", "aliases": [], "options": {"filetype": "md", "title_icon": "exclamation-circle", "collapsible": false, "default_open": true}, "date_created": "2018-08-06T03:09:55.543206+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-05-09T09:31:34.537494+00:00"}, "schema_version": "2", "@id": "/static-sections/621e8359-3885-40ce-965d-91894aa7b758/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "621e8359-3885-40ce-965d-91894aa7b758", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267228139"]}, "display_title": "Data Usage Guidelines", "external_references": [], "content": "\n**Data Use Guidelines:** This is a data set generated by the \n4DN Network and made freely available to the scientific \ncommunity. If you are intending to use these data for a \npublication, we ask that you please contact the data \ngenerating lab to discuss possible coordinated publication. \nIn your manuscript, please cite the 4DN White Paper \n([doi:10.1038/nature23884](https://doi.org/10.1038/nature23884)) \nand the 4DN Data Portal paper \n([doi:10.1038/s41467-022-29697-4](https://doi.org/10.1038/s41467-022-29697-4)), \nand please acknowledge the 4DN lab which generated the data. Please direct any questions to the [Data Coordination and Integration Center](mailto:support@4dnucleome.org).", "filetype": "md", "content_as_html": "<div class=\"markdown-container\"><p><strong>Data Use Guidelines:</strong> This is a data set generated by the \n4DN Network and made freely available to the scientific \ncommunity. If you are intending to use these data for a \npublication, we ask that you please contact the data \ngenerating lab to discuss possible coordinated publication. \nIn your manuscript, please cite the 4DN White Paper \n(<a href=\"https://doi.org/10.1038/nature23884\" rel=\"noopener noreferrer\" target=\"_blank\">doi:10.1038/nature23884</a>) \nand the 4DN Data Portal paper \n(<a href=\"https://doi.org/10.1038/s41467-022-29697-4\" rel=\"noopener noreferrer\" target=\"_blank\">doi:10.1038/s41467-022-29697-4</a>), \nand please acknowledge the 4DN lab which generated the data. Please direct any questions to the <a href=\"mailto:support@4dnucleome.org\">Data Coordination and Integration Center</a>.</p></div>"}], "project_release": "2018-03-02", "experiments_in_set": [{"status": "released", "accession": "4DNEXZUFAK2G", "files": [{"href": "/files-fastq/4DNFIBF7PDVS/@@download/4DNFIBF7PDVS.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_classification": "raw file", "display_title": "4DNFIBF7PDVS.fastq.gz", "extra_files": [], "paired_end": "1", "upload_key": "e0e0e7c1-2530-48c8-ae92-aad20924b82e/4DNFIBF7PDVS.fastq.gz", "accession": "4DNFIBF7PDVS", "md5sum": "896a04105bce38f5d116554aabd4c63b", "file_size": 111080177, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/e0e0e7c1-2530-48c8-ae92-aad20924b82e/4DNFIBF7PDVS.fastq.gz", "file_type": "reads", "file_type_detailed": "reads (fastq)", "uuid": "e0e0e7c1-2530-48c8-ae92-aad20924b82e", "@id": "/files-fastq/4DNFIBF7PDVS/", "related_files": 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