{"lab": {"title": "Steve Henikoff, FREDHUTCH", "display_title": "Steve Henikoff, FREDHUTCH", "@id": "/labs/steve-henikoff-lab/", "correspondence": [{"contact_email": "c3RldmVoQGZoY3JjLm9yZw==", "@id": "/users/bed386a9-7ee0-4ac0-ab50-741018edf928/", "display_title": "Steve Henikoff"}], "status": "current", "uuid": "3a41e042-a9f3-4205-a28a-4c20ba2edda2", "@type": ["Lab", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3a41e042-a9f3-4205-a28a-4c20ba2edda2"]}}, "award": {"@type": ["Award", "Item"], "status": "current", "@id": "/awards/TCPA-2017-04/", "uuid": "4ddcac2d-72b6-40a7-ac68-67efba21a0d0", "display_title": "TETHERED NUCLEASE STRATEGIES FOR IN SITU MAPPING OF 3D NUCLEAR ORGANIZATION", "center_title": "TCPA - Henikoff", "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.", "name": "TCPA-2017-04", "project": "4DN", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["henikoff_lab:cutnrun_180326_H1_CTCF_repset"], "accession": "4DNES1RQBHPK", "condition": "Millipore 07-729", "description": "Replicates CUT&RUN experiments on H1 cells using CTCF (Millipore 07-729)", "date_created": "2019-06-20T22:08:50.119835+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "CTCF - H1-ESC", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-01-13T16:53:45.125729+00:00"}, "public_release": "2019-06-27", "replicate_exps": [{"bio_rep_no": 5, "tec_rep_no": 1, "replicate_exp": {"@type": ["ExperimentSeq", "Experiment", "Item"], "status": "released", "accession": "4DNEX65LZI8G", "@id": "/experiments-seq/4DNEX65LZI8G/", "display_title": "CUT&RUN against CTCF protein on H1-hESC (Tier 1) - 4DNEX65LZI8G", "uuid": "f19948ee-8482-4746-a691-ac2b60b00205", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 6, "tec_rep_no": 1, "replicate_exp": {"@type": ["ExperimentSeq", "Experiment", "Item"], "status": "released", "accession": "4DNEXUS23EIB", "@id": "/experiments-seq/4DNEXUS23EIB/", "display_title": "CUT&RUN against CTCF protein on H1-hESC (Tier 1) - 4DNEXUS23EIB", "uuid": "e6577d9d-bb81-45fb-8862-019a8dcac24d", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"@type": ["ExperimentSeq", "Experiment", "Item"], "status": "released", "accession": "4DNEXIHB6H1I", "@id": "/experiments-seq/4DNEXIHB6H1I/", "display_title": "CUT&RUN against CTCF protein on H1-hESC (Tier 1) - 4DNEXIHB6H1I", "uuid": "f699f8a5-7489-454f-a777-81332451c07f", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 1, "replicate_exp": {"@type": ["ExperimentSeq", "Experiment", "Item"], "status": "released", "accession": "4DNEXCZB2WY3", "@id": "/experiments-seq/4DNEXCZB2WY3/", "display_title": "CUT&RUN against CTCF protein on H1-hESC (Tier 1) - 4DNEXCZB2WY3", "uuid": "bc7bcc03-6a16-4a46-b19e-7c73faab5186", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 3, "tec_rep_no": 1, "replicate_exp": {"@type": ["ExperimentSeq", "Experiment", "Item"], "status": "released", "accession": "4DNEXJ5UFKWU", "@id": "/experiments-seq/4DNEXJ5UFKWU/", "display_title": "CUT&RUN against CTCF protein on H1-hESC (Tier 1) - 4DNEXJ5UFKWU", "uuid": "36497d75-4330-4c33-b69a-d8389ec8d831", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 4, "tec_rep_no": 1, "replicate_exp": {"@type": ["ExperimentSeq", "Experiment", "Item"], "status": "released", "accession": "4DNEXR1FX8LV", "@id": "/experiments-seq/4DNEXR1FX8LV/", "display_title": "CUT&RUN against CTCF protein on H1-hESC (Tier 1) - 4DNEXR1FX8LV", "uuid": "bcb3c3f3-dfea-4fa1-a722-a12de58b867a", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_content": [{"content": {"lab": {"@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "status": "current", "@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "content_as_html": "<div class=\"markdown-container\"><p>Due to an issue with the 4DN standardized pipeline for CUT&amp;RUN some of the recently released files generated by this pipeline contain additional formatting or may have been incorrectly truncated.  This not only interferes with Higlass visualization but may also lead to incorrect interpretation of results. We have restricted access to the files as we work to correct these errors.  Please <strong>use caution</strong> if you have already obtained any of these files and plan to utilize them in your analyses.  </p></div>", "options": {"filetype": "md", "title_icon": "info", "collapsible": false, "default_open": true}, "name": "item-page-headers.note.cut-n-run-pipeline-result-removed", "title": "NOTE: Processed files temporarily restricted", "@type": ["StaticSection", "UserContent", "Item"], "filetype": "md", "uuid": "7303263f-59c3-410b-a9f8-0f8ea16db2ea", "display_title": "NOTE: Processed files temporarily restricted", "award": {"@type": ["Award", "Item"], "status": "current", "@id": "/awards/2U01CA200059-06/", "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@id": "/static-sections/7303263f-59c3-410b-a9f8-0f8ea16db2ea/", "status": "released", "content": "Due to an issue with the 4DN standardized pipeline for CUT&RUN some of the recently released files generated by this pipeline contain additional formatting or may have been incorrectly truncated.  This not only interferes with Higlass visualization but may also lead to incorrect interpretation of results. We have restricted access to the files as we work to correct these errors.  Please **use caution** if you have already obtained any of these files and plan to utilize them in your analyses.  ", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267227777"]}}, "location": "header"}, {"content": {"lab": {"@id": "/labs/steve-henikoff-lab/", "uuid": "3a41e042-a9f3-4205-a28a-4c20ba2edda2", "status": "current", "@type": ["Lab", "Item"], "display_title": "Steve Henikoff, FREDHUTCH", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3a41e042-a9f3-4205-a28a-4c20ba2edda2"]}}, "content_as_html": "<div class=\"markdown-container\"><p>This experiment set supercedes <a href=\"https://data.4dnucleome.org/experiment-set-replicates/e9d9aaa0-debc-45ca-ab6f-15540931a828/\" rel=\"noopener noreferrer\" target=\"_blank\">4DNES6O3WZM6</a>, <a href=\"https://data.4dnucleome.org/experiment-set-replicates/707742f8-de39-4546-a282-e09c3b43c24f/\" rel=\"noopener noreferrer\" target=\"_blank\">4DNES1BCV6XD</a>, <a href=\"https://data.4dnucleome.org/experiment-set-replicates/f0bde961-f102-4b87-93d9-77349792c510/\" rel=\"noopener noreferrer\" target=\"_blank\">4DNESXA8TW4W</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>", "options": {"filetype": "md", "title_icon": "info", "collapsible": false, "default_open": true}, "name": "static-header.replacing_item_4DNES1RQBHPK", "title": "Note: This Item Supercedes - 4DNES6O3WZM6, 4DNES1BCV6XD, 4DNESXA8TW4W", "@type": ["StaticSection", "UserContent", "Item"], "filetype": "md", "uuid": "6143d4ca-4d73-4a99-9431-7643fc82ab5a", "display_title": "Note: This Item Supercedes - 4DNES6O3WZM6, 4DNES1BCV6XD, 4DNESXA8TW4W", "award": {"@type": ["Award", "Item"], "status": "current", "@id": "/awards/TCPA-2017-04/", "uuid": "4ddcac2d-72b6-40a7-ac68-67efba21a0d0", "display_title": "TETHERED NUCLEASE STRATEGIES FOR IN SITU MAPPING OF 3D NUCLEAR ORGANIZATION", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@id": "/static-sections/6143d4ca-4d73-4a99-9431-7643fc82ab5a/", "status": "released", "content": "This experiment set supercedes [4DNES6O3WZM6](https://data.4dnucleome.org/experiment-set-replicates/e9d9aaa0-debc-45ca-ab6f-15540931a828/), [4DNES1BCV6XD](https://data.4dnucleome.org/experiment-set-replicates/707742f8-de39-4546-a282-e09c3b43c24f/), [4DNESXA8TW4W](https://data.4dnucleome.org/experiment-set-replicates/f0bde961-f102-4b87-93d9-77349792c510/) 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.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267227777"]}}, "location": "header"}, {"content": {"error": "no view permissions"}, "location": "tab:processed-files", "description": "auto_generated_higlass_view_config"}], "static_headers": [{"lab": {"status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "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": {"@type": ["Award", "Item"], "@id": "/awards/1U01CA200059-01/", "status": "current", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "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>"}], "processed_files": [], "project_release": "2019-06-27", "experiments_in_set": [{"files": [{"md5sum": "84962527b4b26177816bf4e68d3079a4", "file_type_detailed": "reads (fastq)", "status": "released", "uuid": "695af540-6ad1-46a1-9e76-2a65ae364e06", "file_classification": "raw file", "upload_key": "695af540-6ad1-46a1-9e76-2a65ae364e06/4DNFIADJVIB1.fastq.gz", "accession": "4DNFIADJVIB1", "display_title": "4DNFIADJVIB1.fastq.gz", "href": "/files-fastq/4DNFIADJVIB1/@@download/4DNFIADJVIB1.fastq.gz", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "file_size": 110945176, "paired_end": "1", "@id": "/files-fastq/4DNFIADJVIB1/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/695af540-6ad1-46a1-9e76-2a65ae364e06/4DNFIADJVIB1.fastq.gz", "quality_metric": {"overall_quality_status": "PASS", "@id": 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Hi-C and Micro-C are widely used 3C protocols that differ in key experimental parameters including cross-linking chemistry and chromatin fragmentation strategy. To understand how the choice of experimental protocol determines the ability to detect and quantify aspects of chromosome folding we have performed a  systematic evaluation of 3C experimental parameters. We identified optimal protocol variants for either loop or compartment detection, optimizing fragment size and cross-linking chemistry. We used this knowledge to develop a greatly improved Hi-C protocol (Hi-C 3.0) that can detect both loops and compartments relatively effectively. 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Following ablation of cohesin-mediated loop extrusion during G1, high-efficiency IZs become diffuse and delocalized at boundaries with complex CTCF motif orientations. Moreover, G1 knockdown of the cohesin unloading factor WAPL results in gained long-range loops and narrowed localization of IZs at the same boundaries. Finally, targeted deletion or insertion of specific boundaries causes local replication timing shifts consistent with IZ loss or gain, respectively. 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