{"lab": {"display_title": "Steve Henikoff, FREDHUTCH", "correspondence": [{"contact_email": "c3RldmVoQGZoY3JjLm9yZw==", "@id": "/users/bed386a9-7ee0-4ac0-ab50-741018edf928/", "display_title": "Steve Henikoff"}], "@type": ["Lab", "Item"], "uuid": "3a41e042-a9f3-4205-a28a-4c20ba2edda2", "@id": "/labs/steve-henikoff-lab/", "title": "Steve Henikoff, FREDHUTCH", "status": "current", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3a41e042-a9f3-4205-a28a-4c20ba2edda2"]}}, "award": {"center_title": "TCPA - Henikoff", "display_title": "TETHERED NUCLEASE STRATEGIES FOR IN SITU MAPPING OF 3D NUCLEAR ORGANIZATION", "@type": ["Award", "Item"], "name": "TCPA-2017-04", "uuid": "4ddcac2d-72b6-40a7-ac68-67efba21a0d0", "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.", "@id": "/awards/TCPA-2017-04/", "status": "current", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["henikoff_lab:cutnrun_180921_Hffc6_K4m3_repset"], "accession": "4DNES8ZSCTFJ", "condition": "Active Motif 39159", "description": "Replicates CUT&RUN experiments on Hffc6 cells using H3K4me3 (Active Motif 39159)", "date_created": "2019-06-20T22:09:28.845831+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "H3K4me3 - HFFc6", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-01-11T06:03:06.508268+00:00"}, "public_release": "2019-06-27", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"uuid": "12c8e3f5-9d3d-4854-aad5-eb336196ff11", "@type": ["ExperimentSeq", "Experiment", "Item"], "accession": "4DNEX67Q84RB", "@id": "/experiments-seq/4DNEX67Q84RB/", "display_title": "CUT&RUN against H3K4me3 on HFFc6 (Tier 1) - 4DNEX67Q84RB", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 1, "replicate_exp": {"uuid": "d32e34c5-9177-402b-8af5-ce5376a44847", "@type": ["ExperimentSeq", "Experiment", "Item"], "accession": "4DNEXRL2LUNJ", "@id": "/experiments-seq/4DNEXRL2LUNJ/", "display_title": "CUT&RUN against H3K4me3 on HFFc6 (Tier 1) - 4DNEXRL2LUNJ", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 3, "tec_rep_no": 1, "replicate_exp": {"uuid": "5eaa59c4-67ea-4b6f-9fa2-9074d3b8cd82", "@type": ["ExperimentSeq", "Experiment", "Item"], "accession": "4DNEXQ8TTJJ5", "@id": "/experiments-seq/4DNEXQ8TTJJ5/", "display_title": "CUT&RUN against H3K4me3 on HFFc6 (Tier 1) - 4DNEXQ8TTJJ5", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 4, "tec_rep_no": 1, "replicate_exp": {"uuid": "f194e87d-9047-403d-a98c-b4c49c4612e6", "@type": ["ExperimentSeq", "Experiment", "Item"], "accession": "4DNEX62TLS34", "@id": "/experiments-seq/4DNEX62TLS34/", "display_title": "CUT&RUN against H3K4me3 on HFFc6 (Tier 1) - 4DNEX62TLS34", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_content": [{"content": {"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.  ", "lab": {"@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "status": "current", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "filetype": "md", "@id": "/static-sections/7303263f-59c3-410b-a9f8-0f8ea16db2ea/", "display_title": "NOTE: Processed files temporarily restricted", "name": "item-page-headers.note.cut-n-run-pipeline-result-removed", "award": {"@type": ["Award", "Item"], "@id": "/awards/2U01CA200059-06/", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "status": "current", "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "7303263f-59c3-410b-a9f8-0f8ea16db2ea", "title": "NOTE: Processed files temporarily restricted", "options": {"filetype": "md", "title_icon": "info", "collapsible": false, "default_open": true}, "@type": ["StaticSection", "UserContent", "Item"], "status": "released", "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": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "status": "current", "display_title": "4DN DCIC, HMS", "@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": {"@id": "/awards/1U01CA200059-01/", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "status": "current", "@type": ["Award", "Item"], "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": "<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\" target=\"_blank\" rel=\"noopener noreferrer\">doi:10.1038/nature23884</a>) \nand the 4DN Data Portal paper \n(<a href=\"https://doi.org/10.1038/s41467-022-29697-4\" target=\"_blank\" rel=\"noopener noreferrer\">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>"}], "processed_files": [], "project_release": "2019-06-27", "experiments_in_set": [{"files": [{"upload_key": "ddb5ff15-81e8-46c4-966a-6ea51637d234/4DNFI14ZGQI9.fastq.gz", "file_type": "reads", "paired_end": "1", "file_type_detailed": "reads (fastq)", "uuid": "ddb5ff15-81e8-46c4-966a-6ea51637d234", "@id": "/files-fastq/4DNFI14ZGQI9/", "display_title": "4DNFI14ZGQI9.fastq.gz", "accession": "4DNFI14ZGQI9", "href": "/files-fastq/4DNFI14ZGQI9/@@download/4DNFI14ZGQI9.fastq.gz", "file_classification": "raw file", "file_size": 111908206, "md5sum": "66a60131b72078a24acc4f82f6d00518", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/ddb5ff15-81e8-46c4-966a-6ea51637d234/4DNFI14ZGQI9.fastq.gz", "@type": ["FileFastq", "File", "Item"], "dbxrefs": ["SRA:SRR13601417"], "status": "released", "lab": {"name": "steve-henikoff-lab", "@id": "/labs/steve-henikoff-lab/", "uuid": "3a41e042-a9f3-4205-a28a-4c20ba2edda2", "display_title": "Steve Henikoff, FREDHUTCH", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3a41e042-a9f3-4205-a28a-4c20ba2edda2"]}}, "quality_metric": {"display_title": "QualityMetricFastqc from 2019-06-21", "uuid": "09f3b5a4-e9e8-42f2-b4e2-d2abd8262ead", "overall_quality_status": "PASS", "status": "released", "@id": "/quality-metrics-fastqc/09f3b5a4-e9e8-42f2-b4e2-d2abd8262ead/", "Total Sequences": 4000000, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI14ZGQI9/fastqc_report.html", "Sequence length": "25", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "adde81d0-3d0d-4b05-954e-c7845c4de85f", "@id": "/files-fastq/4DNFIDW7PPUH/", "file_type_detailed": "reads (fastq)", "status": "released", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIDW7PPUH.fastq.gz", "file_type": "reads", "accession": "4DNFIDW7PPUH", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Steve Henikoff, FREDHUTCH", "experiment_type": "CUT&RUN", "experiment_bucket": "raw file", "assay_info": "H3K4me3", "dataset": "H3K4me3 - 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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. In addition to providing benchmarked protocols, this work produced ultra-deep chromatin interaction maps using Micro-C, conventional Hi-C and Hi-C 3.0 for key cell lines used by the 4D Nucleome project.", "title": "Systematic evaluation of chromosome conformation capture assays.", "status": "current", "date_published": "2021-09", "display_title": "Akgol Oksuz B et al. 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