{"lab": {"display_title": "4DN DCIC, HMS", "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@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"]}}, "award": {"status": "current", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "@type": ["Award", "Item"], "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "@id": "/awards/1U01CA200059-01/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "CUT&RUN", "status": "released", "cfde_term": {"status": "released", "@id": "/ontology-terms/OBI:0003033/", "uuid": "2b234eee-666b-467e-a5d6-bf1a8035bb4c", "display_title": "cleavage under targets and release using nuclease assay", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "other_tags": ["1D"], "date_created": "2019-03-28T15:16:14.669046+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2023-03-01T20:12:19.612269+00:00"}, "raw_file_types": "Reads (fastq) provided by lab", "reference_pubs": [{"@type": ["Publication", "Item"], "authors": ["Skene PJ", "Henikoff S"], "uuid": "059e0fe2-eca8-441d-86c5-20e57d531b87", "status": "current", "journal": "eLife", "short_attribution": "Skene PJ and Henikoff S (2017)", "@id": "/publications/059e0fe2-eca8-441d-86c5-20e57d531b87/", "date_published": "2017-01-16", "display_title": "Skene PJ and Henikoff S (2017) doi:10.7554/eLife.21856", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "schema_version": "1", "static_content": [{"content": {"@id": "/static-sections/8e72f1e7-7173-49fd-887d-0f6adfc1f4f4/", "contributing_labs": [{"display_title": "Steve Henikoff, FREDHUTCH", "@type": ["Lab", "Item"], "uuid": "3a41e042-a9f3-4205-a28a-4c20ba2edda2", "status": "current", "@id": "/labs/steve-henikoff-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3a41e042-a9f3-4205-a28a-4c20ba2edda2"]}}], "content": "**CUT&RUN**\n\nCleavage under targets and release using nuclease (CUT&RUN) is \nan epigenomic profiling strategy in which antibody-targeted \ncontrolled cleavage by micrococcal nuclease releases specific \nprotein\u2013DNA complexes into the supernatant for paired-end DNA \nsequencing. CUT&RUN can be performed on the bench-top in a day \nfrom live cells to purified DNA, and has been adapted for full \nautomation. As only the targeted fragments enter into solution,\n and the vast majority of DNA is left behind, CUT&RUN has \nexceptionally low background levels, which reduces sequencing \ncosts. CUT&RUN provides near base-pair resolution, is free of \nsolubility and DNA accessibility artifacts, and has been used \nto profile histone modifications and transcription factors in \nsmall samples and single cells. The method can be used to \ndetect long-range 3D contacts without cross-linking and when \nused with salt fractionation CUT&RUN can profile chromatin \nfeatures based on solubility. CUT&RUN supernatants have also \nbeen used as input for chromatin immunoprecipitation with \nsequencing to map specific components of chromatin complexes \ngenome-wide.\n\n<div>\n<img style=\"width: 600px;\" src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/CUT%26RUN_summary_image_4DN.png\"/>\n  <br/><br/>\n  <em>Image source: Skene & Henikoff, ELife 2017 Figure 1A</em>\n</div>", "content_as_html": "<div class=\"markdown-container\"><p><strong>CUT&amp;RUN</strong></p>\n<p>Cleavage under targets and release using nuclease (CUT&amp;RUN) is \nan epigenomic profiling strategy in which antibody-targeted \ncontrolled cleavage by micrococcal nuclease releases specific \nprotein\u2013DNA complexes into the supernatant for paired-end DNA \nsequencing. CUT&amp;RUN can be performed on the bench-top in a day \nfrom live cells to purified DNA, and has been adapted for full \nautomation. As only the targeted fragments enter into solution,\n and the vast majority of DNA is left behind, CUT&amp;RUN has \nexceptionally low background levels, which reduces sequencing \ncosts. CUT&amp;RUN provides near base-pair resolution, is free of \nsolubility and DNA accessibility artifacts, and has been used \nto profile histone modifications and transcription factors in \nsmall samples and single cells. The method can be used to \ndetect long-range 3D contacts without cross-linking and when \nused with salt fractionation CUT&amp;RUN can profile chromatin \nfeatures based on solubility. CUT&amp;RUN supernatants have also \nbeen used as input for chromatin immunoprecipitation with \nsequencing to map specific components of chromatin complexes \ngenome-wide.</p>\n<div>\n<img src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/CUT%26RUN_summary_image_4DN.png\" style=\"width: 600px;\"/>\n<br/><br/>\n<em>Image source: Skene &amp; Henikoff, ELife 2017 Figure 1A</em>\n</div></div>", "uuid": "8e72f1e7-7173-49fd-887d-0f6adfc1f4f4", "name": "item-page-headers.ExperimentType.cutnrun", "lab": {"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "title": "Assay Description", "@type": ["StaticSection", "UserContent", "Item"], "display_title": "Assay Description", "options": {"filetype": "md", "collapsible": false, "default_open": true}, "filetype": "md", "award": {"display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "status": "current", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "@id": "/awards/1U01CA200059-01/", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.e2324f87-0625-4bbc-803b-d47677aebe08"]}}, "location": "tab:overview"}], "controlled_term": {"term_name": "CUT&RUN", "uuid": "1e765025-fdc3-458f-b3ec-fecf1e30c455", "preferred_name": "CUT&RUN", "@id": "/ontology-terms/EFO:0009973/", "@type": ["OntologyTerm", "Item"], "term_url": "http://www.ebi.ac.uk/efo/EFO_0009973", "term_id": "EFO:0009973", "display_title": "CUT&RUN", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_name": "cut-n-run", "valid_item_types": ["ExperimentSeq"], "reference_protocol": {"link": "https://www.protocols.io/view/cut-amp-run-targeted-in-situ-genome-wide-profiling-zcpf2vn", "title": "CUT&RUN v3: Targeted in situ genome-wide profiling"}, "experiment_category": "Sequencing", "assay_classification": "Linear DNA Enrichment", "assay_subclass_short": "DNA binding", "assay_subclassification": "DNA Binding", "@id": "/experiment-types/cut-n-run/", "@type": ["ExperimentType", "Item"], "uuid": "64166b28-444f-46d6-bf98-f419eb72ccac", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "CUT&RUN", "external_references": [], "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}