{"lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "award": {"display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "@type": ["Award", "Item"], "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "status": "current", "@id": "/awards/1U01CA200059-01/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "pA-DamID", "status": "released", "cfde_term": {"display_title": "DamID-seq", "@id": "/ontology-terms/OBI:0003299/", "@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "c3a6ab93-5212-43b8-aa0d-47a30b7e662c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "other_tags": ["1D"], "date_created": "2019-12-13T18:53:21.401799+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2023-03-01T20:48:40.301961+00:00"}, "raw_file_types": "Reads (fastq) provided by lab", "schema_version": "1", "static_content": [{"content": {"display_title": "Assay Description", "content": "**pA-DamID**\n\nThe proteinA-DamID (pA-DamID) method is a hybrid of the CUT&RUN [(Skene, 2017)](https://data.4dnucleome.org/publications/059e0fe2-eca8-441d-86c5-20e57d531b87/) and DamID [(Vogel, 2007)](https://data.4dnucleome.org/publications/68c22d31-7818-4871-8dad-5ac29674dbfa/) technologies.\n\nCells are permeabilized with digitonin and incubated with an antibody against a nuclear protein of interest, followed by binding with pA-Dam. Subsequent activation of the tethered Dam by its methyldonor S-adenosyl-methionine (SAM) results in in situ Gm6ATC methylation of DNA sequences that are in molecular proximity to the protein of interest. The pattern of deposited m6A can be mapped genome-wide as in conventional DamID. The labeled DNA can also be visualized using the m6A-Tracer (Kind, 2013), providing a powerful quality control and possibly new biological insights. In addition, labeled cells can be sorted to study (rare) subpopulations of interest.\n\n<div>\n<img style=\"width: 600px;\" src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/pADamID_summary_image_4DN.png\"/>\n  <br/><br/>\n  <em>Image source: van Steensel Lab</em>\n</div>", "uuid": "9e49b57b-05c0-4977-aed3-14aa6ca50503", "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "award": {"@type": ["Award", "Item"], "status": "current", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "@id": "/awards/1U01CA200059-01/", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Assay Description", "options": {"filetype": "md", "collapsible": false, "default_open": true}, "name": "item-page-section.ExperimentType.pADamID", "status": "released", "filetype": "md", "content_as_html": "<div class=\"markdown-container\"><p><strong>pA-DamID</strong></p>\n<p>The proteinA-DamID (pA-DamID) method is a hybrid of the CUT&amp;RUN <a href=\"https://data.4dnucleome.org/publications/059e0fe2-eca8-441d-86c5-20e57d531b87/\" rel=\"noopener noreferrer\" target=\"_blank\">(Skene, 2017)</a> and DamID <a href=\"https://data.4dnucleome.org/publications/68c22d31-7818-4871-8dad-5ac29674dbfa/\" rel=\"noopener noreferrer\" target=\"_blank\">(Vogel, 2007)</a> technologies.</p>\n<p>Cells are permeabilized with digitonin and incubated with an antibody against a nuclear protein of interest, followed by binding with pA-Dam. Subsequent activation of the tethered Dam by its methyldonor S-adenosyl-methionine (SAM) results in in situ Gm6ATC methylation of DNA sequences that are in molecular proximity to the protein of interest. The pattern of deposited m6A can be mapped genome-wide as in conventional DamID. The labeled DNA can also be visualized using the m6A-Tracer (Kind, 2013), providing a powerful quality control and possibly new biological insights. In addition, labeled cells can be sorted to study (rare) subpopulations of interest.</p>\n<div>\n<img src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/pADamID_summary_image_4DN.png\" style=\"width: 600px;\"/>\n<br/><br/>\n<em>Image source: van Steensel Lab</em>\n</div></div>", "@type": ["StaticSection", "UserContent", "Item"], "@id": "/static-sections/9e49b57b-05c0-4977-aed3-14aa6ca50503/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267227777"]}}, "location": "tab:overview"}], "experiment_name": "pa-damid", "valid_item_types": ["ExperimentDamid"], "experiment_category": "Sequencing", "assay_classification": "Linear DNA Enrichment", "assay_subclass_short": "Proximity-seq", "assay_subclassification": "Proximity to Cellular Component", "@id": "/experiment-types/pa-damid/", "@type": ["ExperimentType", "Item"], "uuid": "eb4f10a1-63ee-4b2d-8e48-ac38bea0fc03", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "pA-DamID", "external_references": [], "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}