{"lab": {"@type": ["Lab", "Item"], "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "sop": {"date_created": "2020-08-25", "protocol_type": "Experimental protocol", "status": "released", "@id": "/protocols/e8cdfd0d-d622-4ae9-96ea-4c5eefc2fe3d/", "uuid": "e8cdfd0d-d622-4ae9-96ea-4c5eefc2fe3d", "@type": ["Protocol", "Item"], "title": "4DN Standard in situ ChIA-PET Protocol", "attachment": {"href": "@@download/attachment/20200820_4DN_in_situ_chiapet_protocol.pdf", "type": "application/pdf", "md5sum": "8077b53c402e744fa1137a9267fda1e2", "blob_id": "52cc5c9f-b4b2-45ee-9d53-607e29fa9df6", "download": "20200820_4DN_in_situ_chiapet_protocol.pdf"}, "display_title": "4DN Standard in situ ChIA-PET Protocol", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "award": {"@id": "/awards/1U01CA200059-01/", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "status": "current", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "in situ ChIA-PET", "status": "released", "date_created": "2019-11-20T16:20:57.215517+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2020-09-23T18:26:24.714726+00:00"}, "raw_file_types": "Reads (fastq) provided by lab", "schema_version": "1", "static_content": [{"content": {"@type": ["StaticSection", "UserContent", "Item"], "lab": {"@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "display_title": "Assay Description", "status": "released", "@id": "/static-sections/d4133739-d2ce-4f16-b4c9-9de080464ea4/", "filetype": "md", "options": {"filetype": "md", "collapsible": false, "default_open": true, "convert_ext_links": true}, "title": "Assay Description", "name": "item-page-headers.ExperimentType.in-situ-chia-pet", "content": "**in situ ChIA-PET**\n\nIn situ ChIA-PET is an improved protocol with the same goal \nas its predecessor Long-Read ChIA-PET, but with higher \nefficiency. This method detects the pairwise chromatin \ninteractions mediated by a specific protein of interest \n*in vivo* \u2014 directly in the cell nucleus. The protocol was \ndeveloped specifically for the 4DN and ENCODE consortia in \n2017. \n\nInspired by the in situ Hi-C method ([Rao et al., 2014](\nhttps://www.ncbi.nlm.nih.gov/pubmed/25497547)), the in situ \nChIA-PET technique employs the nuclear permeabilization and \nrestriction enzyme (AluI) digestion steps to keep the \nchromatin structures intact within the nucleus. The A-tailing\n and proximity ligation are performed inside the cell nucleus,\n followed by the immunoprecipitation step.  Resulting \nmaterials are tagmented, amplified, and sequenced.  Finally, \nthe processed data reveal protein binding intensity, pairwise\n loops, and genome-wide contact maps.  A major advantage of \nthis method over the Long-Read ChIA-PET is its ability to \nefficiently capture the meaningful intra-chromosomal loops, \nowing to the *in situ* digestion and ligation techniques. \n\n<br>\n<center>\n<img src=\"https://4dn-dcic-public.s3.amazonaws.com/static-pages/InfoBoxes/in-situ-chia-pet.png\" alt=\"in situ ChIA-PET\" width=\"1000\"/>\n</center>", "award": {"display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "@id": "/awards/1U01CA200059-01/", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "status": "current", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "d4133739-d2ce-4f16-b4c9-9de080464ea4", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "userid.e2324f87-0625-4bbc-803b-d47677aebe08"]}}, "location": "tab:overview"}], "experiment_name": "in-situ-chia-pet", "valid_item_types": ["ExperimentChiapet"], "experiment_category": "Sequencing", "assay_classification": "3C via Ligation", "assay_subclass_short": "IP-based 3C", "assay_subclassification": "DNA-DNA Pairwise Interactions of Enriched Regions", "@id": "/experiment-types/in-situ-chia-pet/", "@type": ["ExperimentType", "Item"], "uuid": "c66a4e80-8fc7-4705-94ff-8ed136eb7dc7", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "in situ ChIA-PET", "external_references": [], "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}