{"lab": {"status": "current", "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "sop": {"@id": "/protocols/f1c11c3c-0135-420d-acb5-60112dc24557/", "attachment": {"href": "@@download/attachment/4DN_ChIA-PET_protocol_20170724.pdf", "size": 5478076, "type": "application/pdf", "md5sum": "d1287f514560a111598be0149b1ce8a9", "blob_id": "e0bf742d-6efa-4ee9-936d-958278bf5a59", "download": "4DN_ChIA-PET_protocol_20170724.pdf"}, "title": "4DN Standard Long Read ChIA-PET protocol", "display_title": "4DN Standard Long Read ChIA-PET protocol", "date_created": "2017-11-17T18:01:31.517029+00:00", "protocol_type": "Experimental protocol", "status": "released", "@type": ["Protocol", "Item"], "uuid": "f1c11c3c-0135-420d-acb5-60112dc24557", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "award": {"status": "current", "@id": "/awards/1U01CA200059-01/", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "@type": ["Award", "Item"], "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "ChIA-PET", "status": "released", "other_tags": ["DNA-DNA", "Pairwise", "3D"], "date_created": "2019-03-28T15:16:17.758936+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-11-20T16:14:49.930010+00:00"}, "raw_file_types": "Reads (fastq) provided by lab", "reference_pubs": [{"@id": "/publications/fb5cd1c5-942e-4da0-a7c8-d559fa6d6b47/", "authors": ["Li X", "Luo OJ", "Wang P", "Zheng M", "Wang D", "Piecuch E", "Zhu JJ", "Tian SZ", "Tang Z", "Li G", "Ruan Y"], "@type": ["Publication", "Item"], "status": "current", "display_title": "Li X et al. (2017) PMID:28358394", "uuid": "fb5cd1c5-942e-4da0-a7c8-d559fa6d6b47", "short_attribution": "Li X et al. (2017)", "date_published": "2017-05", "journal": "Nature protocols", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "schema_version": "1", "static_content": [{"content": {"display_title": "Assay Description", "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"]}}, "content": "**ChIA-PET**\n\nChIA-PET is a method for detecting the pairwise chromatin \ninteractions mediated by a specific protein of interest, and \nLong-Read ChIA-PET is the second version of this assay (and \nis used for the ChIA-PET experiments in the 4DN data portal).\n The name \u201clong read\u201d is relative to the original ChIA-PET \nprotocol ([Fullwood et al., 2009](https://www.ncbi.nlm.nih.gov/pubmed/19890323)) \nthat used a Type IIS restriction enzyme (MmeI) to generate \n\u201cshort read\u201d (2x20 bp) paired-end tags (PET) from the \nchromatin DNA templates by proximity ligation. The key \nmodifications of Long-Read ChIA-PET from the original \nChIA-PET method are 1) the use of Tn5 transposase to cut the \nproximity-ligated chromatin DNA fragments randomly, \ngenerating longer DNA templates for sequencing analysis by \npaired-end reads (2x150 bp). Therefore, most of the PET reads\n are up to 200 bp in length by 2x200 bp paired End reading \nmodel by ILLUMINA sequencing. A minor change in the protocol \nis to use one \u201cbridge\u201d linker instead of two \u201cA-B\u201d linkers, \nfurther simplifying the protocol.  \n\nThe protocol involves dual-crosslinking the cells with \nformaldehyde and EGS to fix potential contacts between \nphysically proximal regions.  Subsequently, both the cell and \nnuclear membranes are lysed, and the fragmentation step \nfollows.  An antibody is used to pull down interactions \ninvolving a specific protein factor.  The resulting chromatin \nmaterial goes through the proximity ligation by A-tailing and \nlinker ligation.  Reverse crosslinking removes the protein, \nleaving the DNA fragments to be amplified and sequenced. \nFinally, the processed data reveal protein binding intensity, \npairwise loops, and genome-wide contact maps.\n\nSee [Li et al., 2017](https://www.ncbi.nlm.nih.gov/pubmed/28358394)\n for more details on Long-Read ChIA-PET. \n\n![ChIA-PET](\nhttps://4dn-dcic-public.s3.amazonaws.com/static-pages/InfoBoxes/chia-pet.png)", "lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "uuid": "8e2535fa-bee2-47fc-872f-91506135be5b", "status": "released", "title": "Assay Description", "name": "item-page-headers.ExperimentType.chia-pet", "@type": ["StaticSection", "UserContent", "Item"], "filetype": "md", "options": {"filetype": "md", "collapsible": false, "default_open": false, "convert_ext_links": true}, "@id": "/static-sections/8e2535fa-bee2-47fc-872f-91506135be5b/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "userid.e2324f87-0625-4bbc-803b-d47677aebe08"]}}, "location": "tab:overview"}], "controlled_term": {"status": "released", "preferred_name": "Chia-PET", "uuid": "66a468f5-83db-4994-9518-2c8a1856eae5", "display_title": "Chia-PET", "term_url": "http://www.ebi.ac.uk/efo/EFO_0008684", "@id": "/ontology-terms/EFO:0008684/", "term_name": "Chia-PET", "term_id": "EFO:0008684", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_name": "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/chia-pet/", "@type": ["ExperimentType", "Item"], "uuid": "f1338cf6-8644-41e1-baaa-6691a178ac34", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "ChIA-PET", "external_references": [], "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}