{"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"]}}, "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": "sci-Hi-C", "status": "released", "other_tags": ["DNA-DNA", "Single Cell", "3D", "Pairwise"], "date_created": "2019-03-28T17:41:51.709383+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-02-18T21:01:19.282909+00:00"}, "raw_file_types": "Reads (fastq) provided by lab", "reference_pubs": [{"authors": ["Ramani V", "Deng X", "Qiu R", "Gunderson KL", "Steemers FJ", "Disteche CM", "Noble WS", "Duan Z", "Shendure J"], "uuid": "020f16a3-8ef1-46d5-b208-dde61d81290a", "display_title": "Ramani V et al. (2017) PMID:28135255", "@id": "/publications/020f16a3-8ef1-46d5-b208-dde61d81290a/", "status": "current", "date_published": "2017-03", "@type": ["Publication", "Item"], "journal": "Nature methods", "short_attribution": "Ramani V et al. (2017)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "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/ae5a6470-0694-4ba3-893a-40b170401bc0/", "filetype": "md", "options": {"filetype": "md", "collapsible": false, "default_open": false, "convert_ext_links": true}, "title": "Assay Description", "name": "item-page-headers.ExperimentType.sciHiC", "content": "**Sci-Hi-C**\n\n\nSci-Hi-C is a method to detect and quantify chromatin interactions in large numbers of single cells. This massively multiplexed method was developed in 2017 and it enables characterization of 3D genome architecture in thousands of single cells in parallel without requiring compartmentalization of each cell or microfluidic manipulation.\n\nThis protocol involves cross-linking the cells with formaldehyde. The cells are then permeabilized with their nuclei intact. A 4-cutter restriction enzyme DpnII is used to fragment the chromatin. Nuclei are then distributed to 96 wells, wherein the first barcode is introduced through ligation of barcoded biotinylated double-stranded bridge adaptors. Intact nuclei are then pooled and subjected to proximity ligation, followed by dilution and redistribution to a second 96-well plate. Importantly, this dilution is carried out such that each well in this second plate contains at most 25 nuclei. Following lysis, a second barcode is introduced through ligation of barcoded Y-adaptors. As the number of barcode combinations (96 \u00d7 96) exceeds the number of nuclei (96 \u00d7 25), the vast majority of single nuclei are tagged by a unique combination of barcodes. All material is once again pooled, and biotinylated junctions are purified with streptavidin beads, restriction digested, and further processed to Illumina sequencing libraries. Sequencing these molecules with relatively long paired-end reads (i.e., 2 \u00d7 250 base pairs) allows one to identify not only the genome-derived fragments of conventional Hi-C, but also external and internal barcodes,  which enable decomposition of the Hi-C data into single-cell contact probability maps.\n\n\nSee [Ramani et al 2017](https://www.nature.com/articles/nmeth.4155) for more details on in sci-Hi-C.\n\n<dl>\n<a href=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/sciHiC.jpg\" target=\"_blank\">\n<img src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/sciHiC.jpg\" style=\"width:1000px\" />  \n</a>\n<br/><br/>\n<em>Image source: Ramani et. al. Nature Methods 2017, Figure 1a </em>\n</dl>", "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": "ae5a6470-0694-4ba3-893a-40b170401bc0", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "userid.56c9c683-bb11-471b-b590-c656f7dc03c1"]}}, "location": "tab:overview"}], "controlled_term": {"term_url": "http://www.ebi.ac.uk/efo/EFO_0009977", "@type": ["OntologyTerm", "Item"], "uuid": "896bbafe-12a5-4ea2-8852-6611152bbb68", "term_name": "sci-Hi-C", "status": "released", "preferred_name": "sci-Hi-C", "@id": "/ontology-terms/EFO:0009977/", "term_id": "EFO:0009977", "display_title": "sci-Hi-C", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_name": "sci-hi-c", "valid_item_types": ["ExperimentHiC"], "experiment_category": "Sequencing", "assay_classification": "3C via Ligation", "assay_subclass_short": "Hi-C (single cell)", "assay_subclassification": "DNA-DNA Pairwise Interactions - Single Cell", "@id": "/experiment-types/sci-hi-c/", "@type": ["ExperimentType", "Item"], "uuid": "358540cb-e1b8-4d5a-b0ab-7c1b433a17ce", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "sci-Hi-C", "external_references": [], "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}