{"lab": {"status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "award": {"status": "current", "@id": "/awards/1U01CA200059-01/", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "TSA-seq", "status": "released", "cfde_term": {"status": "released", "@type": ["OntologyTerm", "Item"], "uuid": "cf5aaec3-553e-4b62-8361-e1a3763ab73d", "display_title": "tyramide signal amplification sequencing assay", "@id": "/ontology-terms/OBI:0003297/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "other_tags": ["1D"], "date_created": "2019-03-28T15:16:15.557297+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-07-26T17:22:10.892103+00:00"}, "raw_file_types": "Reads (fastq) provided by lab", "reference_pubs": [{"display_title": "Chen Y et al. (2018) doi:10.1083/jcb.201807108", "journal": "The Journal of cell biology", "short_attribution": "Chen Y et al. (2018)", "@id": "/publications/0cbf34ae-fd3e-4b9d-a02f-cc80f1f8a872/", "@type": ["Publication", "Item"], "status": "current", "authors": ["Chen Y", "Zhang Y", "Wang Y", "Zhang L", "Brinkman EK", "Adam SA", "Goldman R", "van Steensel B", "Ma J", "Belmont AS"], "uuid": "0cbf34ae-fd3e-4b9d-a02f-cc80f1f8a872", "date_published": "2018-11-05", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "schema_version": "1", "static_content": [{"content": {"filetype": "html", "title": "Assay Description", "name": "item-page-headers.ExperimentType.tsa-seq", "@id": "/static-sections/a991040c-591d-4534-8a6e-a33bb0e5ce44/", "@type": ["StaticSection", "UserContent", "Item"], "content_as_html": "<div class=\"html-container\"><p><strong>TSA sequencing (TSA-Seq)</strong>, is a genomic method that allows the estimation of cytological distances of chromosome loci genome-wide relative to a particular nuclear compartment and can be used to infer chromosome trajectories from one compartment to another. This is a method for measuring distances on a scale of ~100-1000 nm.</p>\n<p>TSA uses an antibody-coupled HRP in conjunction with an antibody targeting a specific protein or compartment to catalyze the formation of diffusible biotin-tyramide free radicals and create a free radical concentration gradient centered at the target in fixed nuclei.  The TSA reaction is followed by the reversal of formaldehyde cross-linking, DNA isolation, pulldown of biotinylated DNA, and high-throughput sequencing.  TSA labels DNA directly and the steady-state concentration of tyramide free radicals during the TSA reaction can be modeled by a simple exponential decay proportional to the distance from the target.</p>\n<p>TSA enrichment genomic maps are generated by plotting the log2 ratio of the normalized pulldown read density versus the normalized read density of input DNA over a 20-kbp sliding window and can be visualized as normalized counts in 1D bigwig tracks.</p></div>", "status": "released", "display_title": "Assay Description", "content": "<p><strong>TSA sequencing (TSA-Seq)</strong>, is a genomic method that allows the estimation of cytological distances of chromosome loci genome-wide relative to a particular nuclear compartment and can be used to infer chromosome trajectories from one compartment to another. This is a method for measuring distances on a scale of ~100-1000 nm.</p>\n<p>TSA uses an antibody-coupled HRP in conjunction with an antibody targeting a specific protein or compartment to catalyze the formation of diffusible biotin-tyramide free radicals and create a free radical concentration gradient centered at the target in fixed nuclei.  The TSA reaction is followed by the reversal of formaldehyde cross-linking, DNA isolation, pulldown of biotinylated DNA, and high-throughput sequencing.  TSA labels DNA directly and the steady-state concentration of tyramide free radicals during the TSA reaction can be modeled by a simple exponential decay proportional to the distance from the target.</p>\n<p>TSA enrichment genomic maps are generated by plotting the log2 ratio of the normalized pulldown read density versus the normalized read density of input DNA over a 20-kbp sliding window and can be visualized as normalized counts in 1D bigwig tracks.</p>", "lab": {"status": "current", "@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "award": {"@id": "/awards/1U01CA200059-01/", "@type": ["Award", "Item"], "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "status": "current", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "options": {"filetype": "html", "collapsible": false, "default_open": true}, "uuid": "a991040c-591d-4534-8a6e-a33bb0e5ce44", "contributing_labs": [{"status": "current", "@id": "/labs/andrew-belmont-lab/", "display_title": "Andrew Belmont, ILLINOIS", "uuid": "b2c2deeb-e883-4ac0-b9e2-906e598884d6", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b2c2deeb-e883-4ac0-b9e2-906e598884d6"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267227777"]}}, "location": "tab:overview"}], "controlled_term": {"display_title": "TSA-seq", "@type": ["OntologyTerm", "Item"], "term_url": "http://www.ebi.ac.uk/efo/EFO_0009971", "status": "released", "preferred_name": "TSA-seq", "term_id": "EFO:0009971", "term_name": "TSA-seq", "@id": "/ontology-terms/EFO:0009971/", "uuid": "b6020531-57f8-4aa5-9870-17ab0992fcc0", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_name": "tsa-seq", "current_pipeline": "RepliSeq_Pipeline_v16.1_step1", "valid_item_types": ["ExperimentTsaseq"], "accepted_pipelines": ["RepliSeq_Pipeline_v13.1_step1", "RepliSeq_Pipeline_v14_step1", "RepliSeq_Pipeline_v16_step1"], "experiment_category": "Sequencing", "assay_classification": "Linear DNA Enrichment", "assay_subclass_short": "Proximity-seq", "assay_subclassification": "Proximity to Cellular Component", "@id": "/experiment-types/tsa-seq/", "@type": ["ExperimentType", "Item"], "uuid": "75d7181c-e329-463e-b776-a467433aa4db", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "TSA-seq", "external_references": [], "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}