{"lab": {"status": "current", "correspondence": [{"contact_email": "IGJhcnQuZGVwbGFuY2tlQGVwZmwuY2g=", "@id": "/users/a1a6b714-436a-4bb7-9f7b-4d9fe6cac9be/", "display_title": "Bart Deplancke"}], "display_title": "Deplancke Lab", "uuid": "d111721a-0880-4795-a5d5-835e3c318769", "@type": ["Lab", "Item"], "@id": "/labs/bart-deplancke-lab/", "title": "Deplancke Lab", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.d111721a-0880-4795-a5d5-835e3c318769"]}}, "award": {"description": "Funding source is from outside 4DN.", "@type": ["Award", "Item"], "status": "current", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "@id": "/awards/external-award/", "name": "external-award", "center_title": "External", "project": "External", "center": "External", "display_title": "EXTERNAL AWARD", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["bart-deplancke-lab:expset_lcl_homozygous"], "accession": "4DNESFAJCG4W", "condition": "homozygous reference", "description": "Multiplexed FISH in  lymphoblastoid cell line used as a homozygous reference.", "date_created": "2025-07-08T14:41:04.228141+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "Multiplexed FISH in lymphoblastoid cell line", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-07-10T14:32:05.221617+00:00"}, "public_release": "2025-07-10", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-mic/4DNEX1MX8Y7L/", "@type": ["ExperimentMic", "Experiment", "Item"], "status": "released", "accession": "4DNEX1MX8Y7L", "uuid": "e7a1ef05-fb7b-4914-9753-4f0f586cfd68", "display_title": "multiplexed FISH on B-lymphocyte - 4DNEX1MX8Y7L", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-mic/4DNEX5ICQCRY/", "@type": ["ExperimentMic", "Experiment", "Item"], "status": "released", "accession": "4DNEX5ICQCRY", "uuid": "b61ee99e-ed3c-4b41-923c-3a0a66cd1be1", "display_title": "multiplexed FISH on B-lymphocyte - 4DNEX5ICQCRY", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "project_release": "2025-07-10", "experiments_in_set": [{"@type": ["ExperimentMic", "Experiment", "Item"], "@id": "/experiments-mic/4DNEX1MX8Y7L/", "status": "released", "uuid": "e7a1ef05-fb7b-4914-9753-4f0f586cfd68", "display_title": "multiplexed FISH on B-lymphocyte - 4DNEX1MX8Y7L", "accession": "4DNEX1MX8Y7L", "biosample": {"treatments_summary": "None", "status": "released", "biosample_type": "primary cells", "@type": ["Biosample", "Item"], "biosource_summary": "B-lymphocyte", "@id": "/biosamples/4DNBSLQVWGGC/", "accession": "4DNBSLQVWGGC", "biosample_category": ["Primary Cells"], "display_title": "4DNBSLQVWGGC", "modifications_summary": "None", "uuid": "33f196e9-aadc-496f-9734-804186aee6ef", "tissue_organ_info": {"organ_system": ["mesoderm", "blood"], "tissue_source": "blood"}, "biosource": [{"uuid": "f306c98f-3502-4128-95d8-ecca84216c65", "@id": "/biosources/4DNSR2VO3WVV/", "status": "released", "biosource_type": "primary cell", "accession": "4DNSR2VO3WVV", "@type": ["Biosource", "Item"], "cell_line_tier": "Unclassified", "display_title": "B-lymphocyte - 4DNSR2VO3WVV", "tissue": {"display_title": "blood", "@id": "/ontology-terms/UBERON:0000178/", "status": "released", "synonyms": ["portion of blood", "vertebrate blood"], "uuid": "111147bc-8535-4448-903e-854af460a233", "term_name": "blood", "preferred_name": "blood", "@type": ["OntologyTerm", "Item"], "term_id": "UBERON:0000178", "slim_terms": [{"@id": "/ontology-terms/UBERON:0000926/", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "mesoderm", "uuid": "111120bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/UBERON:0000178/", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "blood", "uuid": "111147bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"term_name": "lymphocyte of B lineage", "@type": ["OntologyTerm", "Item"], "display_title": "B-lymphocyte", "uuid": "0c98ef0b-9a03-43f3-b409-fb091e62e2f8", "status": "released", "preferred_name": "B-lymphocyte", "term_id": "CL:0000945", "@id": "/ontology-terms/CL:0000945/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "@id": "/ontology-terms/CL:0000000/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "uuid": "111133bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "display_title": "immune system", "@id": "/ontology-terms/UBERON:0002405/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "@id": "/ontology-terms/GO:0005623/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "organism": {"scientific_name": "Homo sapiens", "name": "human", "@type": ["Organism", "Item"], "status": "released", "@id": "/organisms/9606/", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "display_title": "H. sapiens", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "@type": ["FileFormat", "Item"], "display_title": "csv", "@id": "/file-formats/csv/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@id": "/files-processed/4DNFIZ37CGLR/", "display_title": "4DNFIZ37CGLR.csv", "upload_key": "e1e963ad-5af5-4d7b-ab25-ddece8f531dd/4DNFIZ37CGLR.csv", "@type": ["FileProcessed", "File", "Item"], "md5sum": "c5dc63fe9080502c250246a5b9cfa00c", "accession": "4DNFIZ37CGLR", "uuid": "e1e963ad-5af5-4d7b-ab25-ddece8f531dd", "file_size": 551586, "genome_assembly": "GRCh38", "file_type_detailed": "FOF-CT - DNA-spot/trace core (csv)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/e1e963ad-5af5-4d7b-ab25-ddece8f531dd/4DNFIZ37CGLR.csv", "file_type": "FOF-CT - DNA-spot/trace core", "file_classification": "processed file", "status": "released", "href": "/files-processed/4DNFIZ37CGLR/@@download/4DNFIZ37CGLR.csv", "last_modified": {"date_modified": "2025-09-05T17:18:55.416566+00:00"}, "track_and_facet_info": {"experimental_lab": "Deplancke Lab", "experiment_type": "multiplexed FISH", "experiment_bucket": "processed file", "assay_info": "GRCh38:17:63486119-63686118 region", "dataset": "Multiplexed FISH in lymphoblastoid cell line", "condition": "homozygous reference", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "B-lymphocyte", "lab_name": "Deplancke Lab"}, "lab": {"display_title": "Deplancke Lab", "status": "current", "uuid": "d111721a-0880-4795-a5d5-835e3c318769", "@id": "/labs/bart-deplancke-lab/", "@type": ["Lab", "Item"], "name": "bart-deplancke-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.d111721a-0880-4795-a5d5-835e3c318769"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "@type": ["FileFormat", "Item"], "display_title": "csv", "@id": "/file-formats/csv/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@id": "/files-processed/4DNFICBJZ2JM/", "display_title": "4DNFICBJZ2JM.csv", "upload_key": "301eb4c3-7856-4e0b-81bb-311edc857105/4DNFICBJZ2JM.csv", "@type": ["FileProcessed", "File", "Item"], "md5sum": "569637639eefafc508ee36bb5c092fab", "accession": "4DNFICBJZ2JM", "uuid": "301eb4c3-7856-4e0b-81bb-311edc857105", "file_size": 111796, "genome_assembly": "GRCh38", "file_type_detailed": "FOF-CT - spot quality (csv)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/301eb4c3-7856-4e0b-81bb-311edc857105/4DNFICBJZ2JM.csv", "file_type": "FOF-CT - spot quality", "file_classification": "processed file", "status": "released", "href": "/files-processed/4DNFICBJZ2JM/@@download/4DNFICBJZ2JM.csv", "last_modified": {"date_modified": "2025-09-05T17:18:53.487363+00:00"}, "track_and_facet_info": {"experimental_lab": "Deplancke Lab", "experiment_type": "multiplexed FISH", "experiment_bucket": "processed file", "assay_info": "GRCh38:17:63486119-63686118 region", "dataset": "Multiplexed FISH in lymphoblastoid cell line", "condition": "homozygous reference", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "B-lymphocyte", "lab_name": "Deplancke Lab"}, "lab": {"display_title": "Deplancke Lab", "status": "current", "uuid": "d111721a-0880-4795-a5d5-835e3c318769", "@id": "/labs/bart-deplancke-lab/", "@type": ["Lab", "Item"], "name": "bart-deplancke-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.d111721a-0880-4795-a5d5-835e3c318769"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "@type": ["FileFormat", "Item"], "display_title": "csv", "@id": "/file-formats/csv/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@id": "/files-processed/4DNFIDULRZLF/", "display_title": "4DNFIDULRZLF.csv", "upload_key": "546efa5d-1dfa-4d25-822f-aecdca934a04/4DNFIDULRZLF.csv", "@type": ["FileProcessed", "File", "Item"], "md5sum": "501dd9028e4649c7b6926e09698cc476", "accession": "4DNFIDULRZLF", "uuid": "546efa5d-1dfa-4d25-822f-aecdca934a04", "file_size": 10496, "genome_assembly": "GRCh38", "file_type_detailed": "FOF-CT - trace data (csv)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/546efa5d-1dfa-4d25-822f-aecdca934a04/4DNFIDULRZLF.csv", "file_type": "FOF-CT - trace data", "file_classification": "processed file", "status": "released", "href": "/files-processed/4DNFIDULRZLF/@@download/4DNFIDULRZLF.csv", "last_modified": {"date_modified": "2025-09-05T17:18:51.585832+00:00"}, "track_and_facet_info": {"experimental_lab": "Deplancke Lab", "experiment_type": "multiplexed FISH", "experiment_bucket": "processed file", "assay_info": "GRCh38:17:63486119-63686118 region", "dataset": "Multiplexed FISH in lymphoblastoid cell line", "condition": "homozygous reference", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "B-lymphocyte", "lab_name": "Deplancke Lab"}, "lab": {"display_title": "Deplancke Lab", "status": "current", "uuid": "d111721a-0880-4795-a5d5-835e3c318769", "@id": "/labs/bart-deplancke-lab/", "@type": ["Lab", "Item"], "name": "bart-deplancke-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.d111721a-0880-4795-a5d5-835e3c318769"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"combined": "Target: GRCh38:17:63486119-63686118 region", "field": "Target", "value": "GRCh38:17:63486119-63686118 region"}, "experiment_type": {"@type": ["ExperimentType", "Item"], "title": "multiplexed FISH", "uuid": "bcdda46a-489d-4d22-be80-c9c21552c915", "status": "released", "experiment_category": "Microscopy", "@id": "/experiment-types/multiplexed-fish/", "other_tags": ["Single Cell"], "assay_subclass_short": "FISH", "assay_classification": "Fluorescence Localization", "display_title": "multiplexed FISH", "assay_subclassification": "Chromatin Tracing", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "last_modified": {"date_modified": "2025-08-21T15:14:43.706193+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["ExperimentMic", "Experiment", "Item"], "@id": "/experiments-mic/4DNEX5ICQCRY/", "status": "released", "uuid": "b61ee99e-ed3c-4b41-923c-3a0a66cd1be1", "display_title": "multiplexed FISH on B-lymphocyte - 4DNEX5ICQCRY", "accession": "4DNEX5ICQCRY", "biosample": {"treatments_summary": "None", "status": "released", "biosample_type": "primary cells", "@type": ["Biosample", "Item"], "biosource_summary": "B-lymphocyte", "@id": "/biosamples/4DNBSQFLSWT1/", "accession": "4DNBSQFLSWT1", "biosample_category": ["Primary Cells"], "display_title": "4DNBSQFLSWT1", "modifications_summary": "None", "uuid": "0894a39a-9612-4c31-8e7f-a3907593957e", "tissue_organ_info": {"organ_system": ["mesoderm", "blood"], "tissue_source": "blood"}, "biosource": [{"uuid": "f306c98f-3502-4128-95d8-ecca84216c65", "@id": "/biosources/4DNSR2VO3WVV/", "status": "released", "biosource_type": "primary cell", "accession": "4DNSR2VO3WVV", "@type": ["Biosource", "Item"], "cell_line_tier": "Unclassified", "display_title": "B-lymphocyte - 4DNSR2VO3WVV", "tissue": {"display_title": "blood", "@id": "/ontology-terms/UBERON:0000178/", "status": "released", "synonyms": ["portion of blood", "vertebrate blood"], "uuid": "111147bc-8535-4448-903e-854af460a233", "term_name": "blood", "preferred_name": "blood", "@type": ["OntologyTerm", "Item"], "term_id": "UBERON:0000178", "slim_terms": [{"@id": "/ontology-terms/UBERON:0000926/", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "mesoderm", "uuid": "111120bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/UBERON:0000178/", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "blood", "uuid": "111147bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"term_name": "lymphocyte of B lineage", "@type": ["OntologyTerm", "Item"], "display_title": "B-lymphocyte", "uuid": "0c98ef0b-9a03-43f3-b409-fb091e62e2f8", "status": "released", "preferred_name": "B-lymphocyte", "term_id": "CL:0000945", "@id": "/ontology-terms/CL:0000945/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "@id": "/ontology-terms/CL:0000000/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "uuid": "111133bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "display_title": "immune system", "@id": "/ontology-terms/UBERON:0002405/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "@id": "/ontology-terms/GO:0005623/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "organism": {"scientific_name": "Homo sapiens", "name": "human", "@type": ["Organism", "Item"], "status": "released", "@id": "/organisms/9606/", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "display_title": "H. sapiens", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "@type": ["FileFormat", "Item"], "display_title": "csv", "@id": "/file-formats/csv/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@id": "/files-processed/4DNFIXSTIVTW/", "display_title": "4DNFIXSTIVTW.csv", "upload_key": "e898080d-3e8c-4f87-bd54-fd98e6e1d209/4DNFIXSTIVTW.csv", "@type": ["FileProcessed", "File", "Item"], "md5sum": "c8e4de4dd4b9046e8b05ca5364fde2d1", "accession": "4DNFIXSTIVTW", "uuid": "e898080d-3e8c-4f87-bd54-fd98e6e1d209", "file_size": 2316112, "genome_assembly": "GRCh38", "file_type_detailed": "FOF-CT - DNA-spot/trace core (csv)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/e898080d-3e8c-4f87-bd54-fd98e6e1d209/4DNFIXSTIVTW.csv", "file_type": "FOF-CT - DNA-spot/trace core", "file_classification": "processed file", "status": "released", "href": "/files-processed/4DNFIXSTIVTW/@@download/4DNFIXSTIVTW.csv", "last_modified": {"date_modified": "2025-09-05T17:18:49.918859+00:00"}, "track_and_facet_info": {"experimental_lab": "Deplancke Lab", "experiment_type": "multiplexed FISH", "experiment_bucket": "processed file", "assay_info": "GRCh38:17:63486119-63686118 region", "dataset": "Multiplexed FISH in lymphoblastoid cell line", "condition": "homozygous reference", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "B-lymphocyte", "lab_name": "Deplancke Lab"}, "lab": {"display_title": "Deplancke Lab", "status": "current", "uuid": "d111721a-0880-4795-a5d5-835e3c318769", "@id": "/labs/bart-deplancke-lab/", "@type": ["Lab", "Item"], "name": "bart-deplancke-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.d111721a-0880-4795-a5d5-835e3c318769"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "@type": ["FileFormat", "Item"], "display_title": "csv", "@id": "/file-formats/csv/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@id": "/files-processed/4DNFIT99WH4F/", "display_title": "4DNFIT99WH4F.csv", "upload_key": "c3b24ec3-2816-4022-ac14-e75066507811/4DNFIT99WH4F.csv", "@type": ["FileProcessed", "File", "Item"], "md5sum": "633231aaef73e819199544988dde2882", "accession": "4DNFIT99WH4F", "uuid": "c3b24ec3-2816-4022-ac14-e75066507811", "file_size": 476926, "genome_assembly": "GRCh38", "file_type_detailed": "FOF-CT - spot quality (csv)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/c3b24ec3-2816-4022-ac14-e75066507811/4DNFIT99WH4F.csv", "file_type": "FOF-CT - spot quality", "file_classification": "processed file", "status": "released", "href": "/files-processed/4DNFIT99WH4F/@@download/4DNFIT99WH4F.csv", "last_modified": {"date_modified": "2025-09-05T17:18:47.971750+00:00"}, "track_and_facet_info": {"experimental_lab": "Deplancke Lab", "experiment_type": "multiplexed FISH", "experiment_bucket": "processed file", "assay_info": "GRCh38:17:63486119-63686118 region", "dataset": "Multiplexed FISH in lymphoblastoid cell line", "condition": "homozygous reference", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "B-lymphocyte", "lab_name": "Deplancke Lab"}, "lab": {"display_title": "Deplancke Lab", "status": "current", "uuid": "d111721a-0880-4795-a5d5-835e3c318769", "@id": "/labs/bart-deplancke-lab/", "@type": ["Lab", "Item"], "name": "bart-deplancke-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.d111721a-0880-4795-a5d5-835e3c318769"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "@type": ["FileFormat", "Item"], "display_title": "csv", "@id": "/file-formats/csv/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@id": "/files-processed/4DNFI8TFEFP1/", "display_title": "4DNFI8TFEFP1.csv", "upload_key": "06c0a48b-a4f5-4483-af3a-77a716ea4ac6/4DNFI8TFEFP1.csv", "@type": ["FileProcessed", "File", "Item"], "md5sum": "4f00a280f33fee36b77b35ac3e85637b", "accession": "4DNFI8TFEFP1", "uuid": "06c0a48b-a4f5-4483-af3a-77a716ea4ac6", "file_size": 35535, "genome_assembly": "GRCh38", "file_type_detailed": "FOF-CT - trace data (csv)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/06c0a48b-a4f5-4483-af3a-77a716ea4ac6/4DNFI8TFEFP1.csv", "file_type": "FOF-CT - trace data", "file_classification": "processed file", "status": "released", "href": "/files-processed/4DNFI8TFEFP1/@@download/4DNFI8TFEFP1.csv", "last_modified": {"date_modified": "2025-09-05T17:18:46.173848+00:00"}, "track_and_facet_info": {"experimental_lab": "Deplancke Lab", "experiment_type": "multiplexed FISH", "experiment_bucket": "processed file", "assay_info": "GRCh38:17:63486119-63686118 region", "dataset": "Multiplexed FISH in lymphoblastoid cell line", "condition": "homozygous reference", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "B-lymphocyte", "lab_name": "Deplancke Lab"}, "lab": {"display_title": "Deplancke Lab", "status": "current", "uuid": "d111721a-0880-4795-a5d5-835e3c318769", "@id": "/labs/bart-deplancke-lab/", "@type": ["Lab", "Item"], "name": "bart-deplancke-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.d111721a-0880-4795-a5d5-835e3c318769"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"combined": "Target: GRCh38:17:63486119-63686118 region", "field": "Target", "value": "GRCh38:17:63486119-63686118 region"}, "experiment_type": {"@type": ["ExperimentType", "Item"], "title": "multiplexed FISH", "uuid": "bcdda46a-489d-4d22-be80-c9c21552c915", "status": "released", "experiment_category": "Microscopy", "@id": "/experiment-types/multiplexed-fish/", "other_tags": ["Single Cell"], "assay_subclass_short": "FISH", "assay_classification": "Fluorescence Localization", "display_title": "multiplexed FISH", "assay_subclassification": "Chromatin Tracing", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "last_modified": {"date_modified": "2025-08-21T15:14:44.036372+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experimentset_type": "replicate", "other_processed_files": [{"type": "supplementary", "files": [{"file_format": {"@type": ["FileFormat", "Item"], "display_title": "bed", "status": "released", "@id": "/file-formats/bed/", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "24eaf323017581b0a5dc093b5e11ec3f", "file_type": "target regions", "display_title": "4DNFID3DR3R9.bed.gz", "@type": ["FileReference", "File", "Item"], "file_type_detailed": "target regions (bed)", "status": "released", "href": "/files-reference/4DNFID3DR3R9/@@download/4DNFID3DR3R9.bed.gz", "uuid": "723aa8f6-634c-4280-85f8-8bc389245235", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/723aa8f6-634c-4280-85f8-8bc389245235/4DNFID3DR3R9.bed.gz", "accession": "4DNFID3DR3R9", "genome_assembly": "GRCh38", "@id": "/files-reference/4DNFID3DR3R9/", "file_size": 432, "higlass_uid": "cV8paO-dRkCRyuObb6EdVA", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"status": "released", "@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFID3DR3R9", "uuid": "741031c8-8484-4b2f-9d95-b22f1d4cd477", "@id": "/higlass-view-configs/741031c8-8484-4b2f-9d95-b22f1d4cd477/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "lab": {"@id": "/labs/bart-deplancke-lab/", "status": "current", "uuid": "d111721a-0880-4795-a5d5-835e3c318769", "@type": ["Lab", "Item"], "name": "bart-deplancke-lab", "display_title": "Deplancke Lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.d111721a-0880-4795-a5d5-835e3c318769"]}}, "track_and_facet_info": {"lab_name": "Deplancke Lab"}, "last_modified": {"date_modified": "2025-09-05T17:47:04.678167+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "title": "Submitter provided files", "description": "Bed files with genomic coordinates (1-based,hg 38) of 200-kb for the 25 8-kb segments used for ORCA targets", "higlass_view_config": {"status": "released", "display_title": "4DNESFAJCG4W - Submitter provided files", "@id": "/higlass-view-configs/b053f74a-b6ff-494d-b9ca-ead20a06e7ec/", "uuid": "b053f74a-b6ff-494d-b9ca-ead20a06e7ec", "description": "Supplementary Files (Submitter provided files) for 4DNESFAJCG4W (Multiplexed FISH in  lymphoblastoid cell line used as a homozygous reference.): 4DNFID3DR3R9", "@type": ["HiglassViewConfig", "UserContent", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}, "last_modified": {"date_modified": "2025-07-10T14:32:06.747701+00:00"}}}], "@id": "/experiment-set-replicates/4DNESFAJCG4W/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "13165dd3-956d-4244-b509-a5319a19b41f", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNESFAJCG4W", "external_references": [], "produced_in_pub": {"abstract": "Non-coding variants coordinate transcription factor (TF) binding and chromatin  mark enrichment changes over regions spanning >100 kb. These molecularly  coordinated regions are named \"variable chromatin modules\" (VCMs), providing a  conceptual framework of how regulatory variation might shape complex traits. To  better understand the molecular mechanisms underlying VCM formation, here, we  mechanistically dissect a VCM-modulating noncoding variant that is associated  with reduced chronic lymphocytic leukemia (CLL) predisposition and disease  progression. This common, germline variant constitutes a 5-bp indel that controls  the activity of an AXIN2 gene-linked VCM by creating a MEF2 binding site, which,  upon binding, activates a super-enhancer-like regulatory element. This triggers a  large change in TF binding activity and chromatin state at an enhancer cluster  spanning >150 kb, coinciding with subtle, long-range chromatin compaction and  robust AXIN2 up-regulation. Our results support a model in which the indel acts  as an AXIN2 VCM-activating TF nucleation event, which modulates CLL pathology.", "status": "current", "url": "https://www.ncbi.nlm.nih.gov/pubmed/35440565", "journal": "Nature communications", "@type": ["Publication", "Item"], "authors": ["Llimos G", "Gardeux V", "Koch U", "Kribelbauer JF", "Hafner A", "Alpern D", "Pezoldt J", "Litovchenko M", "Russeil J", "Dainese R", "Moia R", "Mahmoud AM", "Rossi D", "Gaidano G", "Plass C", "Lutsik P", "Gerhauser C", "Waszak SM", "Boettiger A", "Radtke F", "Deplancke B"], "date_published": "2022-04-19", "@id": "/publications/b87c4200-5443-460f-9f1c-2f8092c7cafb/", "title": "A leukemia-protective germline variant mediates chromatin module formation via  transcription factor nucleation.", "ID": "PMID:35440565", "short_attribution": "Llimos G et al. (2022)", "uuid": "b87c4200-5443-460f-9f1c-2f8092c7cafb", "display_title": "Llimos G et al. (2022) PMID:35440565", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"uuid": "b87c4200-5443-460f-9f1c-2f8092c7cafb", "date_published": "2022-04-19", "authors": ["Llimos G", "Gardeux V", "Koch U", "Kribelbauer JF", "Hafner A", "Alpern D", "Pezoldt J", "Litovchenko M", "Russeil J", "Dainese R", "Moia R", "Mahmoud AM", "Rossi D", "Gaidano G", "Plass C", "Lutsik P", "Gerhauser C", "Waszak SM", "Boettiger A", "Radtke F", "Deplancke B"], "display_title": "Llimos G et al. (2022) PMID:35440565", "status": "current", "abstract": "Non-coding variants coordinate transcription factor (TF) binding and chromatin  mark enrichment changes over regions spanning >100 kb. These molecularly  coordinated regions are named \"variable chromatin modules\" (VCMs), providing a  conceptual framework of how regulatory variation might shape complex traits. To  better understand the molecular mechanisms underlying VCM formation, here, we  mechanistically dissect a VCM-modulating noncoding variant that is associated  with reduced chronic lymphocytic leukemia (CLL) predisposition and disease  progression. This common, germline variant constitutes a 5-bp indel that controls  the activity of an AXIN2 gene-linked VCM by creating a MEF2 binding site, which,  upon binding, activates a super-enhancer-like regulatory element. This triggers a  large change in TF binding activity and chromatin state at an enhancer cluster  spanning >150 kb, coinciding with subtle, long-range chromatin compaction and  robust AXIN2 up-regulation. Our results support a model in which the indel acts  as an AXIN2 VCM-activating TF nucleation event, which modulates CLL pathology.", "title": "A leukemia-protective germline variant mediates chromatin module formation via  transcription factor nucleation.", "ID": "PMID:35440565", "journal": "Nature communications", "@id": "/publications/b87c4200-5443-460f-9f1c-2f8092c7cafb/", "@type": ["Publication", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 2, "imaging_paths": [{"path": {"uuid": "4c561984-7ea4-434f-bdb1-affb00f17b87", "@id": "/imaging-paths/4c561984-7ea4-434f-bdb1-affb00f17b87/", "status": "released", "override_display_title": "200-kb at 8-kb resolution on chr 17 (AXIN2 VCM) targeted by oligo probe library (with Cy3-labeled fiducial oligo probes)", "display_title": "200-kb at 8-kb resolution on chr 17 (AXIN2 VCM) targeted by oligo probe library (with Cy3-labeled fiducial oligo probes)", "labeled_probe": "DNA primer", "@type": ["ImagingPath", "Item"], "target": [{"status": "released", "@id": "/bio-features/b924813f-7a21-4a76-a90a-ccb6b8f377f7/", "uuid": "b924813f-7a21-4a76-a90a-ccb6b8f377f7", "organism_name": "human", "@type": ["BioFeature", "Item"], "display_title": "GRCh38:17:63486119-63686118 region", "genome_location": [{"status": "released", "chromosome": "17", "end_coordinate": 63686118, "@type": ["GenomicRegion", "Item"], "display_title": "GRCh38:17:63486119-63686118", "genome_assembly": "GRCh38", "@id": "/genomic-regions/27e72aeb-cdbb-4802-9821-be01359a57c3/", "start_coordinate": 63486119, "uuid": "27e72aeb-cdbb-4802-9821-be01359a57c3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "feature_type": {"@id": "/ontology-terms/SO:0000001/", "term_url": "http://purl.obolibrary.org/obo/SO_0000001", "preferred_name": "region", "status": "released", "term_name": "region", "@type": ["OntologyTerm", "Item"], "term_id": "SO:0000001", "display_title": "region", "uuid": "41b7a2c5-f2d9-46b4-a49d-51502fe61bb3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "channel": "ch00"}, {"path": {"uuid": "c566dbd8-8728-46db-9635-28e41955735d", "@id": "/imaging-paths/c566dbd8-8728-46db-9635-28e41955735d/", "status": "released", "override_display_title": "200-kb at 8-kb resolution on chr 17 (AXIN2 VCM) targeted by oligo probe library (with Cy5-labeled fiducial oligo probes)", "display_title": "200-kb at 8-kb resolution on chr 17 (AXIN2 VCM) targeted by oligo probe library (with Cy5-labeled fiducial oligo probes)", "labeled_probe": "DNA primer", "@type": ["ImagingPath", "Item"], "target": [{"status": "released", "@id": "/bio-features/b924813f-7a21-4a76-a90a-ccb6b8f377f7/", "uuid": "b924813f-7a21-4a76-a90a-ccb6b8f377f7", "organism_name": "human", "@type": ["BioFeature", "Item"], "display_title": "GRCh38:17:63486119-63686118 region", "genome_location": [{"status": "released", "chromosome": "17", "end_coordinate": 63686118, "@type": ["GenomicRegion", "Item"], "display_title": "GRCh38:17:63486119-63686118", "genome_assembly": "GRCh38", "@id": "/genomic-regions/27e72aeb-cdbb-4802-9821-be01359a57c3/", "start_coordinate": 63486119, "uuid": "27e72aeb-cdbb-4802-9821-be01359a57c3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "feature_type": {"@id": "/ontology-terms/SO:0000001/", "term_url": "http://purl.obolibrary.org/obo/SO_0000001", "preferred_name": "region", "status": "released", "term_name": "region", "@type": ["OntologyTerm", "Item"], "term_id": "SO:0000001", "display_title": "region", "uuid": "41b7a2c5-f2d9-46b4-a49d-51502fe61bb3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "channel": "ch01"}], "@context": "/terms/", "aggregated-items": {"badges": []}, "validation-errors": []}