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For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "@id": "/files-processed/4DNFICGKJ1NW/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/2f1f11c1-6d87-4b14-98f5-05dd339c47fe/4DNFICGKJ1NW.bw", "accession": "4DNFICGKJ1NW", "file_classification": "processed file", "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "display_title": "4DNFICGKJ1NW - normalized counts for HCT116 (Tier 2) TSA-seq NIFK protein", "uuid": "42f47708-5905-4495-89e7-69c75725474a", "@id": "/higlass-view-configs/42f47708-5905-4495-89e7-69c75725474a/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "lab": {"name": "andrew-belmont-lab", "@type": ["Lab", "Item"], "display_title": "Andrew Belmont, ILLINOIS", "@id": "/labs/andrew-belmont-lab/", "uuid": "b2c2deeb-e883-4ac0-b9e2-906e598884d6", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b2c2deeb-e883-4ac0-b9e2-906e598884d6"]}}, "last_modified": {"date_modified": "2024-02-22T17:48:58.763163+00:00"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Andrew Belmont, ILLINOIS", "experiment_type": "TSA-seq", "experiment_bucket": "processed file", "assay_info": "NIFK protein", "dataset": "TSA-seq MKI67IP in  HCT116 cells", "condition": "condition2 - conditionC or conditionE - anti-MKI67IP", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Andrew Belmont, ILLINOIS", "track_title": "normalized counts for HCT116 (Tier 2) TSA-seq NIFK protein"}}], "external_references": [{"ref": "GEO:GSM8231868", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM8231868"}, {"ref": "GEO:SAMN41084472", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=SAMN41084472"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"combined": "Target: NIFK protein", "field": "Target", "value": "NIFK protein"}, "last_modified": {"date_modified": "2025-05-30T16:54:30.885021+00:00"}}], "experimentset_type": "replicate", "completed_processes": ["RepliSeq_Pipeline_v16_step1"], "other_processed_files": [{"type": "preliminary", "files": [], "title": "Repli-Seq Pipeline - Preliminary Files", "higlass_item_uuid": null, "higlass_view_config": {"@id": "/higlass-view-configs/cec6bb23-ae02-421a-b9aa-fbb3df1e4f25/", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "uuid": "cec6bb23-ae02-421a-b9aa-fbb3df1e4f25", "display_title": "4DNESAHA7E69 - Repli-Seq Pipeline - Preliminary Files", "description": "Supplementary Files (Repli-Seq Pipeline - Preliminary Files) for 4DNESAHA7E69 (Replicates of MKI67IP TSA-seq Reaction  Condition C (PBS 50% Sucrose, 1:3000 tyramide biotin) or Condition E (PBS 50% Sucrose, 1:300 tyramide biotin) 30 minute reaction on HCT116  cells): 4DNFIA2MJRI8, 4DNFIIBO2AAB", "last_modified": {"date_modified": "2023-11-03T15:41:41.975653+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "@id": "/experiment-set-replicates/4DNESAHA7E69/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "908132a3-b8e4-4854-a14d-c5cf7ecc6756", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNESAHA7E69", "external_references": [], "produced_in_pub": {"journal": "Communications biology", "authors": ["Kumar P", "Gholamalamdari O", "Zhang Y", "Zhang L", "Vertii A", "van Schaik T", "Peric-Hupkes D", "Sasaki T", "Gilbert DM", "van Steensel B", "Ma J", "Kaufman PD", "Belmont AS"], "title": "Nucleolus and centromere Tyramide Signal Amplification-Seq reveals variable  localization of heterochromatin in different cell types.", "url": "https://www.ncbi.nlm.nih.gov/pubmed/39271748", "short_attribution": "Kumar P et al. (2024)", "ID": "PMID:39271748", "display_title": "Kumar P et al. (2024) PMID:39271748", "date_published": "2024-09-13", "@type": ["Publication", "Item"], "@id": "/publications/22e02dc4-37b9-4891-9084-6d85f6683252/", "status": "current", "abstract": "Genome differential positioning within interphase nuclei remains poorly explored.  We extended and validated Tyramide Signal Amplification (TSA)-seq to map genomic  regions near nucleoli and pericentric heterochromatin in four human cell lines.  Our study confirmed that smaller chromosomes localize closer to nucleoli but  further deconvolved this by revealing a preference for chromosome arms below  36-46 Mbp in length. We identified two lamina associated domain subsets through  their differential nuclear lamina versus nucleolar positioning in different cell  lines which showed distinctive patterns of DNA replication timing and gene  expression across all cell lines. Unexpectedly, active, nuclear  speckle-associated genomic regions were found near typically repressive nuclear  compartments, which is attributable to the close proximity of nuclear speckles  and nucleoli in some cell types, and association of centromeres with nuclear  speckles in human embryonic stem cells (hESCs). Our study points to a more  complex and variable nuclear genome organization than suggested by current  models, as revealed by our TSA-seq methodology.", "uuid": "22e02dc4-37b9-4891-9084-6d85f6683252", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [{"@id": "/publications/f2b3b3fb-e9af-484d-abeb-fe4316ffdc1a/", "display_title": "Gholamalamdari O et al. (2025) PMID:38712201", "@type": ["Publication", "Item"], "uuid": "f2b3b3fb-e9af-484d-abeb-fe4316ffdc1a", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "publications_of_set": [{"authors": ["Gholamalamdari O", "van Schaik T", "Wang Y", "Kumar P", "Zhang L", "Zhang Y", "Gonzalez GAH", "Vouzas AE", "Zhao PA", "Gilbert DM", "Ma J", "van Steensel B", "Belmont AS"], "@id": "/publications/f2b3b3fb-e9af-484d-abeb-fe4316ffdc1a/", "journal": "bioRxiv : the preprint server for biology", "ID": "PMID:38712201", "title": "Beyond A and B Compartments: how major nuclear locales define nuclear genome  organization and function.", "status": "current", "@type": ["Publication", "Item"], "display_title": "Gholamalamdari O et al. (2025) PMID:38712201", "uuid": "f2b3b3fb-e9af-484d-abeb-fe4316ffdc1a", "date_published": "2025-02-26", "abstract": "Models of nuclear genome organization often propose a binary division into active  versus inactive compartments yet typically overlook nuclear bodies. Here we  integrated analysis of sequencing and image-based data to compare genome  organization in four human cell types relative to three different nuclear  locales: the nuclear lamina, nuclear speckles, and nucleoli. Whereas gene  expression correlates mostly with nuclear speckle proximity, DNA replication  timing correlates with proximity to multiple nuclear locales. Speckle attachment  regions emerge as DNA replication initiation zones whose replication timing and  gene composition vary with their attachment frequency. Most facultative LADs  retain a partially repressed state as iLADs, despite their positioning in the  nuclear interior. Knock out of two lamina proteins, Lamin A and LBR, causes a  shift of H3K9me3-enriched LADs from lamina to nucleolus, and a reciprocal  relocation of H3K27me3-enriched partially repressed iLADs from nucleolus to  lamina. Thus, these partially repressed iLADs appear to compete with LADs for  nuclear lamina attachment with consequences for replication timing. The nuclear  organization in adherent cells is polarized with nuclear bodies and genomic  regions segregating both radially and relative to the equatorial plane. Together,  our results underscore the importance of considering genome organization relative  to nuclear locales for a more complete understanding of the spatial and  functional organization of the human genome.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"authors": ["Kumar P", "Gholamalamdari O", "Zhang Y", "Zhang L", "Vertii A", "van Schaik T", "Peric-Hupkes D", "Sasaki T", "Gilbert DM", "van Steensel B", "Ma J", "Kaufman PD", "Belmont AS"], "@id": "/publications/22e02dc4-37b9-4891-9084-6d85f6683252/", "journal": "Communications biology", "ID": "PMID:39271748", "title": "Nucleolus and centromere Tyramide Signal Amplification-Seq reveals variable  localization of heterochromatin in different cell types.", "status": "current", "@type": ["Publication", "Item"], "display_title": "Kumar P et al. (2024) PMID:39271748", "uuid": "22e02dc4-37b9-4891-9084-6d85f6683252", "date_published": "2024-09-13", "abstract": "Genome differential positioning within interphase nuclei remains poorly explored.  We extended and validated Tyramide Signal Amplification (TSA)-seq to map genomic  regions near nucleoli and pericentric heterochromatin in four human cell lines.  Our study confirmed that smaller chromosomes localize closer to nucleoli but  further deconvolved this by revealing a preference for chromosome arms below  36-46 Mbp in length. We identified two lamina associated domain subsets through  their differential nuclear lamina versus nucleolar positioning in different cell  lines which showed distinctive patterns of DNA replication timing and gene  expression across all cell lines. Unexpectedly, active, nuclear  speckle-associated genomic regions were found near typically repressive nuclear  compartments, which is attributable to the close proximity of nuclear speckles  and nucleoli in some cell types, and association of centromeres with nuclear  speckles in human embryonic stem cells (hESCs). Our study points to a more  complex and variable nuclear genome organization than suggested by current  models, as revealed by our TSA-seq methodology.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 2, "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSCJG8AVN/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "warning": null, "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "@id": "/badges/gold-biosample/", "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "description": "Gold biosample"}}}]}, "validation-errors": []}