{"lab": {"title": "Andrew Belmont, ILLINOIS", "@id": "/labs/andrew-belmont-lab/", "@type": ["Lab", "Item"], "display_title": "Andrew Belmont, ILLINOIS", "status": "current", "uuid": "b2c2deeb-e883-4ac0-b9e2-906e598884d6", "correspondence": [{"contact_email": "YXNiZWxAaWxsaW5vaXMuZWR1", "@id": "/users/92f90aed-7df1-4bd9-9e74-a472cb50d663/", "display_title": "Andrew Belmont"}], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b2c2deeb-e883-4ac0-b9e2-906e598884d6"]}}, "award": {"status": "current", "@type": ["Award", "Item"], "@id": "/awards/1U54DK107965-01/", "display_title": "COMBINED CYTOLOGICAL, GENOMIC, AND FUNCTIONAL MAPPING OF NUCLEAR GENOME ORGANIZATION", "center_title": "NOFIC - Belmont", "uuid": "91b694c3-f4d7-4ddd-8278-16f94e15c1c5", "description": "NOFIC: Decades of microscopy have revealed that the nucleus is not a homogeneous organelle, but rather consists of distinct compartments such as nucleoli, nuclear speckles, the nuclear lamina, among other structures. Increasing evidence indicates that specific genomic regions each associate with these compartments. This genome compartmentalization has been linked to various functions, but these links are still poorly understood. Interestingly, Lamina Associated Domains (LADs) share specific heterochromatin marks, defining chromatin domains with distinct genetic and epigenetic properties. Genomic regions associating with other nuclear compartments may similarly define distinct classes of chromatin domains. One major bottleneck towards a deeper understanding of nuclear organization has been the inability to convert microscopy views of nuclear compartments into genome-wide maps that show which loci are associated with which compartment, and how the chromosomal fiber traverses between compartments. In addition, there is an urgent need for more efficient methods to dissect the mechanisms by which large genomic regions are targeted to specific nuclear compartments. Finally, there is an urgent need for high-throughput approaches that query the functional relevance of genome compartmentalization. For this Center grant, we propose to meet these needs through the following Aims: 1. Develop a strategy that connects microscopy views to genome-wide maps that, together with modeling, reveal the localization and dynamics of genomic regions relative to all major nuclear compartments. 2. Develop methods for efficient manipulation of the genome in order to elucidate mechanisms that target loci to specific compartments. 3. Develop methods to measure, model, and validate the functional relevance of nuclear compartments. The combined results of these approaches will reveal causal relationships now hidden among entangled genomic, epigenetic, and nuclear organization features. Deliverables of this proposal include a wide range of structural and functional maps of nuclear organization, reagents for visualizing endogenous chromosome loci, a powerful pipeline for synthesis of ~100kb DNA fragments, and cell lines facilitating repeated, high-fidelity insertio of these large fragments back into selected sites in the genome. These resources will provide a powerful complement to other 4D Nucleome Consortium efforts. A key strength of this Center proposal is the experience and complementary research capabilities of its five Investigators. Together they will pool their expertise for a concerted investigation into the biological functions of nuclear compartmentalization.", "project": "4DN", "name": "1U54DK107965-01", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "badges": [{"badge": {"warning": "Replicate Numbers", "title": "Replicate Numbers", "badge_icon": "/static/img/badges/replicates-orange-circle.svg", "uuid": "24a64a84-3c33-4d76-aaf2-e5ef45eff347", "display_title": "Replicate Numbers", "description": "Issues with replicate numbers", "@id": "/badges/replicate-numbers/", "status": "released", "badge_classification": "Warning", "@type": ["Badge", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "messages": ["Replicate set contains only a single biological replicate"]}], "status": "released", "aliases": ["belmont-lab:input-nucleolin-tsa-seq-hct116-conc"], "accession": "4DNES7A6HTEN", "condition": "input - condition2 - conditionC -  anti-Nucleolin", "description": "Set of Input for Nucleolin TSA-seq Reaction Condition C (PBS 50% Sucrose, 1:3000 tyramide biotin) 30 minute reaction on HCT116 cells", "date_created": "2021-11-02T19:42:15.680946+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "TSA-seq Nucleolin in HCT116 cells", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2023-11-07T20:45:26.577680+00:00"}, "public_release": "2023-11-03", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"uuid": "dad8cee3-7563-46ff-8cd6-0104ba9489f4", "display_title": "TSA-seq against NCL protein on HCT116 (Tier 2) - 4DNEXSCA7VQF", "accession": "4DNEXSCA7VQF", "status": "released", "@id": "/experiments-tsaseq/4DNEXSCA7VQF/", "@type": ["ExperimentTsaseq", "Experiment", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "project_release": "2023-11-03", "experiments_in_set": [{"display_title": "TSA-seq against NCL protein on HCT116 (Tier 2) - 4DNEXSCA7VQF", "@id": "/experiments-tsaseq/4DNEXSCA7VQF/", "files": [{"file_size": 1932222122, "file_type": "reads", "uuid": "bc21e17d-f1f5-4afc-a420-6fbeda91bb6d", "href": "/files-fastq/4DNFI9GU6QSD/@@download/4DNFI9GU6QSD.fastq.gz", "accession": "4DNFI9GU6QSD", "@type": ["FileFastq", "File", "Item"], "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/bc21e17d-f1f5-4afc-a420-6fbeda91bb6d/4DNFI9GU6QSD.fastq.gz", "display_title": "4DNFI9GU6QSD.fastq.gz", "file_classification": "raw file", "file_type_detailed": "reads (fastq)", "upload_key": "bc21e17d-f1f5-4afc-a420-6fbeda91bb6d/4DNFI9GU6QSD.fastq.gz", "md5sum": "5b0ed3071b22588ffb6c31da88dddf17", "@id": "/files-fastq/4DNFI9GU6QSD/", "quality_metric": {"display_title": "QualityMetricFastqc from 2021-11-04", "Total Sequences": 40772896, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "4c1fc38b-d218-4606-9a67-af4eadb8c31d", "overall_quality_status": "PASS", "status": "released", "Sequence length": "100", "@id": "/quality-metrics-fastqc/4c1fc38b-d218-4606-9a67-af4eadb8c31d/", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI9GU6QSD/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Andrew Belmont, ILLINOIS", "experiment_type": "TSA-seq", "experiment_bucket": "raw file", "assay_info": "NCL protein", "dataset": "TSA-seq Nucleolin in HCT116 cells", "condition": "input - condition2 - conditionC -  anti-Nucleolin", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Andrew Belmont, ILLINOIS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "lab": {"display_title": "Andrew Belmont, ILLINOIS", "uuid": "b2c2deeb-e883-4ac0-b9e2-906e598884d6", "status": "current", "@id": "/labs/andrew-belmont-lab/", "name": "andrew-belmont-lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b2c2deeb-e883-4ac0-b9e2-906e598884d6"]}}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": []}], "@type": ["ExperimentTsaseq", "Experiment", "Item"], "accession": "4DNEXSCA7VQF", "status": "released", "uuid": "dad8cee3-7563-46ff-8cd6-0104ba9489f4", "biosample": {"biosource_summary": "HCT116 (Tier 2)", "treatments_summary": "None", "modifications_summary": "None", "@type": ["Biosample", "Item"], "accession": "4DNBSKRLQJMM", "uuid": "c368ead3-5eea-4ea6-8a51-458cb8243b8c", "biosample_type": "immortalized cells", "@id": "/biosamples/4DNBSKRLQJMM/", "status": "released", "display_title": "4DNBSKRLQJMM", "biosample_category": ["Tier 2"], "biosource": [{"status": "released", "biosource_type": "immortalized cell line", "accession": "4DNSRMYUIVGD", "display_title": "HCT116 (Tier 2) - 4DNSRMYUIVGD", "cell_line_tier": "Tier 2", "@type": ["Biosource", "Item"], "@id": "/biosources/4DNSRMYUIVGD/", "uuid": "393880ea-f928-406d-a4bf-78435b8975ef", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "cell_line": {"@id": "/ontology-terms/EFO:0002824/", "term_id": "EFO:0002824", "@type": ["OntologyTerm", "Item"], "term_name": "HCT116", "display_title": "HCT116", "uuid": "49d090b2-5326-40ce-9c19-7a214c682272", "status": "released", "synonyms": ["HCT-116 cell", "HCT116 cell"], "preferred_name": "HCT116", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"status": "current", "@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "organism": {"display_title": "H. sapiens", "name": "human", "status": "released", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "scientific_name": "Homo sapiens", "@type": ["Organism", "Item"], "@id": "/organisms/9606/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"display_title": "colon", "uuid": "3e39f551-bc0b-4bee-b932-29d71956fb94", "preferred_name": "colon", "@type": ["OntologyTerm", "Item"], "term_id": "UBERON:0001155", "synonyms": ["large bowel", "posterior intestine"], "term_name": "colon", "status": "released", "@id": "/ontology-terms/UBERON:0001155/", "slim_terms": [{"uuid": "111174bc-8535-4448-903e-854af460a233", "display_title": "large intestine", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0000059/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "111129bc-8535-4448-903e-854af460a233", "display_title": "digestive system", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0001007/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "badges": [{"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": {"badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "display_title": "Gold Biosample", "@type": ["Badge", "Item"], "description": "Gold biosample", "commendation": "Gold Biosample", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "badge_classification": "Commendation", "status": "released", "@id": "/badges/gold-biosample/", "title": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "cell_culture_details": [{"in_vitro_differentiated": "No", "display_title": "BiosampleCellCulture from 2021-11-02", "uuid": "d9c80b67-84db-42fa-b0eb-a5d92d125183", "@id": "/biosample-cell-cultures/d9c80b67-84db-42fa-b0eb-a5d92d125183/", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "tissue_organ_info": {"tissue_source": "colon", "organ_system": ["large intestine", "digestive system"]}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"@id": "/experiment-types/tsa-seq/", "title": "TSA-seq", "assay_subclassification": "Proximity to Cellular Component", "assay_classification": "Linear DNA Enrichment", "status": "released", "display_title": "TSA-seq", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "Proximity-seq", "@type": ["ExperimentType", "Item"], "uuid": "75d7181c-e329-463e-b776-a467433aa4db", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "other_processed_files": [{"type": "preliminary", "title": "Repli-Seq Pipeline - Preliminary Files", "files": [{"file_size": 1833214129, "file_type_detailed": "alignments (bam)", "href": "/files-processed/4DNFI1LCW8JE/@@download/4DNFI1LCW8JE.bam", "@id": "/files-processed/4DNFI1LCW8JE/", "@type": ["FileProcessed", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/0bf32c45-8482-4cfa-ac9b-c473a33c33a1/4DNFI1LCW8JE.bam", "file_type": "alignments", "display_title": "4DNFI1LCW8JE.bam", "accession": "4DNFI1LCW8JE", "md5sum": "2451177ff5537c459320160803f1aa72", "uuid": "0bf32c45-8482-4cfa-ac9b-c473a33c33a1", "status": "released", "genome_assembly": "GRCh38", "contributing_labs": [{"status": "current", "@id": "/labs/andrew-belmont-lab/", "uuid": "b2c2deeb-e883-4ac0-b9e2-906e598884d6", "@type": ["Lab", "Item"], "display_title": "Andrew Belmont, ILLINOIS", "name": "andrew-belmont-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b2c2deeb-e883-4ac0-b9e2-906e598884d6"]}}], "quality_metric": {"status": "released", "overall_quality_status": "PASS", "display_title": "QualityMetricDedupqcRepliseq from 2021-11-17", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "@id": "/quality-metrics-dedupqc-repliseq/0907218c-e761-4bae-abb2-9b49736ef014/", "uuid": "0907218c-e761-4bae-abb2-9b49736ef014", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "36392808", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "14.666", "tooltip": "Percent of total aligned reads (=5.34m)", "numberType": "percent"}]}, "lab": {"@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "status": "current", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "file_format": {"file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Andrew Belmont, ILLINOIS", "experiment_type": "TSA-seq", "experiment_bucket": "Repli-Seq Pipeline - Preliminary Files", "assay_info": "NCL protein", "dataset": "TSA-seq Nucleolin in HCT116 cells", "condition": "input - condition2 - conditionC -  anti-Nucleolin", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "4DN DCIC, HMS"}, "last_modified": {"date_modified": "2024-02-22T17:26:16.622682+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_size": 816143, "file_type_detailed": "normalized counts (bg)", "href": "/files-processed/4DNFIJPTKJDS/@@download/4DNFIJPTKJDS.bedGraph.gz", "@id": "/files-processed/4DNFIJPTKJDS/", "@type": ["FileProcessed", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/9be51d4e-b692-4552-bb8f-d5037c6bf34f/4DNFIJPTKJDS.bedGraph.gz", "file_type": "normalized counts", "display_title": "4DNFIJPTKJDS.bedGraph.gz", "higlass_uid": "0e47c312-b4a3-4bf8-821e-95ef2f1306a2", "accession": "4DNFIJPTKJDS", "md5sum": "e32e2e5280243b9800ff8edce1891500", "uuid": "9be51d4e-b692-4552-bb8f-d5037c6bf34f", "status": "released", "genome_assembly": "GRCh38", "contributing_labs": [{"status": "current", "@id": "/labs/andrew-belmont-lab/", "uuid": "b2c2deeb-e883-4ac0-b9e2-906e598884d6", "@type": ["Lab", "Item"], "display_title": "Andrew Belmont, ILLINOIS", "name": "andrew-belmont-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b2c2deeb-e883-4ac0-b9e2-906e598884d6"]}}], "lab": {"@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "status": "current", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "file_format": {"file_format": "bg", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/bg/", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "bg", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "@id": "/higlass-view-configs/5aa3978c-f8d9-4ea0-8df2-fece843143c2/", "display_title": "4DNFIJPTKJDS - normalized counts for HCT116 (Tier 2) TSA-seq NCL protein", "uuid": "5aa3978c-f8d9-4ea0-8df2-fece843143c2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "track_and_facet_info": {"experimental_lab": "Andrew Belmont, ILLINOIS", "experiment_type": "TSA-seq", "experiment_bucket": "Repli-Seq Pipeline - Preliminary Files", "assay_info": "NCL protein", "dataset": "TSA-seq Nucleolin in HCT116 cells", "condition": "input - condition2 - conditionC -  anti-Nucleolin", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for HCT116 (Tier 2) TSA-seq NCL protein"}, "last_modified": {"date_modified": "2024-02-22T17:47:38.047315+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}], "experiment_categorizer": {"combined": "Target: NCL protein", "field": "Target", "value": "NCL protein"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-11-03T15:41:57.452078+00:00"}, "external_references": []}], "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": {"display_title": "4DNES7A6HTEN - Repli-Seq Pipeline - Preliminary Files", "@id": "/higlass-view-configs/4ade4abc-4048-48d0-9b1e-1402a1f5da61/", "@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "4ade4abc-4048-48d0-9b1e-1402a1f5da61", "description": "Supplementary Files (Repli-Seq Pipeline - Preliminary Files) for 4DNES7A6HTEN (Set of Input for Nucleolin TSA-seq Reaction Condition C (PBS 50% Sucrose, 1:3000 tyramide biotin) 30 minute reaction on HCT116 cells): 4DNFIJPTKJDS", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}, "last_modified": {"date_modified": "2023-11-03T15:41:44.109415+00:00"}}}], "@id": "/experiment-set-replicates/4DNES7A6HTEN/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "dff879d4-928c-4ea0-9387-b1171b3467c6", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNES7A6HTEN", "external_references": [], "produced_in_pub": {"short_attribution": "Kumar P et al. (2023)", "ID": "doi:10.1101/2023.10.29.564613", "status": "current", "@id": "/publications/395f743d-4d9a-49a8-9712-6bd832a66e35/", "uuid": "395f743d-4d9a-49a8-9712-6bd832a66e35", "journal": "bioRxiv : the preprint server for biology", "date_published": "2023-11-01", "url": "https://www.ncbi.nlm.nih.gov/pubmed/37961445", "display_title": "Kumar P et al. (2023) doi:10.1101/2023.10.29.564613", "abstract": "Genome differential positioning within interphase nuclei remains poorly explored.  We extended and validated 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 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.", "@type": ["Publication", "Item"], "title": "Nucleolus and centromere TSA-Seq reveals variable localization of heterochromatin  in different cell types.", "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"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"title": "Nucleolus and centromere TSA-Seq reveals variable localization of heterochromatin  in different cell types.", "display_title": "Kumar P et al. (2023) doi:10.1101/2023.10.29.564613", "date_published": "2023-11-01", "ID": "doi:10.1101/2023.10.29.564613", "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"], "abstract": "Genome differential positioning within interphase nuclei remains poorly explored.  We extended and validated 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 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": "395f743d-4d9a-49a8-9712-6bd832a66e35", "journal": "bioRxiv : the preprint server for biology", "@id": "/publications/395f743d-4d9a-49a8-9712-6bd832a66e35/", "status": "current", "@type": ["Publication", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 1, "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSKRLQJMM/", "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"}}}, {"parent": "/experiment-set-replicates/4DNES7A6HTEN/", "embedded_path": "badges", "item": {"messages": ["Replicate set contains only a single biological replicate"], "badge": {"commendation": null, "warning": "Replicate Numbers", "uuid": "24a64a84-3c33-4d76-aaf2-e5ef45eff347", "@id": "/badges/replicate-numbers/", "badge_icon": "/static/img/badges/replicates-orange-circle.svg", "description": "Issues with replicate numbers"}}}]}, "validation-errors": []}