{"lab": {"uuid": "d7005432-7c8d-4a88-a10b-c0a5dcf2d861", "correspondence": [{"contact_email": "c2w2ODJAY29sdW1iaWEuZWR1", "@id": "/users/472214a6-c8dd-4ac6-9dad-2995905c20ea/", "display_title": "Stavros Lomvardas"}], "display_title": "Stavros Lomvardas, COLUMBIA", "status": "current", "title": "Stavros Lomvardas, COLUMBIA", "@id": "/labs/stavros-lomvardas-lab/", "@type": ["Lab", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.d7005432-7c8d-4a88-a10b-c0a5dcf2d861"]}}, "award": {"@id": "/awards/1U01DA040582-01/", "@type": ["Award", "Item"], "project": "4DN", "description": "NBC: The stochastic and monoallelic expression of one out of a thousand olfactory receptor (OR) genes in mammals is a complex process governed by the spatial compartmentalization of active and silent OR alleles in olfactory sensory neurons (OSNs). During OSN differentiation OR loci from multiple chromosomes converge into distinct, OSN-specific nuclear foci characterized by the hallmarks of constitutive heterochromatin. Absent from these unusual nuclear bodies is the OR allele that is transcriptionally active in each OSN, which typically resides on euchromatic nuclear compartments and is surrounded by numerous enhancer elements recruited from several chromosomes. This intricate network of interchromosomal interactions is responsible for both the robust transcription of the chosen OR allele and the complete silencing of the repressed ones. The extraordinary number of OR family members and the unprecedented extent of long-range genomic interactions that culminate to the remarkable organization of the OR nucleome, make the olfactory system ideal for they study of the molecular principles that organize the mammalian nuclear architecture in vivo. For a comprehensive interrogation of the OR nucleome, we assembled a multidisciplinary team seeking to combine novel genetic manipulations with a one of a kind imaging system, a state of the art proteomics facility, and innovative genomic analyses. With CRISPR, phiC31 integrase and in utero DNA electroporation we will tag OR loci and enhancers, making the OR subgenome accessible by three novel experimental strategies: High resolution imaging by correlated soft X-ray tomography and cryo- SIM; biochemical purification by sequence specific tagging with Halo and APEX followed by sophisticated mass spectrometry; and genomic analysis of long range interactions occurring during OSN differentiation using two different DNA modifying enzymes and single molecule real time sequencing. This ambitious experimental project not only will reveal molecular mechanisms that govern the nuclear organization of OR genes but also generally applicable principles and powerful technologies for the study of the mammalian nucleome in vivo.", "status": "current", "name": "1U01DA040582-01", "uuid": "c7883cb7-0f06-4833-ba75-654d81e1415f", "display_title": "DECIPHERING NUCLEAR BODIES AND COMPARTMENTS THAT GOVERN SINGULAR OLFACTORY RECEPTOR EXPRESSION.", "center_title": "NBC - Lomvardas", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "badges": [{"badge": {"warning": "Replicate Numbers", "badge_classification": "Warning", "@type": ["Badge", "Item"], "display_title": "Replicate Numbers", "uuid": "24a64a84-3c33-4d76-aaf2-e5ef45eff347", "description": "Issues with replicate numbers", "@id": "/badges/replicate-numbers/", "title": "Replicate Numbers", "badge_icon": "/static/img/badges/replicates-orange-circle.svg", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "messages": ["Replicate set contains only a single biological replicate"]}], "status": "released", "aliases": ["lomvardas-lab:rnaseq-on-osn-human-covid134"], "accession": "4DNESFDLC34P", "condition": "SARS-Cov2 infected", "description": "RNA-seq on SARS-Cov2 infected human olfactory epithelium - hOE134", "date_created": "2021-02-16T21:23:09.664442+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "RNA-seq on human olfactory epithelium", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-01-06T15:46:48.595727+00:00"}, "public_release": "2021-03-11", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"@type": ["ExperimentSeq", "Experiment", "Item"], "display_title": "RNA-seq on olfactory epithelium - 4DNEX8UXPBJV", "@id": "/experiments-seq/4DNEX8UXPBJV/", "accession": "4DNEX8UXPBJV", "status": "released", "uuid": "11dba8f0-658b-4139-a4eb-803889fe5faf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_content": [{"content": {"uuid": "a2c014ec-0253-4485-9ade-de48e71971d5", "@id": "/higlass-view-configs/a2c014ec-0253-4485-9ade-de48e71971d5/", "lab": {"@type": ["Lab", "Item"], "display_title": "Stavros Lomvardas, COLUMBIA", "@id": "/labs/stavros-lomvardas-lab/", "uuid": "d7005432-7c8d-4a88-a10b-c0a5dcf2d861", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.d7005432-7c8d-4a88-a10b-c0a5dcf2d861"]}}, "status": "released", "display_title": "4DNESFDLC34P - Processed files", "title": "4DNESFDLC34P - Processed files", "description": "4DNESFDLC34P (RNA-seq on SARS-Cov2 infected human olfactory epithelium - hOE134): 4DNFII8VIOXH, 4DNFIRHT2LW9", "contributing_labs": [], "award": {"uuid": "c7883cb7-0f06-4833-ba75-654d81e1415f", "@id": "/awards/1U01DA040582-01/", "@type": ["Award", "Item"], "display_title": "DECIPHERING NUCLEAR BODIES AND COMPARTMENTS THAT GOVERN SINGULAR OLFACTORY RECEPTOR EXPRESSION.", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "name": "a2c014ec-0253-4485-9ade-de48e71971d5", "@type": ["HiglassViewConfig", "UserContent", "Item"], "filetype": "HiglassViewConfig", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}, "location": "tab:processed-files", "description": "auto_generated_higlass_view_config"}], "project_release": "2021-03-11", "experiments_in_set": [{"@id": "/experiments-seq/4DNEX8UXPBJV/", "display_title": "RNA-seq on olfactory epithelium - 4DNEX8UXPBJV", "@type": ["ExperimentSeq", "Experiment", "Item"], "status": "released", "uuid": "11dba8f0-658b-4139-a4eb-803889fe5faf", "accession": "4DNEX8UXPBJV", "files": [{"accession": "4DNFINQVT2BG", "md5sum": "b94e410adc51af485a98ae4d8a0b52ca", "paired_end": "1", "file_type": "reads", "status": "restricted", "upload_key": "c944908d-716d-4a8f-a968-9cdb924bb962/4DNFINQVT2BG.fastq.gz", "file_type_detailed": "reads (fastq)", "file_size": 2407424835, "href": "/files-fastq/4DNFINQVT2BG/@@download/4DNFINQVT2BG.fastq.gz", "@type": ["FileFastq", "File", "Item"], "uuid": "c944908d-716d-4a8f-a968-9cdb924bb962", "file_classification": "raw file", "@id": "/files-fastq/4DNFINQVT2BG/", "display_title": "4DNFINQVT2BG.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"uuid": "4a55ba7f-4bd1-433b-9a3a-d1dfe6fd1b1c", "accession": "4DNFISE1PG6R", "@type": ["FileFastq", "File", "Item"], "status": "restricted", "paired_end": "2", "file_type": "reads", "@id": "/files-fastq/4DNFISE1PG6R/", "display_title": "4DNFISE1PG6R.fastq.gz", "file_type_detailed": "reads (fastq)", "file_format": {"status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "file_format": "fastq", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"display_title": "QualityMetricFastqc from 2021-02-25", "Sequence length": "35-75", "uuid": "211081ff-9a0a-4058-9ba1-b4926dfb1791", "Total Sequences": 55547579, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFINQVT2BG/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/211081ff-9a0a-4058-9ba1-b4926dfb1791/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "stavros-lomvardas-lab", "@type": ["Lab", "Item"], "@id": "/labs/stavros-lomvardas-lab/", "display_title": "Stavros Lomvardas, COLUMBIA", "status": "current", "uuid": "d7005432-7c8d-4a88-a10b-c0a5dcf2d861", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.d7005432-7c8d-4a88-a10b-c0a5dcf2d861"]}}, "file_format": {"@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Stavros Lomvardas, COLUMBIA", "experiment_type": "RNA-seq", "experiment_bucket": "raw file", "dataset": "RNA-seq on human olfactory epithelium", "condition": "SARS-Cov2 infected", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "olfactory epithelium", "lab_name": "Stavros Lomvardas, COLUMBIA"}}, {"accession": "4DNFISE1PG6R", "md5sum": "2ecab95c2ad9ec209ba6dc436d265904", "paired_end": "2", "file_type": "reads", "status": "restricted", "upload_key": "4a55ba7f-4bd1-433b-9a3a-d1dfe6fd1b1c/4DNFISE1PG6R.fastq.gz", "file_type_detailed": "reads (fastq)", "file_size": 2461298686, "href": "/files-fastq/4DNFISE1PG6R/@@download/4DNFISE1PG6R.fastq.gz", "@type": ["FileFastq", "File", "Item"], "uuid": "4a55ba7f-4bd1-433b-9a3a-d1dfe6fd1b1c", "file_classification": "raw file", "@id": "/files-fastq/4DNFISE1PG6R/", "display_title": "4DNFISE1PG6R.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"uuid": "c944908d-716d-4a8f-a968-9cdb924bb962", "accession": "4DNFINQVT2BG", "@type": ["FileFastq", "File", "Item"], "status": "restricted", "paired_end": "1", "file_type": "reads", "@id": "/files-fastq/4DNFINQVT2BG/", "display_title": "4DNFINQVT2BG.fastq.gz", "file_type_detailed": "reads (fastq)", "file_format": {"status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "file_format": "fastq", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"display_title": "QualityMetricFastqc from 2021-02-25", "Sequence length": "35-75", "uuid": "03da71e5-eca8-4105-b0f8-ecc6e0aafba2", "Total Sequences": 55547579, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFISE1PG6R/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/03da71e5-eca8-4105-b0f8-ecc6e0aafba2/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "stavros-lomvardas-lab", "@type": ["Lab", "Item"], "@id": "/labs/stavros-lomvardas-lab/", "display_title": "Stavros Lomvardas, COLUMBIA", "status": "current", "uuid": "d7005432-7c8d-4a88-a10b-c0a5dcf2d861", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.d7005432-7c8d-4a88-a10b-c0a5dcf2d861"]}}, "file_format": {"@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Stavros Lomvardas, COLUMBIA", "experiment_type": "RNA-seq", "experiment_bucket": "raw file", "dataset": "RNA-seq on human olfactory epithelium", "condition": "SARS-Cov2 infected", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "olfactory epithelium", "lab_name": "Stavros Lomvardas, COLUMBIA"}}, {"accession": "4DNFIZLQKU8F", "md5sum": "9b29926065f1798a10102a2e35feeffc", "paired_end": "1", "file_type": "reads", "status": "restricted", "upload_key": "8959cb02-5295-46a1-800e-8ec04a1aef7b/4DNFIZLQKU8F.fastq.gz", "file_type_detailed": "reads (fastq)", "file_size": 3058927054, "href": "/files-fastq/4DNFIZLQKU8F/@@download/4DNFIZLQKU8F.fastq.gz", "@type": ["FileFastq", "File", "Item"], "uuid": "8959cb02-5295-46a1-800e-8ec04a1aef7b", "file_classification": "raw file", "@id": "/files-fastq/4DNFIZLQKU8F/", "display_title": "4DNFIZLQKU8F.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"uuid": "fa7e113d-f957-46c5-bd47-c9d0dcb57d7a", "accession": "4DNFID2CBS45", "@type": ["FileFastq", "File", "Item"], "status": "restricted", "paired_end": "2", "file_type": "reads", "@id": "/files-fastq/4DNFID2CBS45/", "display_title": "4DNFID2CBS45.fastq.gz", "file_type_detailed": "reads (fastq)", "file_format": {"status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "file_format": "fastq", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"display_title": "QualityMetricFastqc from 2021-02-25", "Sequence length": "35-75", "uuid": "1e0c1032-30ac-4863-b3c6-2e9d436e60bb", "Total Sequences": 67815416, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIZLQKU8F/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/1e0c1032-30ac-4863-b3c6-2e9d436e60bb/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "stavros-lomvardas-lab", "@type": ["Lab", "Item"], "@id": "/labs/stavros-lomvardas-lab/", "display_title": "Stavros Lomvardas, COLUMBIA", "status": "current", "uuid": "d7005432-7c8d-4a88-a10b-c0a5dcf2d861", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.d7005432-7c8d-4a88-a10b-c0a5dcf2d861"]}}, "file_format": {"@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Stavros Lomvardas, COLUMBIA", "experiment_type": "RNA-seq", "experiment_bucket": "raw file", "dataset": "RNA-seq on human olfactory epithelium", "condition": "SARS-Cov2 infected", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "olfactory epithelium", "lab_name": "Stavros Lomvardas, COLUMBIA"}}, {"accession": "4DNFID2CBS45", "md5sum": "519310a63ed9467727d7ba842995bb81", "paired_end": "2", "file_type": "reads", "status": "restricted", "upload_key": "fa7e113d-f957-46c5-bd47-c9d0dcb57d7a/4DNFID2CBS45.fastq.gz", "file_type_detailed": "reads (fastq)", "file_size": 3134507044, "href": "/files-fastq/4DNFID2CBS45/@@download/4DNFID2CBS45.fastq.gz", "@type": ["FileFastq", "File", "Item"], "uuid": "fa7e113d-f957-46c5-bd47-c9d0dcb57d7a", "file_classification": "raw file", "@id": "/files-fastq/4DNFID2CBS45/", "display_title": "4DNFID2CBS45.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"uuid": "8959cb02-5295-46a1-800e-8ec04a1aef7b", "accession": "4DNFIZLQKU8F", "@type": ["FileFastq", "File", "Item"], "status": "restricted", "paired_end": "1", "file_type": "reads", "@id": "/files-fastq/4DNFIZLQKU8F/", "display_title": "4DNFIZLQKU8F.fastq.gz", "file_type_detailed": "reads (fastq)", "file_format": {"status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "file_format": "fastq", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"display_title": "QualityMetricFastqc from 2021-02-25", "Sequence length": "35-75", "uuid": "97a5c217-90f1-40f3-bd27-744371e72ca7", "Total Sequences": 67815416, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFID2CBS45/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/97a5c217-90f1-40f3-bd27-744371e72ca7/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "stavros-lomvardas-lab", "@type": ["Lab", "Item"], "@id": "/labs/stavros-lomvardas-lab/", "display_title": "Stavros Lomvardas, COLUMBIA", "status": "current", "uuid": "d7005432-7c8d-4a88-a10b-c0a5dcf2d861", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.d7005432-7c8d-4a88-a10b-c0a5dcf2d861"]}}, "file_format": {"@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Stavros Lomvardas, COLUMBIA", "experiment_type": "RNA-seq", "experiment_bucket": "raw file", "dataset": "RNA-seq on human olfactory epithelium", "condition": "SARS-Cov2 infected", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "olfactory epithelium", "lab_name": "Stavros Lomvardas, COLUMBIA"}}], "biosample": {"display_title": "4DNBS8EZCNHP", "treatments_summary": "None", "accession": "4DNBS8EZCNHP", "uuid": "64a8e500-219d-4103-ac0f-bacf7c9b8c93", "status": "released", "biosample_type": "tissue", "biosample_category": ["Multicellular Tissue"], "@id": "/biosamples/4DNBS8EZCNHP/", "@type": ["Biosample", "Item"], "biosource_summary": "olfactory epithelium", "modifications_summary": "None", "tissue_organ_info": {"organ_system": ["nose", "endoderm", "olfactory organ", "peripheral nervous system", "respiratory system", "sensory system", "ectoderm"], "tissue_source": "olfactory epithelium"}, "biosource": [{"accession": "4DNSRDDDF18N", "@id": "/biosources/4DNSRDDDF18N/", "display_title": "olfactory epithelium - 4DNSRDDDF18N", "status": "released", "uuid": "14456b79-33a6-4504-a020-2bad9e6ddd10", "biosource_type": "tissue", "cell_line_tier": "Unclassified", "@type": ["Biosource", "Item"], "tissue": {"term_name": "olfactory epithelium", "display_title": "olfactory epithelium", "term_id": "UBERON:0001997", "synonyms": ["olfactory membrane", "main olfactory epithelium", "sensory olfactory epithelium", "olfactory sensory epithelium", "nasal cavity olfactory epithelium"], "status": "released", "uuid": "9fa0e2b1-15fc-42a2-95ac-422bd8892386", "preferred_name": "olfactory epithelium", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0001997/", "slim_terms": [{"@type": ["OntologyTerm", "Item"], "uuid": "111159bc-8535-4448-903e-854af460a233", "display_title": "nose", "status": "released", "@id": "/ontology-terms/UBERON:0000004/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "uuid": "111121bc-8535-4448-903e-854af460a233", "display_title": "endoderm", "status": "released", "@id": "/ontology-terms/UBERON:0000925/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "uuid": "111161bc-8535-4448-903e-854af460a233", "display_title": "olfactory organ", "status": "released", "@id": "/ontology-terms/UBERON:0002268/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "uuid": "111137bc-8535-4448-903e-854af460a233", "display_title": "peripheral nervous system", "status": "released", "@id": "/ontology-terms/UBERON:0000010/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "uuid": "111128bc-8535-4448-903e-854af460a233", "display_title": "respiratory system", "status": "released", "@id": "/ontology-terms/UBERON:0001004/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "uuid": "111135bc-8535-4448-903e-854af460a233", "display_title": "sensory system", "status": "released", "@id": "/ontology-terms/UBERON:0001032/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "uuid": "111119bc-8535-4448-903e-854af460a233", "display_title": "ectoderm", "status": "released", "@id": "/ontology-terms/UBERON:0000924/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"scientific_name": "Homo sapiens", "@id": "/organisms/9606/", "@type": ["Organism", "Item"], "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "status": "released", "name": "human", "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": [{"uuid": "b45dfdc8-1bf1-43ef-9385-7272e2c5b23f", "file_type": "read positions", "file_type_detailed": "read positions (bam)", "status": "restricted", "file_size": 11265302528, "upload_key": "b45dfdc8-1bf1-43ef-9385-7272e2c5b23f/4DNFITF7NRRN.bam", "@id": "/files-processed/4DNFITF7NRRN/", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFITF7NRRN", "file_classification": "processed file", "href": "/files-processed/4DNFITF7NRRN/@@download/4DNFITF7NRRN.bam", "file_format": {"display_title": "bam", "status": "released", "@id": "/file-formats/bam/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "c8eff5e6edd4fdd508fdc9252f7fd95f", "genome_assembly": "GRCh38", "display_title": "4DNFITF7NRRN.bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "status": "current", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"name": "stavros-lomvardas-lab", "@id": "/labs/stavros-lomvardas-lab/", "status": "current", "@type": ["Lab", "Item"], "display_title": "Stavros Lomvardas, COLUMBIA", "uuid": "d7005432-7c8d-4a88-a10b-c0a5dcf2d861", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.d7005432-7c8d-4a88-a10b-c0a5dcf2d861"]}}], "last_modified": {"date_modified": "2021-12-17T16:28:28.204811+00:00"}, "quality_metric": {"display_title": "QualityMetricRnaseq from 2021-03-04", "@id": "/quality-metrics-rnaseq/c6d9f91b-b037-411d-b5d7-4a4370d0c351/", "overall_quality_status": "PASS", "@type": ["QualityMetricRnaseq", "QualityMetric", "Item"], "status": "released", "uuid": "c6d9f91b-b037-411d-b5d7-4a4370d0c351", "quality_metric_summary": [{"title": "Total mapped reads (genome)", "value": "117110483", "numberType": "integer"}, {"title": "Total uniquely mapped reads (genome)", "value": "33011132", "numberType": "integer"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Stavros Lomvardas, COLUMBIA", "experiment_type": "RNA-seq", "experiment_bucket": "processed file", "dataset": "RNA-seq on human olfactory epithelium", "condition": "SARS-Cov2 infected", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "olfactory epithelium", "lab_name": "4DN DCIC, HMS"}}, {"higlass_uid": "9543e32c-3dd8-4046-8bc7-65191e7d4be6", "uuid": "b3bf443e-27a8-43be-8c1d-6f3e6d646d4d", "file_type": "read counts (plus)", "file_type_detailed": "read counts (plus) (bw)", "status": "released", "file_size": 190498360, "upload_key": "b3bf443e-27a8-43be-8c1d-6f3e6d646d4d/4DNFII8VIOXH.bw", "@id": "/files-processed/4DNFII8VIOXH/", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFII8VIOXH", "file_classification": "processed file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/b3bf443e-27a8-43be-8c1d-6f3e6d646d4d/4DNFII8VIOXH.bw", "href": "/files-processed/4DNFII8VIOXH/@@download/4DNFII8VIOXH.bw", "file_format": {"display_title": "bw", "status": "released", "@id": "/file-formats/bw/", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "8e5d053a662b07f28abb54529ba251fd", "genome_assembly": "GRCh38", "display_title": "4DNFII8VIOXH.bw", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "status": "current", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"name": "stavros-lomvardas-lab", "@id": "/labs/stavros-lomvardas-lab/", "status": "current", "@type": ["Lab", "Item"], "display_title": "Stavros Lomvardas, COLUMBIA", "uuid": "d7005432-7c8d-4a88-a10b-c0a5dcf2d861", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.d7005432-7c8d-4a88-a10b-c0a5dcf2d861"]}}], "last_modified": {"date_modified": "2022-01-06T15:46:46.850564+00:00"}, "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"status": "released", "display_title": "4DNFII8VIOXH - read counts (plus) for olfactory epithelium RNA-seq", "uuid": "0d4d6f4a-4530-418d-9206-eedcb494228c", "@type": ["HiglassViewConfig", "UserContent", "Item"], "@id": "/higlass-view-configs/0d4d6f4a-4530-418d-9206-eedcb494228c/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "external_references": [], "track_and_facet_info": {"experimental_lab": "Stavros Lomvardas, COLUMBIA", "experiment_type": "RNA-seq", "experiment_bucket": "processed file", "dataset": "RNA-seq on human olfactory epithelium", "condition": "SARS-Cov2 infected", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "olfactory epithelium", "lab_name": "4DN DCIC, HMS", "track_title": "read counts (plus) for olfactory epithelium RNA-seq"}}, {"higlass_uid": "734f701c-2e1b-4b97-ac5b-2ab26c0b1377", "uuid": "9a10ee00-5c75-4388-931e-d6014f26d196", "file_type": "read counts (minus)", "file_type_detailed": "read counts (minus) (bw)", "status": "released", "file_size": 183711838, "upload_key": "9a10ee00-5c75-4388-931e-d6014f26d196/4DNFIRHT2LW9.bw", "@id": "/files-processed/4DNFIRHT2LW9/", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIRHT2LW9", "file_classification": "processed file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/9a10ee00-5c75-4388-931e-d6014f26d196/4DNFIRHT2LW9.bw", "href": "/files-processed/4DNFIRHT2LW9/@@download/4DNFIRHT2LW9.bw", "file_format": {"display_title": "bw", "status": "released", "@id": "/file-formats/bw/", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "84127256a59c7932ea07db7ebddd764c", "genome_assembly": "GRCh38", "display_title": "4DNFIRHT2LW9.bw", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "status": "current", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"name": "stavros-lomvardas-lab", "@id": "/labs/stavros-lomvardas-lab/", "status": "current", "@type": ["Lab", "Item"], "display_title": "Stavros Lomvardas, COLUMBIA", "uuid": "d7005432-7c8d-4a88-a10b-c0a5dcf2d861", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.d7005432-7c8d-4a88-a10b-c0a5dcf2d861"]}}], "last_modified": {"date_modified": "2022-01-06T15:46:45.270977+00:00"}, "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"status": "released", "display_title": "4DNFIRHT2LW9 - read counts (minus) for olfactory epithelium RNA-seq", "uuid": "f2da17bd-ca70-4e14-aea7-a6662be15806", "@type": ["HiglassViewConfig", "UserContent", "Item"], "@id": "/higlass-view-configs/f2da17bd-ca70-4e14-aea7-a6662be15806/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "external_references": [], "track_and_facet_info": {"experimental_lab": "Stavros Lomvardas, COLUMBIA", "experiment_type": "RNA-seq", "experiment_bucket": "processed file", "dataset": "RNA-seq on human olfactory epithelium", "condition": "SARS-Cov2 infected", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "olfactory epithelium", "lab_name": "4DN DCIC, HMS", "track_title": "read counts (minus) for olfactory epithelium RNA-seq"}}, {"uuid": "9a992cc7-fbec-4cad-855c-ee704fd3ccd8", "file_type": "gene expression", "file_type_detailed": "gene expression (tsv)", "status": "released", "file_size": 11044060, "upload_key": "9a992cc7-fbec-4cad-855c-ee704fd3ccd8/4DNFIFU74RC3.tsv", "@id": "/files-processed/4DNFIFU74RC3/", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIFU74RC3", "file_classification": "processed file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/9a992cc7-fbec-4cad-855c-ee704fd3ccd8/4DNFIFU74RC3.tsv", "href": "/files-processed/4DNFIFU74RC3/@@download/4DNFIFU74RC3.tsv", "file_format": {"display_title": "tsv", "status": "released", "@id": "/file-formats/tsv/", "uuid": "5e8f64b8-6323-410a-8af2-05aba0472f8e", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "ad665be34a9654454593466fe3b3fe09", "genome_assembly": "GRCh38", "display_title": "4DNFIFU74RC3.tsv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "status": "current", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"name": "stavros-lomvardas-lab", "@id": "/labs/stavros-lomvardas-lab/", "status": "current", "@type": ["Lab", "Item"], "display_title": "Stavros Lomvardas, COLUMBIA", "uuid": "d7005432-7c8d-4a88-a10b-c0a5dcf2d861", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.d7005432-7c8d-4a88-a10b-c0a5dcf2d861"]}}], "last_modified": {"date_modified": "2022-01-06T15:26:40.242881+00:00"}, "quality_metric": {"display_title": "QualityMetricRnaseq from 2021-03-04", "@id": "/quality-metrics-rnaseq/b163ba6d-ca86-46cf-8567-5b4303eef34d/", "overall_quality_status": "PASS", "@type": ["QualityMetricRnaseq", "QualityMetric", "Item"], "status": "released", "uuid": "b163ba6d-ca86-46cf-8567-5b4303eef34d", "quality_metric_summary": [{"title": "Reads mapped to protein-coding genes", "value": "17506602", "numberType": "integer"}, {"title": "Reads mapped to rRNA", "value": "73668", "numberType": "integer"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Stavros Lomvardas, COLUMBIA", "experiment_type": "RNA-seq", "experiment_bucket": "processed file", "dataset": "RNA-seq on human olfactory epithelium", "condition": "SARS-Cov2 infected", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "olfactory epithelium", "lab_name": "4DN DCIC, HMS"}}, {"uuid": "bc408de3-59f0-4781-b51d-baff40e2d819", "file_type": "isoform expression", "file_type_detailed": "isoform expression (tsv)", "status": "released", "file_size": 31489369, "upload_key": "bc408de3-59f0-4781-b51d-baff40e2d819/4DNFIJ7FK83E.tsv", "@id": "/files-processed/4DNFIJ7FK83E/", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIJ7FK83E", "file_classification": "processed file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/bc408de3-59f0-4781-b51d-baff40e2d819/4DNFIJ7FK83E.tsv", "href": "/files-processed/4DNFIJ7FK83E/@@download/4DNFIJ7FK83E.tsv", "file_format": {"display_title": "tsv", "status": "released", "@id": "/file-formats/tsv/", "uuid": "5e8f64b8-6323-410a-8af2-05aba0472f8e", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "97dc456efb493a484fdb1a2c213fa30b", "genome_assembly": "GRCh38", "display_title": "4DNFIJ7FK83E.tsv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "status": "current", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"name": "stavros-lomvardas-lab", "@id": "/labs/stavros-lomvardas-lab/", "status": "current", "@type": ["Lab", "Item"], "display_title": "Stavros Lomvardas, COLUMBIA", "uuid": "d7005432-7c8d-4a88-a10b-c0a5dcf2d861", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.d7005432-7c8d-4a88-a10b-c0a5dcf2d861"]}}], "last_modified": {"date_modified": "2022-01-06T15:26:30.821858+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Stavros Lomvardas, COLUMBIA", "experiment_type": "RNA-seq", "experiment_bucket": "processed file", "dataset": "RNA-seq on human olfactory epithelium", "condition": "SARS-Cov2 infected", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "olfactory epithelium", "lab_name": "4DN DCIC, HMS"}}], "experiment_type": {"display_title": "RNA-seq", "@id": "/experiment-types/rna-seq/", "title": "RNA-seq", "uuid": "19f848e6-7c52-4b8b-8aa8-e82ea0a968ce", "assay_subclass_short": "Transcription", "assay_classification": "RNA Quantification", "assay_subclassification": "Transcription", "experiment_category": "Sequencing", "status": "released", "other_tags": ["1D"], "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Default"}, "last_modified": {"date_modified": "2021-03-11T22:30:11.662463+00:00"}, "external_references": []}], "experimentset_type": "replicate", "completed_processes": ["ENCODE_RNAseq_Pipeline_1.1"], "@id": "/experiment-set-replicates/4DNESFDLC34P/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "1c5de528-273e-4483-9a3f-a279061be8ed", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNESFDLC34P", "external_references": [], "produced_in_pub": {"authors": ["Zazhytska M", "Kodra A", "Hoagland DA", "Fullard JF", "Shayya H", "Omer A", "Firestein S", "Gong Q", "Canoll PD", "Goldman JE", "Roussos P", "tenOever BR", "Overdevest JB", "Lomvardas S"], "@type": ["Publication", "Item"], "journal": "bioRxiv : the preprint server for biology", "abstract": "Olfaction relies on a coordinated partnership between odorant flow and neuronal communication. Disruption in our ability to detect odors, or anosmia, has emerged as a hallmark symptom of infection with SARS-CoV-2, yet the mechanism behind this abrupt sensory deficit remains elusive. Here, using molecular evaluation of human olfactory epithelium (OE) from subjects succumbing to COVID-19 and a hamster model of SARS-CoV-2 infection, we discovered widespread downregulation of olfactory receptors (ORs) as well as key components of their signaling pathway. OR downregulation likely represents a non-cell autonomous effect, since SARS-CoV-2 detection in OSNs is extremely rare both in human and hamster OEs. A likely explanation for the reduction of OR transcription is the striking reorganization of nuclear architecture observed in the OSN lineage, which disrupts multi-chromosomal compartments regulating OR expression in humans and hamsters. Our experiments uncover a novel molecular mechanism by which a virus with a very selective tropism can elicit persistent transcriptional changes in cells that evade it, contributing to the severity of COVID-19.", "display_title": "Zazhytska M et al. (2021) doi:10.1101/2021.02.09.430314", "url": "https://www.ncbi.nlm.nih.gov/pubmed/33594368", "status": "current", "date_published": "2021-02-09", "@id": "/publications/14aefcd7-cec0-49b5-904f-851a9a1466f8/", "uuid": "14aefcd7-cec0-49b5-904f-851a9a1466f8", "ID": "doi:10.1101/2021.02.09.430314", "title": "Disruption of nuclear architecture as a cause of COVID-19 induced anosmia.", "short_attribution": "Zazhytska M et al. (2021)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"abstract": "Olfaction relies on a coordinated partnership between odorant flow and neuronal communication. Disruption in our ability to detect odors, or anosmia, has emerged as a hallmark symptom of infection with SARS-CoV-2, yet the mechanism behind this abrupt sensory deficit remains elusive. Here, using molecular evaluation of human olfactory epithelium (OE) from subjects succumbing to COVID-19 and a hamster model of SARS-CoV-2 infection, we discovered widespread downregulation of olfactory receptors (ORs) as well as key components of their signaling pathway. OR downregulation likely represents a non-cell autonomous effect, since SARS-CoV-2 detection in OSNs is extremely rare both in human and hamster OEs. A likely explanation for the reduction of OR transcription is the striking reorganization of nuclear architecture observed in the OSN lineage, which disrupts multi-chromosomal compartments regulating OR expression in humans and hamsters. Our experiments uncover a novel molecular mechanism by which a virus with a very selective tropism can elicit persistent transcriptional changes in cells that evade it, contributing to the severity of COVID-19.", "@id": "/publications/14aefcd7-cec0-49b5-904f-851a9a1466f8/", "ID": "doi:10.1101/2021.02.09.430314", "@type": ["Publication", "Item"], "uuid": "14aefcd7-cec0-49b5-904f-851a9a1466f8", "display_title": "Zazhytska M et al. (2021) doi:10.1101/2021.02.09.430314", "title": "Disruption of nuclear architecture as a cause of COVID-19 induced anosmia.", "authors": ["Zazhytska M", "Kodra A", "Hoagland DA", "Fullard JF", "Shayya H", "Omer A", "Firestein S", "Gong Q", "Canoll PD", "Goldman JE", "Roussos P", "tenOever BR", "Overdevest JB", "Lomvardas S"], "status": "current", "journal": "bioRxiv : the preprint server for biology", "date_published": "2021-02-09", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 1, "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/experiment-set-replicates/4DNESFDLC34P/", "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": []}