{"lab": {"title": "Yijun Ruan, JAX", "display_title": "Yijun Ruan, JAX", "@id": "/labs/yijun-ruan-lab/", "correspondence": [{"contact_email": "eWlqdW4ucnVhbkBqYXgub3Jn", "@id": "/users/d8ac229e-ec08-4411-be38-dc779520ea62/", "display_title": "Yijun Ruan"}], "status": "current", "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "@type": ["Lab", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "award": {"@type": ["Award", "Item"], "status": "current", "@id": "/awards/1U54DK107967-01/", "uuid": "029a2578-43dc-4343-8f41-694518cce304", "display_title": "NUCLEOME POSITIONING SYSTEM FOR SPATIOTEMPORAL GENOME ORGANIZATION AND REGULATION", "center_title": "NOFIC - Ruan", "description": "NOFIC: This proposal seeks to fulfill a community need for a comprehensive, high-resolution genome-mapping platform that will enable investigation of the structural, functional and spatiotemporal organization of the human genome. Our ultimate goal is to deliver complex chromatin interaction network maps in the context of 3D genome structures from which the dynamics of individual genomic elements can be monitored and referenced. Here, we propose to develop a Nucleome Positioning System (NPS)-comprised of 1) a robust genome- wide mapping technology platform, 2) advanced computational modeling algorithms and 3) state-of-the-art nuclear imaging methods-that will allow users community-wide to uncover the regulatory functions of 3D genome organization in human cells. NPS will be based upon the established ChIA-PET method (1,2), enhanced by process optimizations-i.e., microfluidic-based miniaturization and Tn5-transposase-based library preparation-to facilitate the study of chromatin interactions mediated by protein factors across a broader range of human cell types (Aim 1, see also Mapping Technology Development Component). We will also optimize RICh-PET for the comprehensive mapping of chromatin interactions mediated by non-coding RNAs (Aim 1). The high-quality mapping data generated through these optimization efforts will be analyzed by a new computational platform (Three-Dimensional Nucleome Modeling Engine, or 3D-NOME) that makes use of hierarchical multi-scaling to model 3D genome structures (Aim 2, Data Analysis and Modeling component). We will also complement the 3D modeling with transcriptome, epigenome and SNP data associated with genetic diseases (GWAS) to provide functional annotation to structural units (Aim 2). We will continue by developing strategies to validate the nucleome geometry predicted by 3D-NOME both structurally, using new nuclear imaging technologies, and functionally, using cutting-edge genome- and epigenome-editing approaches, in both human cell lines and mouse models (Aim 3, Biological Validation Component). Finally, we will implement NPS to generate pilot 3D genome maps from a wide range of human cell lines and primary immune cells sorted from whole blood, to elucidate the spatiotemporal dynamics of human genome organization over major developmental and hematopoietic cell lineages, as well as among differentiating lymphocytes involved in the immune response (Aim 4, Data Generation Component). Together, these efforts will yield a powerful set of sophisticated, high-quality tools and mapping data for the larger research community, and will help establish the standards for future 3D/4D nucleome studies. They will also provide insights into the broad mechanisms that organize the structure and regulate the function of the human genome, as well as the specific mechanisms by which immune responses are regulated at the nuclear level.", "name": "1U54DK107967-01", "project": "4DN", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "badges": [{"badge": {"badge_icon": "/static/img/badges/replicates-orange-circle.svg", "display_title": "Replicate Numbers", "uuid": "24a64a84-3c33-4d76-aaf2-e5ef45eff347", "warning": "Replicate Numbers", "description": "Issues with replicate numbers", "badge_classification": "Warning", "@id": "/badges/replicate-numbers/", "status": "released", "title": "Replicate Numbers", "@type": ["Badge", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "messages": ["Replicate set contains only a single biological replicate"]}], "status": "released", "aliases": ["ruan-lab:expset_chia-pet_GM12878_RNAPII_ActinomycinD-24h"], "accession": "4DNESBYJGIDU", "condition": "RNAII antibody, ActinomycinD-24h", "description": "in situ ChIA-PET in GM12878 using RNAPII antibody, ActinomycinD-24h", "date_created": "2024-06-28T15:29:38.980522+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "in situ ChIA-PET in GM12878 cell line, ActinomycinD-24h", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-10-21T16:46:47.759826+00:00"}, "public_release": "2024-10-21", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"@type": ["ExperimentChiapet", "Experiment", "Item"], "status": "released", "accession": "4DNEXUNAXTJJ", "@id": "/experiments-chiapet/4DNEXUNAXTJJ/", "display_title": "in situ ChIA-PET against RNA Pol II on GM12878 - 4DNEXUNAXTJJ", "uuid": "d4f8e746-155f-43c3-91e3-5b916461a702", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "project_release": "2024-10-21", "experiments_in_set": [{"files": [{"md5sum": "9e677c79b87a6f5ef85f3166cd8249bb", "file_type_detailed": "reads (fastq)", "status": "released", "uuid": "652e1ecc-036c-48df-ad37-9865aaba1b00", "file_classification": "raw file", "upload_key": "652e1ecc-036c-48df-ad37-9865aaba1b00/4DNFIO8129KX.fastq.gz", "accession": "4DNFIO8129KX", "display_title": "4DNFIO8129KX.fastq.gz", "href": "/files-fastq/4DNFIO8129KX/@@download/4DNFIO8129KX.fastq.gz", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "file_size": 30344319105, "paired_end": "1", "@id": "/files-fastq/4DNFIO8129KX/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/652e1ecc-036c-48df-ad37-9865aaba1b00/4DNFIO8129KX.fastq.gz", "dbxrefs": ["SRA:SRR12762226"], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/a0c0fee7-9266-4127-8202-ff386eaa3710/", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIO8129KX/fastqc_report.html", "Sequence length": "151", "status": "released", "uuid": "a0c0fee7-9266-4127-8202-ff386eaa3710", "Total Sequences": 356152208, "display_title": "QualityMetricFastqc from 2024-08-08", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Yijun Ruan, JAX", "experiment_type": "in situ ChIA-PET", "experiment_bucket": "raw file", "assay_info": "RNA Pol II", "dataset": "in situ ChIA-PET in GM12878 cell line, ActinomycinD-24h", "condition": "RNAII antibody, ActinomycinD-24h", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "GM12878", "lab_name": "Yijun Ruan, JAX"}, "lab": {"display_title": "Yijun Ruan, JAX", "@id": "/labs/yijun-ruan-lab/", "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "name": "yijun-ruan-lab", "@type": ["Lab", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "display_title": "4DNFIYCYQHMV.fastq.gz", "@id": "/files-fastq/4DNFIYCYQHMV/", "accession": "4DNFIYCYQHMV", "uuid": "f44f6977-bc6a-43eb-873d-03da5425b88a", "file_type": "reads", "status": "released", "@type": ["FileFastq", "File", "Item"], "paired_end": "2", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "display_title": "fastq", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "SRA:SRR12762226", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR12762226"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "82025dc2c338f7d113951e5d7fa84da6", "file_type_detailed": "reads (fastq)", "status": "released", "uuid": "f44f6977-bc6a-43eb-873d-03da5425b88a", "file_classification": "raw file", "upload_key": "f44f6977-bc6a-43eb-873d-03da5425b88a/4DNFIYCYQHMV.fastq.gz", "accession": "4DNFIYCYQHMV", "display_title": "4DNFIYCYQHMV.fastq.gz", "href": "/files-fastq/4DNFIYCYQHMV/@@download/4DNFIYCYQHMV.fastq.gz", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "file_size": 34646161866, "paired_end": "2", "@id": "/files-fastq/4DNFIYCYQHMV/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/f44f6977-bc6a-43eb-873d-03da5425b88a/4DNFIYCYQHMV.fastq.gz", "dbxrefs": ["SRA:SRR12762226"], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/ffb18ebc-a8a6-4e2a-8d41-e79d939462f9/", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIYCYQHMV/fastqc_report.html", "Sequence length": "151", "status": "released", "uuid": "ffb18ebc-a8a6-4e2a-8d41-e79d939462f9", "Total Sequences": 356152208, "display_title": "QualityMetricFastqc from 2024-08-05", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Yijun Ruan, JAX", "experiment_type": "in situ ChIA-PET", "experiment_bucket": "raw file", "assay_info": "RNA Pol II", "dataset": "in situ ChIA-PET in GM12878 cell line, ActinomycinD-24h", "condition": "RNAII antibody, ActinomycinD-24h", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "GM12878", "lab_name": "Yijun Ruan, JAX"}, "lab": {"display_title": "Yijun Ruan, JAX", "@id": "/labs/yijun-ruan-lab/", "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "name": "yijun-ruan-lab", "@type": ["Lab", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "display_title": "4DNFIO8129KX.fastq.gz", "@id": "/files-fastq/4DNFIO8129KX/", "accession": "4DNFIO8129KX", "uuid": "652e1ecc-036c-48df-ad37-9865aaba1b00", "file_type": "reads", "status": "released", "@type": ["FileFastq", "File", "Item"], "paired_end": "1", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "display_title": "fastq", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "SRA:SRR12762226", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR12762226"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-chiapet/4DNEXUNAXTJJ/", "uuid": "d4f8e746-155f-43c3-91e3-5b916461a702", "crosslinking_method": "1% Formaldehyde", "status": "released", "display_title": "in situ ChIA-PET against RNA Pol II on GM12878 - 4DNEXUNAXTJJ", "@type": ["ExperimentChiapet", "Experiment", "Item"], "accession": "4DNEXUNAXTJJ", "dbxrefs": ["GEO:GSM5983404", "GEO:SRX14660851"], "biosample": {"treatments_summary": "Chemical (24.0h)", "biosource_summary": "GM12878", "accession": "4DNBSCX7THPV", "biosample_type": "immortalized cells", "biosample_category": ["GM12878", "1000 genomes/Hap Map"], "uuid": "3602ff87-c8b6-45f7-b2af-8ee11e8f05fd", "@id": "/biosamples/4DNBSCX7THPV/", "modifications_summary": "None", "display_title": "4DNBSCX7THPV", "@type": ["Biosample", "Item"], "status": "released", "biosource": [{"biosource_type": "immortalized cell line", "cell_line_tier": "Unclassified", "@type": ["Biosource", "Item"], "@id": "/biosources/4DNSRVYYPJRX/", "uuid": "b1963bed-6a69-427d-9cd6-4cc2a07de075", "status": "released", "accession": "4DNSRVYYPJRX", "display_title": "GM12878 - 4DNSRVYYPJRX", "cell_line": {"uuid": "b9668b9a-be39-47de-8eab-5bf1b0854417", "status": "released", "display_title": "GM12878", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/EFO:0002784/", "term_name": "GM12878", "term_id": "EFO:0002784", "preferred_name": "GM12878", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "status": "current", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "tissue": {"preferred_name": "B-lymphocyte", "term_id": "CL:0000945", "@type": ["OntologyTerm", "Item"], "display_title": "B-lymphocyte", "@id": "/ontology-terms/CL:0000945/", "uuid": "0c98ef0b-9a03-43f3-b409-fb091e62e2f8", "status": "released", "term_name": "lymphocyte of B lineage", "slim_terms": [{"status": "released", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "@id": "/ontology-terms/UBERON:0002405/", "@type": ["OntologyTerm", "Item"], "display_title": "immune system", "uuid": "111133bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "current", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"status": "released", "display_title": "H. sapiens", "@id": "/organisms/9606/", "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "name": "human", "@type": ["Organism", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample missing Cell Culture Details"], "badge": {"uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "title": "Biosample Metadata Incomplete", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "status": "released", "@type": ["Badge", "Item"], "badge_classification": "Warning", "display_title": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "warning": "Biosample Metadata Incomplete", "badge_icon": "/static/img/badges/biosample-icon.svg", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "treatments": [{"display_title": "Chemical (24.0h)", "@type": ["TreatmentAgent", "Treatment", "Item"], "@id": "/treatments-agent/b617c684-5aa4-4174-a049-ecf9a36b9191/", "treatment_type": "Chemical", "uuid": "b617c684-5aa4-4174-a049-ecf9a36b9191", "duration": 24.0, "description": "treatment with actinomycin D", "status": "released", "duration_units": "hour", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "tissue_organ_info": {"organ_system": ["immune system"], "tissue_source": "B-lymphocyte"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "other_processed_files": [{"title": "HiC Processing Pipeline - v0.3.0", "type": "preliminary", "description": "These are files generated using the updated Hi-C processing pipeline. They should be largely similar to those available in the Processed Files tab, which were generated with the previous version of the standard pipeline.  One potential difference of note is that the version of cooler used to generate the mcool file has a bug fix to prevent a pixel duplication issue which is observed in some files generated by the previous version of the pipeline.  Another notable difference is that a filter is applied to remove reads with MAPQ scores below 30 prior to mcool file generation.", "files": [{"display_title": "4DNFI3HOL9UV.bam", "accession": "4DNFI3HOL9UV", "file_type": "alignments", "file_size": 73295560547, "href": "/files-processed/4DNFI3HOL9UV/@@download/4DNFI3HOL9UV.bam", "status": "released", "uuid": "a87ad3ca-d295-4fed-85b5-2186f883245b", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI3HOL9UV/", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/a87ad3ca-d295-4fed-85b5-2186f883245b/4DNFI3HOL9UV.bam", "file_type_detailed": "alignments (bam)", "md5sum": "a2ee1072c787bd1086351e336351f9c1", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "bam", "display_title": "bam", "@id": "/file-formats/bam/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "status": "current", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "last_modified": {"date_modified": "2024-12-03T19:01:52.467822+00:00"}, "contributing_labs": [{"uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "@id": "/labs/yijun-ruan-lab/", "status": "current", "display_title": "Yijun Ruan, JAX", "@type": ["Lab", "Item"], "name": "yijun-ruan-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}], "track_and_facet_info": {"experimental_lab": "Yijun Ruan, JAX", "experiment_type": "in situ ChIA-PET", "experiment_bucket": "HiC Processing Pipeline - v0.3.0", "assay_info": "RNA Pol II", "dataset": "in situ ChIA-PET in GM12878 cell line, ActinomycinD-24h", "condition": "RNAII antibody, ActinomycinD-24h", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "GM12878", "lab_name": "4DN DCIC, HMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "4DNFI4WALYV6.pairs.gz", "accession": "4DNFI4WALYV6", "file_type": "contact list-replicate", "file_size": 2072481386, "href": "/files-processed/4DNFI4WALYV6/@@download/4DNFI4WALYV6.pairs.gz", "status": "released", "uuid": "a8d823b2-8e3e-4716-8f68-bbce34bb9fdb", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI4WALYV6/", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/a8d823b2-8e3e-4716-8f68-bbce34bb9fdb/4DNFI4WALYV6.pairs.gz", "file_type_detailed": "contact list-replicate (pairs)", "md5sum": "a583e2a744cc69462c7359c8302db03f", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "pairs", "display_title": "pairs", "@id": "/file-formats/pairs/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"status": "released", "@id": "/quality-metrics-pairsqc/0566a106-1623-443a-aff0-e71230308267/", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI4WALYV6/pairsqc_report.html", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "display_title": "QualityMetricPairsqc from 2024-09-04", "overall_quality_status": "PASS", "uuid": "0566a106-1623-443a-aff0-e71230308267", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "148481485", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "33.902", "tooltip": "Percent of filtered reads (=50.34m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "56.108", "tooltip": "Percent of filtered reads (=83.31m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "9.99", "tooltip": "Percent of filtered reads (=14.83m)", "numberType": "percent"}]}, "lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "status": "current", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "last_modified": {"date_modified": "2024-12-03T18:53:47.741218+00:00"}, "contributing_labs": [{"uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "@id": "/labs/yijun-ruan-lab/", "status": "current", "display_title": "Yijun Ruan, JAX", "@type": ["Lab", "Item"], "name": "yijun-ruan-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}], "track_and_facet_info": {"experimental_lab": "Yijun Ruan, JAX", "experiment_type": "in situ ChIA-PET", "experiment_bucket": "HiC Processing Pipeline - v0.3.0", "assay_info": "RNA Pol II", "dataset": "in situ ChIA-PET in GM12878 cell line, ActinomycinD-24h", "condition": "RNAII antibody, ActinomycinD-24h", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "GM12878", "lab_name": "4DN DCIC, HMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}], "experiment_type": {"experiment_category": "Sequencing", "assay_subclassification": "DNA-DNA Pairwise Interactions of Enriched Regions", "@id": "/experiment-types/in-situ-chia-pet/", "display_title": "in situ ChIA-PET", "uuid": "c66a4e80-8fc7-4705-94ff-8ed136eb7dc7", "status": "released", "title": "in situ ChIA-PET", "assay_subclass_short": "IP-based 3C", "assay_classification": "3C via Ligation", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-10-21T16:48:36.953608+00:00"}, "external_references": [{"ref": "GEO:GSM5983404", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5983404"}, {"ref": "GEO:SRX14660851", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=SRX14660851"}], "experiment_categorizer": {"value": "RNA Pol II", "combined": "Target: RNA Pol II", "field": "Target"}, "digestion_enzyme": {"status": "released", "@id": "/enzymes/AluI/", "display_title": "AluI", "@type": ["Enzyme", "Item"], "uuid": "1db70ad9-5209-4596-85a5-71ac489c7ee7", "name": "AluI", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experimentset_type": "replicate", "completed_processes": ["HiC_Pipeline_0.3.0"], "other_processed_files": [{"type": "supplementary", "files": [{"@id": "/files-processed/4DNFIXMDJVDD/", "href": "/files-processed/4DNFIXMDJVDD/@@download/4DNFIXMDJVDD.hic", "uuid": "6b609178-9ff6-4dc0-981a-3cef1499acdd", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/6b609178-9ff6-4dc0-981a-3cef1499acdd/4DNFIXMDJVDD.hic", "file_type": "contact matrix", "display_title": "4DNFIXMDJVDD.hic", "genome_assembly": "GRCh38", "file_size": 731163494, "file_format": {"status": "released", "uuid": "d13d11cf-218e-4f61-bbf0-91f226248b2c", "@id": "/file-formats/hic/", "@type": ["FileFormat", "Item"], "display_title": "hic", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "status": "released", "accession": "4DNFIXMDJVDD", "file_type_detailed": "contact matrix (hic)", "md5sum": "b89fae1b637a03b1d8d64c9d551bc759", "lab": {"@id": "/labs/yijun-ruan-lab/", "status": "current", "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "name": "yijun-ruan-lab", "@type": ["Lab", "Item"], "display_title": "Yijun Ruan, JAX", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "track_and_facet_info": {"dataset": "in situ ChIA-PET in GM12878 cell line, ActinomycinD-24h", "condition": "RNAII antibody, ActinomycinD-24h", "experimental_lab": "Yijun Ruan, JAX", "replicate_info": "unreplicated", "experiment_bucket": "Author supplied processed files (bedpe, bedgraph, broadPeak, hic)", "experiment_type": "in situ ChIA-PET", "assay_info": "RNA Pol II", "biosource_name": "GM12878", "lab_name": "Yijun Ruan, JAX"}, "last_modified": {"date_modified": "2024-12-03T17:57:54.957191+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/files-processed/4DNFIVNWGVXD/", "href": "/files-processed/4DNFIVNWGVXD/@@download/4DNFIVNWGVXD.bedpe.gz", "uuid": "35709aba-bff7-405e-ad4e-b4b666f70a88", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/35709aba-bff7-405e-ad4e-b4b666f70a88/4DNFIVNWGVXD.bedpe.gz", "file_type": "long range chromatin interactions", "display_title": "4DNFIVNWGVXD.bedpe.gz", "genome_assembly": "GRCh38", "file_size": 7492927, "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-55f0-94f556118b2c", "@id": "/file-formats/bedpe/", "@type": ["FileFormat", "Item"], "display_title": "bedpe", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "status": "released", "accession": "4DNFIVNWGVXD", "file_type_detailed": "long range chromatin interactions (bedpe)", "md5sum": "e67250d071259dcc832157102483ab4a", "lab": {"@id": "/labs/yijun-ruan-lab/", "status": "current", "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "name": "yijun-ruan-lab", "@type": ["Lab", "Item"], "display_title": "Yijun Ruan, JAX", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "track_and_facet_info": {"dataset": "in situ ChIA-PET in GM12878 cell line, ActinomycinD-24h", "condition": "RNAII antibody, ActinomycinD-24h", "experimental_lab": "Yijun Ruan, JAX", "replicate_info": "unreplicated", "experiment_bucket": "Author supplied processed files (bedpe, bedgraph, broadPeak, hic)", "experiment_type": "in situ ChIA-PET", "assay_info": "RNA Pol II", "biosource_name": "GM12878", "lab_name": "Yijun Ruan, JAX"}, "last_modified": {"date_modified": "2024-12-03T17:57:48.983625+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/files-processed/4DNFIWZTZDVJ/", "href": "/files-processed/4DNFIWZTZDVJ/@@download/4DNFIWZTZDVJ.bedGraph.gz", "uuid": "047ed53e-2bac-4857-bd03-a228bb5fbd22", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/047ed53e-2bac-4857-bd03-a228bb5fbd22/4DNFIWZTZDVJ.bedGraph.gz", "file_type": "intensity values", "display_title": "4DNFIWZTZDVJ.bedGraph.gz", "genome_assembly": "GRCh38", "file_size": 1325309095, "file_format": {"status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/bg/", "@type": ["FileFormat", "Item"], "display_title": "bg", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "status": "released", "accession": "4DNFIWZTZDVJ", "file_type_detailed": "intensity values (bg)", "md5sum": "88379cafd4ce82c1568854ac919f9fb5", "lab": {"@id": "/labs/yijun-ruan-lab/", "status": "current", "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "name": "yijun-ruan-lab", "@type": ["Lab", "Item"], "display_title": "Yijun Ruan, JAX", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "track_and_facet_info": {"dataset": "in situ ChIA-PET in GM12878 cell line, ActinomycinD-24h", "condition": "RNAII antibody, ActinomycinD-24h", "experimental_lab": "Yijun Ruan, JAX", "replicate_info": "unreplicated", "experiment_bucket": "Author supplied processed files (bedpe, bedgraph, broadPeak, hic)", "experiment_type": "in situ ChIA-PET", "assay_info": "RNA Pol II", "biosource_name": "GM12878", "lab_name": "Yijun Ruan, JAX"}, "last_modified": {"date_modified": "2024-12-03T17:57:46.955397+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"higlass_uid": "EoDDkW0qRZSkYKbCNyecrA", "@id": "/files-processed/4DNFIVCRPZHO/", "href": "/files-processed/4DNFIVCRPZHO/@@download/4DNFIVCRPZHO.bed.gz", "uuid": "d8bbc7a4-3848-4d34-a664-c5cfd7a7c53b", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/d8bbc7a4-3848-4d34-a664-c5cfd7a7c53b/4DNFIVCRPZHO.bed.gz", "file_type": "peaks", "display_title": "4DNFIVCRPZHO.bed.gz", "genome_assembly": "GRCh38", "file_size": 2024871, "file_format": {"status": "released", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "@id": "/file-formats/bed/", "@type": ["FileFormat", "Item"], "display_title": "bed", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "status": "released", "accession": "4DNFIVCRPZHO", "file_type_detailed": "peaks (bed)", "md5sum": "30a089b7bcb2c8524d361f51d5675c17", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"display_title": "4DNFIVCRPZHO - peaks for GM12878 in situ ChIA-PET RNA Pol II", "@type": ["HiglassViewConfig", "UserContent", "Item"], "@id": "/higlass-view-configs/30feaca6-f519-4876-a042-e0e978a94c34/", "status": "released", "uuid": "30feaca6-f519-4876-a042-e0e978a94c34", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "lab": {"@id": "/labs/yijun-ruan-lab/", "status": "current", "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "name": "yijun-ruan-lab", "@type": ["Lab", "Item"], "display_title": "Yijun Ruan, JAX", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "track_and_facet_info": {"dataset": "in situ ChIA-PET in GM12878 cell line, ActinomycinD-24h", "condition": "RNAII antibody, ActinomycinD-24h", "experimental_lab": "Yijun Ruan, JAX", "replicate_info": "unreplicated", "experiment_bucket": "Author supplied processed files (bedpe, bedgraph, broadPeak, hic)", "experiment_type": "in situ ChIA-PET", "assay_info": "RNA Pol II", "biosource_name": "GM12878", "lab_name": "Yijun Ruan, JAX", "track_title": "peaks for GM12878 in situ ChIA-PET RNA Pol II"}, "last_modified": {"date_modified": "2024-12-04T20:45:59.438177+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "title": "Author supplied processed files (bedpe, bedgraph, broadPeak, hic)", "description": "Processed files include 1)bedpe: Bedpe file containing ChIA-PET loop (long-range interaction data) data generated by in-house processing pipeline (ChIA-PIPE) where the 7th column of the file denotes the PET counts, filtered to have loops with PET counts greater than or equal to three, 2) bedgraph (.bg): DNA-binding protein coverage files  generated by bedtools (v2.26.0) and sorted by chromosome and coordinate,3) broadPeak:Peaks (broadPeak, bed file type) called by SPP (v1.13), and 4) hic: 2D contact map files  generated using Juicer tools (v1.7.5) which can be visualized using Juicebox app (https://aidenlab.org/juicebox/)", "higlass_view_config": {"@id": "/higlass-view-configs/2d4c5ee0-6206-4c14-b994-5ff6863baedd/", "@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "2d4c5ee0-6206-4c14-b994-5ff6863baedd", "description": "Supplementary Files (Author supplied processed files (bedpe, bedgraph, broadPeak, hic)) for 4DNESBYJGIDU (in situ ChIA-PET in GM12878 using RNAPII antibody, ActinomycinD-24h): 4DNFIVCRPZHO", "status": "released", "display_title": "4DNESBYJGIDU - Author supplied processed files (bedpe, bedgraph, broadPeak, hic)", "last_modified": {"date_modified": "2024-10-21T16:49:03.750667+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "@id": "/experiment-set-replicates/4DNESBYJGIDU/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "517131af-4af3-41c2-99c8-53c0b35bc26a", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNESBYJGIDU", "external_references": [], "produced_in_pub": {"date_published": "2024-03-27", "status": "current", "short_attribution": "Kim M et al. (2024)", "journal": "bioRxiv : the preprint server for biology", "authors": ["Kim M", "Wang P", "Clow PA", "Chien IE", "Wang X", "Peng J", "Chai H", "Liu X", "Lee B", "Ngan CY", "Yue F", "Milenkovic O", "Chuang JH", "Wei CL", "Casellas R", "Cheng AW", "Ruan Y"], "@type": ["Publication", "Item"], "abstract": "Cohesin is required for chromatin loop formation. However, its precise role in  regulating gene transcription remains largely unknown. We investigated the  relationship between cohesin and RNA Polymerase II (RNAPII) using single-molecule  mapping and live-cell imaging methods in human cells. Cohesin-mediated  transcriptional loops were highly correlated with those of RNAPII and followed  the direction of gene transcription. Depleting RAD21, a subunit of cohesin,  resulted in the loss of long-range (>100 kb) loops between distal  (super-)enhancers and promoters of cell-type-specific genes. By contrast, the  short-range (<50 kb) loops were insensitive to RAD21 depletion and connected  genes that are mostly housekeeping. This result explains why only a small  fraction of genes are affected by the loss of long-range chromatin interactions  due to cohesin depletion. Remarkably, RAD21 depletion appeared to up-regulate  genes located in early initiation zones (EIZ) of DNA replication, and the EIZ  signals were amplified drastically without RAD21. Our results revealed new  mechanistic insights of cohesin's multifaceted roles in establishing  transcriptional loops, preserving long-range chromatin interactions for  cell-specific genes, and maintaining timely order of DNA replication.", "display_title": "Kim M et al. (2024) doi:10.1101/2024.03.25.586715", "url": "https://www.ncbi.nlm.nih.gov/pubmed/38585764", "title": "Multifaceted roles of cohesin in regulating transcriptional loops.", "@id": "/publications/a84d089a-b2a0-4da5-a454-07f73987df08/", "uuid": "a84d089a-b2a0-4da5-a454-07f73987df08", "ID": "doi:10.1101/2024.03.25.586715", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"status": "current", "uuid": "a84d089a-b2a0-4da5-a454-07f73987df08", "date_published": "2024-03-27", "display_title": "Kim M et al. (2024) doi:10.1101/2024.03.25.586715", "ID": "doi:10.1101/2024.03.25.586715", "journal": "bioRxiv : the preprint server for biology", "abstract": "Cohesin is required for chromatin loop formation. However, its precise role in  regulating gene transcription remains largely unknown. We investigated the  relationship between cohesin and RNA Polymerase II (RNAPII) using single-molecule  mapping and live-cell imaging methods in human cells. Cohesin-mediated  transcriptional loops were highly correlated with those of RNAPII and followed  the direction of gene transcription. Depleting RAD21, a subunit of cohesin,  resulted in the loss of long-range (>100 kb) loops between distal  (super-)enhancers and promoters of cell-type-specific genes. By contrast, the  short-range (<50 kb) loops were insensitive to RAD21 depletion and connected  genes that are mostly housekeeping. This result explains why only a small  fraction of genes are affected by the loss of long-range chromatin interactions  due to cohesin depletion. Remarkably, RAD21 depletion appeared to up-regulate  genes located in early initiation zones (EIZ) of DNA replication, and the EIZ  signals were amplified drastically without RAD21. Our results revealed new  mechanistic insights of cohesin's multifaceted roles in establishing  transcriptional loops, preserving long-range chromatin interactions for  cell-specific genes, and maintaining timely order of DNA replication.", "@type": ["Publication", "Item"], "@id": "/publications/a84d089a-b2a0-4da5-a454-07f73987df08/", "title": "Multifaceted roles of cohesin in regulating transcriptional loops.", "authors": ["Kim M", "Wang P", "Clow PA", "Chien IE", "Wang X", "Peng J", "Chai H", "Liu X", "Lee B", "Ngan CY", "Yue F", "Milenkovic O", "Chuang JH", "Wei CL", "Casellas R", "Cheng AW", "Ruan Y"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 1, "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSCX7THPV/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["Biosample missing Cell Culture Details"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}, {"parent": "/experiment-set-replicates/4DNESBYJGIDU/", "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": []}