{"lab": {"@id": "/labs/erez-liebermanaiden-lab/", "title": "Erez Lieberman Aiden, BCM", "display_title": "Erez Lieberman Aiden, BCM", "uuid": "5771d772-1d10-43ea-bec1-0ea8c5a58503", "correspondence": [{"contact_email": "ZXJlekBlcmV6LmNvbQ==", "@id": "/users/60938b2e-e120-4c4f-9ddb-001296021df7/", "display_title": "Erez Lieberman Aiden"}], "status": "current", "@type": ["Lab", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.5771d772-1d10-43ea-bec1-0ea8c5a58503"]}}, "award": {"description": "Biological systems contain a large number of components whose physical interactions bring about cellular processes. A fundamental problem in molecular biology is to catalog these interactions and to decipher their functional consequences. High throughput sequencing has made it possible to characterize some of these interactions rapidly, at high-resolution, and in vivo (e.g., protein-DNA binding via ChIP-Seq and protein-RNA binding via RIP-Seq). But many interactions are not susceptible to these methods (e.g., RNA- RNA complexes, ncRNA-DNA binding, and - aside from recent work described below - DNA-DNA contacts and genome folding.) This gap may be bridged by coupling high-throughput sequencing with proximity-ligation-based methods. In proximity ligation, spatially proximate nucleic acids ligate to one another, forming a chimeric oligo. Observation of a chimera composed of X and Y suggests that X and Y must have been near one another in the original sample. As a result, questions about spatial arrangement become questions about sequence composition, making it possible to take advantage of high-throughput sequencing. Nevertheless, the development of these approaches is challenging: they involve subtle molecular biology and produce massive high-dimensional datasets requiring wholly new analytical paradigms including extensive physical modeling. We recently developed Hi-C, the first technology that couples proximity ligation and high-throughput sequencing in an unbiased, genome-wide fashion (Lieberman-Aiden et al., Science, 2009). Hi-C uses a DNA-DNA proximity ligation step to identify long-range physical contacts between genomic DNA loci in vivo. We used Hi-C to create a low-resolution three-dimensional map of the human genome, and made two significant discoveries: (1) genetic regulation is accompanied by the three-dimensional movement of genes from an 'on' compartment to an 'off' compartment, and vice-versa; (2) a never-before-seen macromolecular state, the fractal globule, which couples extraordinary spatial density and a total absence of knots. Here, we propose to dramatically extend the above work, by building a new generation of tools for systematically exploring the spatial organization of genomes, RNAs, and proteins, and by applying these tools to explore how RNAs and proteins establish and regulate the three-dimensional architecture of the genome. We will accomplish this through three specific research aims: (1) We will create an ensemble of new technologies combining proximity ligation and sequencing to enable comprehensive mapping of (a) DNA-RNA contacts [via DNA-RNA proximity ligation]; (b) RNA-RNA complexes [via RNA-RNA proximity ligation]; (c) selected protein-protein complexes [via probe-coupled proximity ligation]. We will use these methods to generate maps of biomolecular contacts in vivo. (2) We will create high-resolution Hi-C maps of mammalian genomes, comprehensively mapping promoter-enhancer contacts and exploring large-scale organizational features such as transcription factories. (3) We will develop new analytical approaches that combine the data produced by (1) and (2) with new (a) informatic tools, (b) computational analyses, (c) physical simulations, and (d) rigorous theoretical methods. We will characterize how physical interactions change during differentiation and tumorigenesis; identify the RNAs, proteins and pathways that that are most crucial in regulating genome folding, and produce detailed physical models of these pathways and how they modulate the physical structure of the genome. We plan to initially apply these techniques to characterize murine ES cells differentiating down a neural lineage, and later to differentiating human ES cells and to primary tumors. This effort will produce powerful new molecular methods which will dramatically improve our ability to assess the spatial arrangement of cellular components. It will transform our understanding of how mammalian genomes fold inside the nucleus. It will reveal how specific physical interactions between DNA, RNA, and protein play a role in differentiation, tumorigenesis, and genome folding, and suggest new drug targets in the process. Finally, this work will generate a series of datasets that will serve as valuable resources for the scientific community as a whole. Public Health Relevance: Biological systems contain a large number of components whose physical interactions bring about cellular processes, but our tools for identifying many of these biomolecular interactions are laborious and slow. We recently developed the Hi-C method for reconstructing the architecture of the human genome, and will extend this technological approach to map interactions between DNA, RNA, and protein in vivo and at high-throughput. We will use these maps to study how genome folding regulates cell function, and to characterize the process of cellular differentiation and tumorigenesis, identifying crucial biomolecular pathways and potential drug targets.", "name": "OD008540-01", "@id": "/awards/OD008540-01/", "project": "External", "status": "current", "uuid": "36a06537-7831-494d-b10d-3e9fea931021", "center_title": "Lieberman Aiden", "@type": ["Award", "Item"], "display_title": "EXPLORING HOW THE GENOME FOLDS THROUGH PROXIMITY LIGATION AND SEQUENCING", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "files": [{"display_title": "4DNFIHU7WJTZ.fastq.gz", "href": "/files-fastq/4DNFIHU7WJTZ/@@download/4DNFIHU7WJTZ.fastq.gz", "@type": ["FileFastq", "File", "Item"], "upload_key": "759aab38-39de-42e4-b69b-bc2b7fe2c993/4DNFIHU7WJTZ.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "dbxrefs": ["SRA:SRR2671401"], "@id": "/files-fastq/4DNFIHU7WJTZ/", "accession": "4DNFIHU7WJTZ", "file_classification": "raw file", "uuid": "759aab38-39de-42e4-b69b-bc2b7fe2c993", "paired_end": "1", "file_size": 161140161, "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webdev-wfoutput/4DNFIHU7WJTZ/fastqc_report.html", "display_title": "QualityMetricFastqc from 2017-06-30", "uuid": "e85ba249-9ccf-496b-9fcc-af929c554bd0", "overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/e85ba249-9ccf-496b-9fcc-af929c554bd0/", "status": "released", "Total Sequences": 3208074, "Sequence length": "80", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "paired_end": "2", "accession": "4DNFI7J7LIMM", "uuid": "d34fbe36-09b4-4c44-84b1-c845c04a6d17", "@id": "/files-fastq/4DNFI7J7LIMM/", "status": "released", "display_title": "4DNFI7J7LIMM.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [{"ref": "SRA:SRR2671401", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR2671401"}]}, {"display_title": "4DNFI7J7LIMM.fastq.gz", "href": "/files-fastq/4DNFI7J7LIMM/@@download/4DNFI7J7LIMM.fastq.gz", "@type": ["FileFastq", "File", "Item"], "upload_key": "d34fbe36-09b4-4c44-84b1-c845c04a6d17/4DNFI7J7LIMM.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "dbxrefs": ["SRA:SRR2671401"], "@id": "/files-fastq/4DNFI7J7LIMM/", "accession": "4DNFI7J7LIMM", "file_classification": "raw file", "uuid": "d34fbe36-09b4-4c44-84b1-c845c04a6d17", "paired_end": "2", "file_size": 165851522, "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webdev-wfoutput/4DNFI7J7LIMM/fastqc_report.html", "display_title": "QualityMetricFastqc from 2017-06-30", "uuid": "4948be77-809d-4d77-9818-281eee9023a7", "overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/4948be77-809d-4d77-9818-281eee9023a7/", "status": "released", "Total Sequences": 3208074, "Sequence length": "80", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "paired_end": "1", "accession": "4DNFIHU7WJTZ", "uuid": "759aab38-39de-42e4-b69b-bc2b7fe2c993", "@id": "/files-fastq/4DNFIHU7WJTZ/", "status": "released", "display_title": "4DNFIHU7WJTZ.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [{"ref": "SRA:SRR2671401", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR2671401"}]}, {"display_title": "4DNFIP2OH6Y3.fastq.gz", "href": "/files-fastq/4DNFIP2OH6Y3/@@download/4DNFIP2OH6Y3.fastq.gz", "@type": ["FileFastq", "File", "Item"], "upload_key": "57a48564-bac8-47cd-bbd4-e714e8724557/4DNFIP2OH6Y3.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "dbxrefs": ["SRA:SRR2671402"], "@id": "/files-fastq/4DNFIP2OH6Y3/", "accession": "4DNFIP2OH6Y3", "file_classification": "raw file", "uuid": "57a48564-bac8-47cd-bbd4-e714e8724557", "paired_end": "1", "file_size": 156003168, "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webdev-wfoutput/4DNFIP2OH6Y3/fastqc_report.html", "display_title": "QualityMetricFastqc from 2017-06-30", "uuid": "48d5392a-d828-43c0-8a4d-5be60a027abd", "overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/48d5392a-d828-43c0-8a4d-5be60a027abd/", "status": "released", "Total Sequences": 3120057, "Sequence length": "80", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "paired_end": "2", "accession": "4DNFI9MZ9IEA", "uuid": "07dfcb0a-c6f2-4cf2-ba3a-db920f0453a2", "@id": "/files-fastq/4DNFI9MZ9IEA/", "status": "released", "display_title": "4DNFI9MZ9IEA.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [{"ref": "SRA:SRR2671402", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR2671402"}]}, {"display_title": "4DNFI9MZ9IEA.fastq.gz", "href": "/files-fastq/4DNFI9MZ9IEA/@@download/4DNFI9MZ9IEA.fastq.gz", "@type": ["FileFastq", "File", "Item"], "upload_key": "07dfcb0a-c6f2-4cf2-ba3a-db920f0453a2/4DNFI9MZ9IEA.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "dbxrefs": ["SRA:SRR2671402"], "@id": "/files-fastq/4DNFI9MZ9IEA/", "accession": "4DNFI9MZ9IEA", "file_classification": "raw file", "uuid": "07dfcb0a-c6f2-4cf2-ba3a-db920f0453a2", "paired_end": "2", "file_size": 161222952, "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webdev-wfoutput/4DNFI9MZ9IEA/fastqc_report.html", "display_title": "QualityMetricFastqc from 2017-06-30", "uuid": "802fa6cd-fe01-4472-b482-f5f6080d45d9", "overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/802fa6cd-fe01-4472-b482-f5f6080d45d9/", "status": "released", "Total Sequences": 3120057, "Sequence length": "80", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "paired_end": "1", "accession": "4DNFIP2OH6Y3", "uuid": "57a48564-bac8-47cd-bbd4-e714e8724557", "@id": "/files-fastq/4DNFIP2OH6Y3/", "status": "released", "display_title": "4DNFIP2OH6Y3.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [{"ref": "SRA:SRR2671402", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR2671402"}]}, {"display_title": "4DNFI1WJD786.fastq.gz", "href": "/files-fastq/4DNFI1WJD786/@@download/4DNFI1WJD786.fastq.gz", "@type": ["FileFastq", "File", "Item"], "upload_key": "9e675fc9-1dd9-423f-bca1-10f58432da2e/4DNFI1WJD786.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "dbxrefs": ["SRA:SRR2671403"], "@id": "/files-fastq/4DNFI1WJD786/", "accession": "4DNFI1WJD786", "file_classification": "raw file", "uuid": "9e675fc9-1dd9-423f-bca1-10f58432da2e", "paired_end": "1", "file_size": 162620666, "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webdev-wfoutput/4DNFI1WJD786/fastqc_report.html", "display_title": "QualityMetricFastqc from 2017-06-30", "uuid": "2930c7c4-362e-4240-b6a1-f2755e9abeac", "overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/2930c7c4-362e-4240-b6a1-f2755e9abeac/", "status": "released", "Total Sequences": 3250802, "Sequence length": "80", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "paired_end": "2", "accession": "4DNFIGX57TZO", "uuid": "a2370c3b-1e36-4324-8d53-a8a140140a85", "@id": "/files-fastq/4DNFIGX57TZO/", "status": "released", "display_title": "4DNFIGX57TZO.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [{"ref": "SRA:SRR2671403", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR2671403"}]}, {"display_title": "4DNFIGX57TZO.fastq.gz", "href": "/files-fastq/4DNFIGX57TZO/@@download/4DNFIGX57TZO.fastq.gz", "@type": ["FileFastq", "File", "Item"], "upload_key": "a2370c3b-1e36-4324-8d53-a8a140140a85/4DNFIGX57TZO.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "dbxrefs": ["SRA:SRR2671403"], "@id": "/files-fastq/4DNFIGX57TZO/", "accession": "4DNFIGX57TZO", "file_classification": "raw file", "uuid": "a2370c3b-1e36-4324-8d53-a8a140140a85", "paired_end": "2", "file_size": 167807313, "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIGX57TZO/fastqc_report.html", "display_title": "QualityMetricFastqc from 2017-08-31", "uuid": "f410957b-d1e2-4909-8401-d938a43c14e7", "overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/f410957b-d1e2-4909-8401-d938a43c14e7/", "status": "released", "Total Sequences": 3250802, "Sequence length": "80", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "paired_end": "1", "accession": "4DNFI1WJD786", "uuid": "9e675fc9-1dd9-423f-bca1-10f58432da2e", "@id": "/files-fastq/4DNFI1WJD786/", "status": "released", "display_title": "4DNFI1WJD786.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [{"ref": "SRA:SRR2671403", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR2671403"}]}, {"display_title": "4DNFIEWOOZKX.fastq.gz", "href": "/files-fastq/4DNFIEWOOZKX/@@download/4DNFIEWOOZKX.fastq.gz", "@type": ["FileFastq", "File", "Item"], "upload_key": "2c155180-00e3-4436-9e39-73c7c6f835e3/4DNFIEWOOZKX.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "dbxrefs": ["SRA:SRR2671404"], "@id": "/files-fastq/4DNFIEWOOZKX/", "accession": "4DNFIEWOOZKX", "file_classification": "raw file", "uuid": "2c155180-00e3-4436-9e39-73c7c6f835e3", "paired_end": "1", "file_size": 160098624, "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIEWOOZKX/fastqc_report.html", "display_title": "QualityMetricFastqc from 2017-08-31", "uuid": "7009402a-24d7-4048-9f7e-b77b5cb12d52", "overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/7009402a-24d7-4048-9f7e-b77b5cb12d52/", "status": "released", "Total Sequences": 3206945, "Sequence length": "80", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "paired_end": "2", "accession": "4DNFIQ594TDS", "uuid": "10f1e43d-91fd-4eed-a43a-291902a9ff08", "@id": "/files-fastq/4DNFIQ594TDS/", "status": "released", "display_title": "4DNFIQ594TDS.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [{"ref": "SRA:SRR2671404", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR2671404"}]}, {"display_title": "4DNFIQ594TDS.fastq.gz", "href": "/files-fastq/4DNFIQ594TDS/@@download/4DNFIQ594TDS.fastq.gz", "@type": ["FileFastq", "File", "Item"], "upload_key": "10f1e43d-91fd-4eed-a43a-291902a9ff08/4DNFIQ594TDS.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "dbxrefs": ["SRA:SRR2671404"], "@id": "/files-fastq/4DNFIQ594TDS/", "accession": "4DNFIQ594TDS", "file_classification": "raw file", "uuid": "10f1e43d-91fd-4eed-a43a-291902a9ff08", "paired_end": "2", "file_size": 165484876, "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIQ594TDS/fastqc_report.html", "display_title": "QualityMetricFastqc from 2017-08-11", "uuid": "05587add-602e-4314-9f57-40f822d3b39b", "overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/05587add-602e-4314-9f57-40f822d3b39b/", "status": "released", "Total Sequences": 3206945, "Sequence length": "80", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "paired_end": "1", "accession": "4DNFIEWOOZKX", "uuid": "2c155180-00e3-4436-9e39-73c7c6f835e3", "@id": "/files-fastq/4DNFIEWOOZKX/", "status": "released", "display_title": "4DNFIEWOOZKX.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [{"ref": "SRA:SRR2671404", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR2671404"}]}], "notes": "Old Target: e2406013-1ea2-4978-bbb0-c451f3d6fad7 198491ec-2951-451f-a5ee-b74c2e396ec4Old Target: f2c5562b-c00c-41bb-8d81-c18fb02b6f23 42855b1d-611d-4886-bb9c-c06d093c5ec4Old Target: 4bdcf493-8eb9-424a-878f-70c6aad3e055 6b246560-99c2-4682-9b89-15c0fc61e86d", "status": "released", "aliases": ["dcic:SR15-hic053"], "dbxrefs": ["SRA:SRX1341923"], "rna_tag": "bio-dCTP", "accession": "4DNEXRZJ37CB", "biosample": {"accession": "4DNBSOFUL6I6", "status": "released", "biosample_type": "immortalized cells", "treatments_summary": "None", "modifications_summary": "Crispr deletion of CTCF site E-reverse in Region 2", "@type": ["Biosample", "Item"], "biosource_summary": "HAP-1", "uuid": "57134036-6e26-4348-b3d8-db0cbbf972cd", "display_title": "4DNBSOFUL6I6", "@id": "/biosamples/4DNBSOFUL6I6/", "biosource": [{"lab": {"display_title": "Erez Lieberman Aiden, BCM", "@type": ["Lab", "Item"], "@id": "/labs/erez-liebermanaiden-lab/", "uuid": "5771d772-1d10-43ea-bec1-0ea8c5a58503", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.5771d772-1d10-43ea-bec1-0ea8c5a58503"]}}, "url": "https://www.horizondiscovery.com/cell-lines/all-products/about-x-man-cell-lines/hap1-cells", "award": {"uuid": "36a06537-7831-494d-b10d-3e9fea931021", "@id": "/awards/OD008540-01/", "status": "current", "display_title": "EXPLORING HOW THE GENOME FOLDS THROUGH PROXIMITY LIGATION AND SEQUENCING", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"@type": ["OntologyTerm", "Item"], "uuid": "0d64fbe2-ed5c-43cd-a30d-d9f0320d27ed", "term_name": "blood cell", "@id": "/ontology-terms/CL:0000081/", "display_title": "blood cell", "slim_terms": [{"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"]}}, {"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"]}}], "preferred_name": "blood cell", "term_id": "CL:0000081", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["dcic:hap1cells"], "accession": "4DNSRNIAESOK", "cell_line": {"uuid": "57d18eec-d662-4bf7-8000-047de03ad84a", "term_name": "HAP-1", "slim_terms": [{"status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "display_title": "cell", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "display_title": "cell", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "term_id": "EFO:0007598", "@id": "/ontology-terms/EFO:0007598/", "preferred_name": "HAP-1", "display_title": "HAP-1", "@type": ["OntologyTerm", "Item"], "status": "released", "synonyms": ["HAP1"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"@type": ["IndividualHuman", "Individual", "Item"], "status": "released", "uuid": "6e37c213-33dd-4aff-aedb-b466a4b2aa45", "display_title": "4DNINGLJ7A6Z", "@id": "/individuals-human/4DNINGLJ7A6Z/", "protected_data": false, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "references": [], "description": "HAP-1 a near haploid cell line", "date_created": "2017-04-10T01:05:47.201162+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-06-05T14:29:58.101324+00:00"}, "modifications": [], "biosource_type": "immortalized cell line", "cell_line_tier": "Unclassified", "public_release": "2017-04-10", "schema_version": "2", "project_release": "2017-04-10", "biosource_vendor": {"display_title": "Horizon Genomics", "uuid": "1fd06d82-b232-46ec-91f7-f18593f43e9d", "status": "released", "@type": ["Vendor", "Item"], "@id": "/vendors/horizon-genomics/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "alternate_accessions": [], "@id": "/biosources/4DNSRNIAESOK/", "@type": ["Biosource", "Item"], "uuid": "18fc203e-0b65-43b7-8373-0c8fdf5eff57", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "HAP-1 - 4DNSRNIAESOK", "external_references": [], "biosource_name": "HAP-1", "biosource_category": ["Tier 2"], "organism": {"@id": "/organisms/9606/", "@type": ["Organism", "Item"], "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "display_title": "H. sapiens", "status": "released", "name": "human", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "modifications": [{"genomic_change": "deletion", "display_title": "Crispr deletion of CTCF site E-reverse in Region 2", "modification_type": "Crispr", "description": "Region 2 motif E-reverse deletion 1", "status": "released", "@type": ["Modification", "Item"], "@id": "/modifications/f4c35df5-aab6-4d6e-95a7-df21b6b0fed2/", "override_modification_name": "Crispr deletion of CTCF site E-reverse in Region 2", "uuid": "f4c35df5-aab6-4d6e-95a7-df21b6b0fed2", "target_of_mod": [{"uuid": "0add481d-fb9f-47ad-bda8-45898309227e", "feature_type": {"uuid": "41b7a2c5-f2d9-46b4-a49d-51502fe61bb3", "@type": ["OntologyTerm", "Item"], "display_title": "region", "status": "released", "@id": "/ontology-terms/SO:0000001/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "display_title": "GRCh38:1:180863366-180863385 region", "status": "released", "organism_name": "human", "genome_location": [{"uuid": "a685f9d3-f525-4283-b4ba-75e818c01ac1", "@id": "/genomic-regions/a685f9d3-f525-4283-b4ba-75e818c01ac1/", "@type": ["GenomicRegion", "Item"], "display_title": "GRCh38:1:180863366-180863385", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/bio-features/0add481d-fb9f-47ad-bda8-45898309227e/", "@type": ["BioFeature", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "treatments": [], "badges": [{"messages": ["Biosample missing Cell Culture Details", "HAP-1 biosample missing ploidy authentication"], "badge": {"badge_icon": "/static/img/badges/biosample-icon.svg", "@type": ["Badge", "Item"], "display_title": "Biosample Metadata Incomplete", "title": "Biosample Metadata Incomplete", "badge_classification": "Warning", "warning": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "status": "released", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "documents": [], "references": [], "description": "Hap1 capture Hi-C 053", "sop_mapping": {"has_sop": "No"}, "date_created": "2017-04-10T01:11:11.036033+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2020-11-04T16:35:26.491396+00:00"}, "digestion_time": 120.0, "public_release": "2017-04-10", "schema_version": "3", "tagging_method": "biotin-dUTP", "experiment_type": {"uuid": "62ddb15e-4907-4b8a-bfca-cdd4371cb179", "display_title": "Capture Hi-C", "assay_subclass_short": "Enrichment Hi-C", "@id": "/experiment-types/capture-hi-c/", "@type": ["ExperimentType", "Item"], "experiment_category": "Sequencing", "title": "Capture Hi-C", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/1747bc44-4b50-4b5e-b24e-3cfb19356223/4DNFI6FAAG3G.bam", "upload_key": "1747bc44-4b50-4b5e-b24e-3cfb19356223/4DNFI6FAAG3G.bam", "file_size": 2064837635, "uuid": "1747bc44-4b50-4b5e-b24e-3cfb19356223", "file_format": {"status": "released", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "file_format": "bam", "@id": "/file-formats/bam/", "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNFI6FAAG3G", "display_title": "4DNFI6FAAG3G.bam", "file_classification": "processed file", "href": "/files-processed/4DNFI6FAAG3G/@@download/4DNFI6FAAG3G.bam", "@id": "/files-processed/4DNFI6FAAG3G/", "status": "released", "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "alignments (bam)", "file_type": "alignments", "quality_metric": {"display_title": "QualityMetricBamqc from 2019-12-21", "@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "status": "released", "@id": "/quality-metrics-bamqc/9f89771f-6859-4899-a0b6-bac3655b16bd/", "uuid": "9f89771f-6859-4899-a0b6-bac3655b16bd", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Reads", "value": "12785878", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "6.008", "tooltip": "Percent of total reads (=0.77m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "25.581", "tooltip": "Percent of total reads (=3.27m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "1.262", "tooltip": "Percent of total reads (=0.16m)", "numberType": "percent"}, {"title": "Walks", "value": "6.24", "tooltip": "Percent of total reads (=0.8m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.482", "tooltip": "Percent of total reads (=0.06m)", "numberType": "percent"}]}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Erez Lieberman Aiden, BCM", "experiment_type": "Capture Hi-C", "experiment_bucket": "processed file", "assay_info": "GRCh38:1:179830865-181830865 region, GRCh38:5:30999893-32999894 region, GRCh38:8:131987753-133987757 region", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HAP-1", "lab_name": "4DN DCIC, HMS"}, "external_references": []}, {"open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/32ea9928-3b0c-4c39-bc00-46ddb983310c/4DNFI9ZFRE7L.pairs.gz", "upload_key": "32ea9928-3b0c-4c39-bc00-46ddb983310c/4DNFI9ZFRE7L.pairs.gz", "file_size": 170699269, "uuid": "32ea9928-3b0c-4c39-bc00-46ddb983310c", "file_format": {"status": "released", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "pairs", "@id": "/file-formats/pairs/", "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNFI9ZFRE7L", "display_title": "4DNFI9ZFRE7L.pairs.gz", "file_classification": "processed file", "href": "/files-processed/4DNFI9ZFRE7L/@@download/4DNFI9ZFRE7L.pairs.gz", "@id": "/files-processed/4DNFI9ZFRE7L/", "status": "released", "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "contact list-replicate (pairs)", "file_type": "contact list-replicate", "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI9ZFRE7L/pairsqc_report.html", "Total reads": 7787715, "display_title": "QualityMetricPairsqc from 2018-03-01", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "status": "released", "@id": "/quality-metrics-pairsqc/09e7529a-3fc3-495d-94b8-a4e57baade43/", "uuid": "09e7529a-3fc3-495d-94b8-a4e57baade43", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "7787715", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "47.337", "tooltip": "Percent of filtered reads (=3.69m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "29.042", "tooltip": "Percent of filtered reads (=2.26m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "23.622", "tooltip": "Percent of filtered reads (=1.84m)", "numberType": "percent"}]}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Erez Lieberman Aiden, BCM", "experiment_type": "Capture Hi-C", "experiment_bucket": "processed file", "assay_info": "GRCh38:1:179830865-181830865 region, GRCh38:5:30999893-32999894 region, GRCh38:8:131987753-133987757 region", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HAP-1", "lab_name": "4DN DCIC, HMS"}, "external_references": []}], "project_release": "2017-04-10", "digestion_enzyme": {"name": "MboI", "display_title": "MboI", "@type": ["Enzyme", "Item"], "@id": "/enzymes/MboI/", "uuid": "d8da42d0-bc20-40e5-bacf-c263b8603e03", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "targeted_regions": [{"target": [{"@type": ["BioFeature", "Item"], "display_title": "GRCh38:8:131987753-133987757 region", "feature_type": {"status": "released", "uuid": "41b7a2c5-f2d9-46b4-a49d-51502fe61bb3", "@id": "/ontology-terms/SO:0000001/", "@type": ["OntologyTerm", "Item"], "display_title": "region", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "b0ddfa0c-6abd-4acc-9ca5-7540a4b2946d", "organism_name": "human", "status": "released", "@id": "/bio-features/b0ddfa0c-6abd-4acc-9ca5-7540a4b2946d/", "genome_location": [{"chromosome": "8", "@type": ["GenomicRegion", "Item"], "start_coordinate": 131987753, "status": "released", "end_coordinate": 133987757, "uuid": "645c1ba7-b082-4518-b57f-2c89cb887e93", "display_title": "GRCh38:8:131987753-133987757", "@id": "/genomic-regions/645c1ba7-b082-4518-b57f-2c89cb887e93/", "location_description": "Region 1", "genome_assembly": "GRCh38", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "oligo_file": {"accession": "4DNFI4FLO6VF", "status": "released", "@id": "/files-reference/4DNFI4FLO6VF/", "display_title": "4DNFI4FLO6VF.fasta.gz", "@type": ["FileReference", "File", "Item"], "href": "/files-reference/4DNFI4FLO6VF/@@download/4DNFI4FLO6VF.fasta.gz", "uuid": "198491ec-2951-451f-a5ee-b74c2e396ec4", "file_format": {"lab": {"display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "url": "https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=BlastHelp", "award": {"status": "current", "@id": "/awards/1U01CA200059-01/", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "assay_types": ["Sequencing"], "description": "This format is used for compressed FASTA files", "file_format": "compressed_fasta", "date_created": "2018-09-18T02:52:39.611716+00:00", "file_content": "sequences", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2020-11-02T15:59:55.761777+00:00"}, "schema_version": "1", "valid_item_types": ["FileReference"], "standard_file_extension": "fasta.gz", "other_allowed_extensions": ["fsa.gz", "fa.gz"], "@id": "/file-formats/compressed_fasta/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-55f0-92f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "compressed_fasta", "external_references": []}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"target": [{"@type": ["BioFeature", "Item"], "display_title": "GRCh38:1:179830865-181830865 region", "feature_type": {"status": "released", "uuid": "41b7a2c5-f2d9-46b4-a49d-51502fe61bb3", "@id": "/ontology-terms/SO:0000001/", "@type": ["OntologyTerm", "Item"], "display_title": "region", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "56ebc735-38ce-40b5-b0f9-d5aee69cea5f", "organism_name": "human", "status": "released", "@id": "/bio-features/56ebc735-38ce-40b5-b0f9-d5aee69cea5f/", "genome_location": [{"chromosome": "1", "@type": ["GenomicRegion", "Item"], "start_coordinate": 179830865, "status": "released", "end_coordinate": 181830865, "uuid": "d7320dc6-c0e8-47b7-bd1e-4c461fb85d97", "display_title": "GRCh38:1:179830865-181830865", "@id": "/genomic-regions/d7320dc6-c0e8-47b7-bd1e-4c461fb85d97/", "location_description": "Region 2", "genome_assembly": "GRCh38", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "oligo_file": {"accession": "4DNFI9P2SCZ7", "status": "released", "@id": "/files-reference/4DNFI9P2SCZ7/", "display_title": "4DNFI9P2SCZ7.fasta.gz", "@type": ["FileReference", "File", "Item"], "href": "/files-reference/4DNFI9P2SCZ7/@@download/4DNFI9P2SCZ7.fasta.gz", "uuid": "42855b1d-611d-4886-bb9c-c06d093c5ec4", "file_format": {"lab": {"display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "url": "https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=BlastHelp", "award": {"status": "current", "@id": "/awards/1U01CA200059-01/", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "assay_types": ["Sequencing"], "description": "This format is used for compressed FASTA files", "file_format": "compressed_fasta", "date_created": "2018-09-18T02:52:39.611716+00:00", "file_content": "sequences", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2020-11-02T15:59:55.761777+00:00"}, "schema_version": "1", "valid_item_types": ["FileReference"], "standard_file_extension": "fasta.gz", "other_allowed_extensions": ["fsa.gz", "fa.gz"], "@id": "/file-formats/compressed_fasta/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-55f0-92f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "compressed_fasta", "external_references": []}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"target": [{"@type": ["BioFeature", "Item"], "display_title": "GRCh38:5:30999893-32999894 region", "feature_type": {"status": "released", "uuid": "41b7a2c5-f2d9-46b4-a49d-51502fe61bb3", "@id": "/ontology-terms/SO:0000001/", "@type": ["OntologyTerm", "Item"], "display_title": "region", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "69b00232-96ea-462c-af3a-18435e6dff3e", "organism_name": "human", "status": "released", "@id": "/bio-features/69b00232-96ea-462c-af3a-18435e6dff3e/", "genome_location": [{"chromosome": "5", "@type": ["GenomicRegion", "Item"], "start_coordinate": 30999893, "status": "released", "end_coordinate": 32999894, "uuid": "0cd3bf69-be4d-4e0d-8901-68416ef7e88d", "display_title": "GRCh38:5:30999893-32999894", "@id": "/genomic-regions/0cd3bf69-be4d-4e0d-8901-68416ef7e88d/", "location_description": "Region 3", "genome_assembly": "GRCh38", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "oligo_file": {"accession": "4DNFIMIV7AHJ", "status": "released", "@id": "/files-reference/4DNFIMIV7AHJ/", "display_title": "4DNFIMIV7AHJ.fasta.gz", "@type": ["FileReference", "File", "Item"], "href": "/files-reference/4DNFIMIV7AHJ/@@download/4DNFIMIV7AHJ.fasta.gz", "uuid": "6b246560-99c2-4682-9b89-15c0fc61e86d", "file_format": {"lab": {"display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "url": "https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=BlastHelp", "award": {"status": "current", "@id": "/awards/1U01CA200059-01/", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "assay_types": ["Sequencing"], "description": "This format is used for compressed FASTA files", "file_format": "compressed_fasta", "date_created": "2018-09-18T02:52:39.611716+00:00", "file_content": "sequences", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2020-11-02T15:59:55.761777+00:00"}, "schema_version": "1", "valid_item_types": ["FileReference"], "standard_file_extension": "fasta.gz", "other_allowed_extensions": ["fsa.gz", "fa.gz"], "@id": "/file-formats/compressed_fasta/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-55f0-92f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "compressed_fasta", "external_references": []}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "crosslinking_time": 10.0, "crosslinking_method": "1% Formaldehyde", "alternate_accessions": [], "digestion_temperature": 37.0, "crosslinking_temperature": 22.0, "@id": "/experiments-capture-c/4DNEXRZJ37CB/", "@type": ["ExperimentCaptureC", "Experiment", "Item"], "uuid": "53882fda-ae4f-4635-809c-85df0be8082c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "Capture Hi-C on HAP-1 with MboI - 4DNEXRZJ37CB", "external_references": [{"ref": "SRA:SRX1341923", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRX1341923"}], "experiment_sets": [{"status": "released", "accession": "4DNESCTABFXV", "@id": "/experiment-sets/4DNESCTABFXV/", "uuid": "bd180a8b-58be-45da-9f76-bbf3580c7ef1", "display_title": "4DNESCTABFXV", "experimentset_type": "custom", "@type": ["ExperimentSet", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "accession": "4DNESNOJ28YT", "@id": "/experiment-set-replicates/4DNESNOJ28YT/", "uuid": "f46bd57d-075d-4663-aa7a-91f16d896cd0", "display_title": "4DNESNOJ28YT", "experimentset_type": "replicate", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"status": "current", "short_attribution": "Sanborn AL et al. (2015)", "display_title": "Sanborn AL et al. (2015) PMID:26499245", "@type": ["Publication", "Item"], "authors": ["Sanborn AL", "Rao SS", "Huang SC", "Durand NC", "Huntley MH", "Jewett AI", "Bochkov ID", "Chinnappan D", "Cutkosky A", "Li J", "Geeting KP", "Gnirke A", "Melnikov A", "McKenna D", "Stamenova EK", "Lander ES", "Aiden EL"], "@id": "/publications/5427c34d-1ff4-409c-9ce1-97c7a5af2965/", "uuid": "5427c34d-1ff4-409c-9ce1-97c7a5af2965", "date_published": "2015-11-25", "title": "Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "abstract": "We recently used in situ Hi-C to create kilobase-resolution 3D maps of mammalian  genomes. Here, we combine these maps with new Hi-C, microscopy, and genome-editing experiments to study the physical structure of chromatin fibers, domains, and loops. We find that the observed contact domains are inconsistent with the equilibrium state for an ordinary condensed polymer. Combining Hi-C data and novel mathematical theorems, we show that contact domains are also not consistent with a fractal globule. Instead, we use physical simulations to study  two models of genome folding. In one, intermonomer attraction during polymer condensation leads to formation of an anisotropic \"tension globule.\" In the other, CCCTC-binding factor (CTCF) and cohesin act together to extrude unknotted  loops during interphase. Both models are consistent with the observed contact domains and with the observation that contact domains tend to form inside loops.  However, the extrusion model explains a far wider array of observations, such as  why loops tend not to overlap and why the CTCF-binding motifs at pairs of loop anchors lie in the convergent orientation. Finally, we perform 13 genome-editing  experiments examining the effect of altering CTCF-binding sites on chromatin folding. The convergent rule correctly predicts the affected loops in every case. Moreover, the extrusion model accurately predicts in silico the 3D maps resulting from each experiment using only the location of CTCF-binding sites in the WT. Thus, we show that it is possible to disrupt, restore, and move loops and domains using targeted mutations as small as a single base pair.", "ID": "PMID:26499245", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"date_published": "2015-11-25", "@type": ["Publication", "Item"], "uuid": "5427c34d-1ff4-409c-9ce1-97c7a5af2965", "ID": "PMID:26499245", "authors": ["Sanborn AL", "Rao SS", "Huang SC", "Durand NC", "Huntley MH", "Jewett AI", "Bochkov ID", "Chinnappan D", "Cutkosky A", "Li J", "Geeting KP", "Gnirke A", "Melnikov A", "McKenna D", "Stamenova EK", "Lander ES", "Aiden EL"], "abstract": "We recently used in situ Hi-C to create kilobase-resolution 3D maps of mammalian  genomes. Here, we combine these maps with new Hi-C, microscopy, and genome-editing experiments to study the physical structure of chromatin fibers, domains, and loops. We find that the observed contact domains are inconsistent with the equilibrium state for an ordinary condensed polymer. Combining Hi-C data and novel mathematical theorems, we show that contact domains are also not consistent with a fractal globule. Instead, we use physical simulations to study  two models of genome folding. In one, intermonomer attraction during polymer condensation leads to formation of an anisotropic \"tension globule.\" In the other, CCCTC-binding factor (CTCF) and cohesin act together to extrude unknotted  loops during interphase. Both models are consistent with the observed contact domains and with the observation that contact domains tend to form inside loops.  However, the extrusion model explains a far wider array of observations, such as  why loops tend not to overlap and why the CTCF-binding motifs at pairs of loop anchors lie in the convergent orientation. Finally, we perform 13 genome-editing  experiments examining the effect of altering CTCF-binding sites on chromatin folding. The convergent rule correctly predicts the affected loops in every case. Moreover, the extrusion model accurately predicts in silico the 3D maps resulting from each experiment using only the location of CTCF-binding sites in the WT. Thus, we show that it is possible to disrupt, restore, and move loops and domains using targeted mutations as small as a single base pair.", "short_attribution": "Sanborn AL et al. (2015)", "@id": "/publications/5427c34d-1ff4-409c-9ce1-97c7a5af2965/", "display_title": "Sanborn AL et al. (2015) PMID:26499245", "title": "Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes.", "status": "current", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Target", "value": "GRCh38:1:179830865-181830865 region, GRCh38:5:30999893-32999894 region, GRCh38:8:131987753-133987757 region", "combined": "Target: GRCh38:1:179830865-181830865 region, GRCh38:5:30999893-32999894 region, GRCh38:8:131987753-133987757 region"}, "experiment_summary": "Capture Hi-C on HAP-1 with MboI", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSOFUL6I6/", "embedded_path": "biosample.badges", "item": {"messages": ["Biosample missing Cell Culture Details", "HAP-1 biosample missing ploidy authentication"], "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."}}}]}, "validation-errors": []}