{"lab": {"status": "current", "@type": ["Lab", "Item"], "@id": "/labs/jay-ashok-shendure-lab/", "correspondence": [{"contact_email": "c2hlbmR1cmVAdXcuZWR1", "@id": "/users/56682066-d5c0-48b5-aec9-9234c1135b22/", "display_title": "Jay Ashok Shendure"}], "uuid": "f9d7e470-cde0-4847-b629-2b70ae4e31cf", "display_title": "Jay Ashok Shendure, UW", "title": "Jay Ashok Shendure, UW", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.f9d7e470-cde0-4847-b629-2b70ae4e31cf"]}}, "tags": ["4DN Joint Analysis 2018"], "award": {"display_title": "UNIVERSITY OF WASHINGTON CENTER FOR NUCLEAR ORGANIZATION AND FUNCTION", "name": "1U54DK107979-01", "center_title": "NOFIC - Shendure", "uuid": "fcc7f634-9252-499f-b79c-380795af2ddd", "status": "current", "description": "NOFIC: A current grand challenge in genomics involves accurately assaying, at all relevant scales, the 3D conformation of DNA in vivo and then linking conformational changes to dynamic processes such as the cell cycle, differentiation and disease. Here we propose to create the University of Washington Center for Nuclear Organization and Function, bringing together an interdisciplinary team of investigators whose diverse areas of expertise - technology development, computational modeling, and mouse and human biology - make them ideally suited to this challenge. Our overall hypothesis is that characterizing and understanding changes in genome architecture over time (the 4D nucleome) will lead to fundamental insights into human biology and disease. We will address this hypothesis by developing a combination of experimental and computational methods development, coupled with their systematic biological validation and application to development- and disease-relevant systems. On the experimental side, we will further optimize our recently developed DNase Hi- C assay, including combinatorial methods for single cells, ultimately aiming to concurrently assay nuclear architecture and gene expression within each of many single cells. On the computational side, we will extend our existing 3D modeling algorithms to account for diploidy, cell-to-cell variabilit, the hierarchical nature of genome architecture, and to explicitly model architectural changes over cell cycle and cell differentiation time scales. We will then employ several complementary computational methods to link our 4D nucleome models to existing, 1D genomics data sets. The outputs of these new experimental and computational technologies will be subjected to orthogonal validation in several well-understood model systems: human cell lines, in vivo tissues from interspecific F1 hybrid mice, mouse embryonic stem cells (ESCs) and skeletal myoblasts. We will also test specific predictions of the models in response to targeted (genome editing) or large-scale (chromosome silencing) perturbations. After initial validation and in parallel with further methods development, we will apply our new tools to the analysis of three biological systems: we will characterize the dynamics of nuclear architecture during the directed differentiation of na\u00efve human ESCs into cardiomyocytes and endothelial cells; we will test the hypothesis that cardiomyopathy-inducing mutations in the nuclear scaffolding protein, lamin A, are associated with derangements in cardiomyocyte nuclear architecture; and we will determine the changes in human cardiomyocyte nuclear architecture induced by trisomy 21. The proposed center will produce new experimental protocols for ascertaining 4D nucleome architecture, two new software toolkits for modeling the 4D nucleome and linking features of the nucleome to other types of genomic data, a variety of publicly available, large-scale 4D nucleome data sets in mouse and human systems, and fundamental insights into human biology and disease. In all of this work, we will work closely and openly with NOFIC and the 4DN Network to maximize the impact of our center and the overall program.", "@type": ["Award", "Item"], "@id": "/awards/1U54DK107979-01/", "project": "4DN", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["shendure:h1esc_scihi-c_repset"], "accession": "4DNESIKGI39T", "condition": "H1-ESC", "description": "Replicate Set of sciHi-C on H1-ESC cells - this Replicate Set is derived from experiments performed on a pure H1-ESC culture (Bio replicate 1) and a pooled mixture of H1-ESC cells and HFFc6 cells (Bio replicate 2).  Bioreplicate 2 raw files will contain reads from both cell types.  Barcode information needs to used to obtain line specific reads.  Processed files for this set will be specific to H1-ESC cells.", "date_created": "2018-02-05T20:54:56.815521+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "sci-Hi-C on five human cell lines - analyzed using topic modeling", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-05-29T15:31:24.784868+00:00"}, "public_release": "2019-02-01", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"uuid": "a2a013bf-65cf-4bdc-b1dc-db6143349a76", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEXJLO3SIH", "@id": "/experiments-hi-c/4DNEXJLO3SIH/", "status": "released", "display_title": "sci-Hi-C on H1-hESC (Tier 1) with DpnII - 4DNEXJLO3SIH", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 1, "tec_rep_no": 2, "replicate_exp": {"uuid": "4361c980-0d85-45ed-a2db-2a0c2de3477e", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEXJD1GLV9", "@id": "/experiments-hi-c/4DNEXJD1GLV9/", "status": "released", "display_title": "sci-Hi-C on H1-hESC (Tier 1) with DpnII - 4DNEXJD1GLV9", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 1, "replicate_exp": {"uuid": "094fc06f-52f9-4366-9d81-8e2ba384c0ab", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEXSXHFNQU", "@id": "/experiments-hi-c/4DNEXSXHFNQU/", "status": "released", "display_title": "sci-Hi-C on H1-hESC (Tier 1) with DpnII - 4DNEXSXHFNQU", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 2, "replicate_exp": {"uuid": "5bd7e989-9073-4777-9d2b-7e23cfd166da", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEXSR13BV7", "@id": "/experiments-hi-c/4DNEXSR13BV7/", "status": "released", "display_title": "sci-Hi-C on H1-hESC (Tier 1) with DpnII - 4DNEXSR13BV7", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_headers": [{"lab": {"@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "status": "current", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "**Sci-Hi-C**\n\n\nSci-Hi-C is a method to detect and quantify chromatin interactions in large numbers of single cells. This massively multiplexed method was developed in 2017 and it enables characterization of 3D genome architecture in thousands of single cells in parallel without requiring compartmentalization of each cell or microfluidic manipulation.\n\nThis protocol involves cross-linking the cells with formaldehyde. The cells are then permeabilized with their nuclei intact. A 4-cutter restriction enzyme DpnII is used to fragment the chromatin. Nuclei are then distributed to 96 wells, wherein the first barcode is introduced through ligation of barcoded biotinylated double-stranded bridge adaptors. Intact nuclei are then pooled and subjected to proximity ligation, followed by dilution and redistribution to a second 96-well plate. Importantly, this dilution is carried out such that each well in this second plate contains at most 25 nuclei. Following lysis, a second barcode is introduced through ligation of barcoded Y-adaptors. As the number of barcode combinations (96 \u00d7 96) exceeds the number of nuclei (96 \u00d7 25), the vast majority of single nuclei are tagged by a unique combination of barcodes. All material is once again pooled, and biotinylated junctions are purified with streptavidin beads, restriction digested, and further processed to Illumina sequencing libraries. Sequencing these molecules with relatively long paired-end reads (i.e., 2 \u00d7 250 base pairs) allows one to identify not only the genome-derived fragments of conventional Hi-C, but also external and internal barcodes,  which enable decomposition of the Hi-C data into single-cell contact probability maps.\n\n\nSee [Ramani et al 2017](https://www.nature.com/articles/nmeth.4155) for more details on in sci-Hi-C.\n\n<dl>\n<a href=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/sciHiC.jpg\" target=\"_blank\">\n<img src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/sciHiC.jpg\" style=\"width:1000px\" />  \n</a>\n<br/><br/>\n<em>Image source: Ramani et. al. Nature Methods 2017, Figure 1a </em>\n</dl>", "name": "item-page-headers.ExperimentType.sciHiC", "award": {"display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "status": "current", "@id": "/awards/1U01CA200059-01/", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Assay Description", "status": "released", "aliases": ["4dn-dcic-lab:experiment_infobox_sciHiC"], "options": {"filetype": "md", "collapsible": false, "default_open": false}, "date_created": "2018-10-10T14:42:45.156523+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-06-14T14:04:34.975645+00:00"}, "schema_version": "2", "@id": "/static-sections/ae5a6470-0694-4ba3-893a-40b170401bc0/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "ae5a6470-0694-4ba3-893a-40b170401bc0", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.56c9c683-bb11-471b-b590-c656f7dc03c1"]}, "display_title": "Assay Description", "external_references": [], "content": "**Sci-Hi-C**\n\n\nSci-Hi-C is a method to detect and quantify chromatin interactions in large numbers of single cells. This massively multiplexed method was developed in 2017 and it enables characterization of 3D genome architecture in thousands of single cells in parallel without requiring compartmentalization of each cell or microfluidic manipulation.\n\nThis protocol involves cross-linking the cells with formaldehyde. The cells are then permeabilized with their nuclei intact. A 4-cutter restriction enzyme DpnII is used to fragment the chromatin. Nuclei are then distributed to 96 wells, wherein the first barcode is introduced through ligation of barcoded biotinylated double-stranded bridge adaptors. Intact nuclei are then pooled and subjected to proximity ligation, followed by dilution and redistribution to a second 96-well plate. Importantly, this dilution is carried out such that each well in this second plate contains at most 25 nuclei. Following lysis, a second barcode is introduced through ligation of barcoded Y-adaptors. As the number of barcode combinations (96 \u00d7 96) exceeds the number of nuclei (96 \u00d7 25), the vast majority of single nuclei are tagged by a unique combination of barcodes. All material is once again pooled, and biotinylated junctions are purified with streptavidin beads, restriction digested, and further processed to Illumina sequencing libraries. Sequencing these molecules with relatively long paired-end reads (i.e., 2 \u00d7 250 base pairs) allows one to identify not only the genome-derived fragments of conventional Hi-C, but also external and internal barcodes,  which enable decomposition of the Hi-C data into single-cell contact probability maps.\n\n\nSee [Ramani et al 2017](https://www.nature.com/articles/nmeth.4155) for more details on in sci-Hi-C.\n\n<dl>\n<a href=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/sciHiC.jpg\" target=\"_blank\">\n<img src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/sciHiC.jpg\" style=\"width:1000px\" />  \n</a>\n<br/><br/>\n<em>Image source: Ramani et. al. Nature Methods 2017, Figure 1a </em>\n</dl>", "filetype": "md", "content_as_html": "<div class=\"markdown-container\"><p><strong>Sci-Hi-C</strong></p>\n<p>Sci-Hi-C is a method to detect and quantify chromatin interactions in large numbers of single cells. This massively multiplexed method was developed in 2017 and it enables characterization of 3D genome architecture in thousands of single cells in parallel without requiring compartmentalization of each cell or microfluidic manipulation.</p>\n<p>This protocol involves cross-linking the cells with formaldehyde. The cells are then permeabilized with their nuclei intact. A 4-cutter restriction enzyme DpnII is used to fragment the chromatin. Nuclei are then distributed to 96 wells, wherein the first barcode is introduced through ligation of barcoded biotinylated double-stranded bridge adaptors. Intact nuclei are then pooled and subjected to proximity ligation, followed by dilution and redistribution to a second 96-well plate. Importantly, this dilution is carried out such that each well in this second plate contains at most 25 nuclei. Following lysis, a second barcode is introduced through ligation of barcoded Y-adaptors. As the number of barcode combinations (96 \u00d7 96) exceeds the number of nuclei (96 \u00d7 25), the vast majority of single nuclei are tagged by a unique combination of barcodes. All material is once again pooled, and biotinylated junctions are purified with streptavidin beads, restriction digested, and further processed to Illumina sequencing libraries. Sequencing these molecules with relatively long paired-end reads (i.e., 2 \u00d7 250 base pairs) allows one to identify not only the genome-derived fragments of conventional Hi-C, but also external and internal barcodes,  which enable decomposition of the Hi-C data into single-cell contact probability maps.</p>\n<p>See <a href=\"https://www.nature.com/articles/nmeth.4155\" rel=\"noopener noreferrer\" target=\"_blank\">Ramani et al 2017</a> for more details on in sci-Hi-C.</p>\n<dl>\n<a href=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/sciHiC.jpg\" rel=\"noopener noreferrer\" target=\"_blank\">\n<img src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/sciHiC.jpg\" style=\"width:1000px\"/>\n</a>\n<br/><br/>\n<em>Image source: Ramani et. al. Nature Methods 2017, Figure 1a </em>\n</dl></div>"}], "project_release": "2018-02-23", "experiments_in_set": [{"display_title": "sci-Hi-C on H1-hESC (Tier 1) with DpnII - 4DNEXJLO3SIH", "accession": "4DNEXJLO3SIH", "@id": "/experiments-hi-c/4DNEXJLO3SIH/", "crosslinking_method": "3.5% Formaldehyde", "uuid": "a2a013bf-65cf-4bdc-b1dc-db6143349a76", "status": "released", "files": [{"display_title": "4DNFIMITB1P4.fastq.gz", "extra_files": [], "file_type_detailed": "reads (fastq)", "paired_end": "1", "uuid": "dbef9117-3e2c-4e60-b548-0b0bf251d71e", "md5sum": "e6f31610c8bb9b3a9d5fc057406cc31e", "upload_key": "dbef9117-3e2c-4e60-b548-0b0bf251d71e/4DNFIMITB1P4.fastq.gz", "file_size": 13677113043, "status": "released", "accession": "4DNFIMITB1P4", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIMITB1P4/", "href": "/files-fastq/4DNFIMITB1P4/@@download/4DNFIMITB1P4.fastq.gz", "file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/dbef9117-3e2c-4e60-b548-0b0bf251d71e/4DNFIMITB1P4.fastq.gz", "file_type": "reads", "lab": {"status": "current", "@id": "/labs/jay-ashok-shendure-lab/", "name": "jay-ashok-shendure-lab", "uuid": "f9d7e470-cde0-4847-b629-2b70ae4e31cf", "display_title": "Jay Ashok Shendure, UW", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.f9d7e470-cde0-4847-b629-2b70ae4e31cf"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "accession": "4DNFI7HWNPBG", "file_type_detailed": "reads (fastq)", "status": "released", "uuid": "66fc16fd-4297-4381-b4a5-0a1ef9547c38", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFI7HWNPBG.fastq.gz", "@id": "/files-fastq/4DNFI7HWNPBG/", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experimental_lab": "Jay Ashok Shendure, UW", "experiment_type": "sci-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "sci-Hi-C on five human cell lines - analyzed using topic modeling", "condition": "H1-ESC", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "Jay Ashok Shendure, UW"}, "quality_metric": {"Sequence length": "250", "@id": "/quality-metrics-fastqc/3453f3e1-a32c-453f-99bb-5327c5023be6/", "overall_quality_status": "PASS", "uuid": "3453f3e1-a32c-453f-99bb-5327c5023be6", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 63240218, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIMITB1P4/fastqc_report.html", "display_title": "QualityMetricFastqc from 2018-02-12", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "4DNFI7HWNPBG.fastq.gz", "extra_files": [], "file_type_detailed": "reads (fastq)", "paired_end": "2", "uuid": "66fc16fd-4297-4381-b4a5-0a1ef9547c38", "md5sum": "494cb7ccdd4a7f0936a13368551f7116", "upload_key": "66fc16fd-4297-4381-b4a5-0a1ef9547c38/4DNFI7HWNPBG.fastq.gz", "file_size": 14221675893, "status": "released", "accession": "4DNFI7HWNPBG", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFI7HWNPBG/", "href": "/files-fastq/4DNFI7HWNPBG/@@download/4DNFI7HWNPBG.fastq.gz", "file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/66fc16fd-4297-4381-b4a5-0a1ef9547c38/4DNFI7HWNPBG.fastq.gz", "file_type": "reads", "lab": {"status": "current", "@id": "/labs/jay-ashok-shendure-lab/", "name": "jay-ashok-shendure-lab", "uuid": "f9d7e470-cde0-4847-b629-2b70ae4e31cf", "display_title": "Jay Ashok Shendure, UW", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.f9d7e470-cde0-4847-b629-2b70ae4e31cf"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "accession": "4DNFIMITB1P4", "file_type_detailed": "reads (fastq)", "status": "released", "uuid": "dbef9117-3e2c-4e60-b548-0b0bf251d71e", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIMITB1P4.fastq.gz", "@id": "/files-fastq/4DNFIMITB1P4/", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experimental_lab": "Jay Ashok Shendure, UW", "experiment_type": "sci-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "sci-Hi-C on five human cell lines - analyzed using topic modeling", "condition": "H1-ESC", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "Jay Ashok Shendure, UW"}, "quality_metric": {"Sequence length": "250", "@id": "/quality-metrics-fastqc/4fd36d94-44d1-4bae-a820-a114b270f1a3/", "overall_quality_status": "PASS", "uuid": "4fd36d94-44d1-4bae-a820-a114b270f1a3", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 63240218, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI7HWNPBG/fastqc_report.html", "display_title": "QualityMetricFastqc from 2018-02-12", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "4DNFILSICU64.fastq.gz", "extra_files": [], "file_type_detailed": "reads (fastq)", "paired_end": "1", "uuid": "e35d6dbe-8c41-4df5-8bcb-e781920729d4", "md5sum": "ea8cbfbeb3ba9b3a32da7fd5e9e5bd48", "upload_key": "e35d6dbe-8c41-4df5-8bcb-e781920729d4/4DNFILSICU64.fastq.gz", "file_size": 23229924682, "status": "released", "accession": "4DNFILSICU64", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFILSICU64/", "href": "/files-fastq/4DNFILSICU64/@@download/4DNFILSICU64.fastq.gz", "file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/e35d6dbe-8c41-4df5-8bcb-e781920729d4/4DNFILSICU64.fastq.gz", "file_type": "reads", "lab": {"status": "current", "@id": "/labs/jay-ashok-shendure-lab/", "name": "jay-ashok-shendure-lab", "uuid": "f9d7e470-cde0-4847-b629-2b70ae4e31cf", "display_title": "Jay Ashok Shendure, UW", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.f9d7e470-cde0-4847-b629-2b70ae4e31cf"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "accession": "4DNFIBQM8JCD", "file_type_detailed": "reads (fastq)", "status": "released", "uuid": "0b435a18-8aff-4b3b-ac5a-b07baab8f3f0", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIBQM8JCD.fastq.gz", "@id": "/files-fastq/4DNFIBQM8JCD/", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experimental_lab": "Jay Ashok Shendure, UW", "experiment_type": "sci-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "sci-Hi-C on five human cell lines - analyzed using topic modeling", "condition": "H1-ESC", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "Jay Ashok Shendure, UW"}, "quality_metric": {"Sequence length": "250", "@id": "/quality-metrics-fastqc/82b55462-873d-48a4-8a0a-a4fbe9181b17/", "overall_quality_status": "PASS", "uuid": "82b55462-873d-48a4-8a0a-a4fbe9181b17", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 107300246, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFILSICU64/fastqc_report.html", "display_title": "QualityMetricFastqc from 2018-02-12", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "4DNFIBQM8JCD.fastq.gz", "extra_files": [], "file_type_detailed": "reads (fastq)", "paired_end": "2", "uuid": "0b435a18-8aff-4b3b-ac5a-b07baab8f3f0", "md5sum": "1881f2f5e407545d1794fccbbb539136", "upload_key": "0b435a18-8aff-4b3b-ac5a-b07baab8f3f0/4DNFIBQM8JCD.fastq.gz", "file_size": 24042154903, "status": "released", "accession": "4DNFIBQM8JCD", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIBQM8JCD/", "href": "/files-fastq/4DNFIBQM8JCD/@@download/4DNFIBQM8JCD.fastq.gz", "file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/0b435a18-8aff-4b3b-ac5a-b07baab8f3f0/4DNFIBQM8JCD.fastq.gz", "file_type": "reads", "lab": {"status": "current", "@id": "/labs/jay-ashok-shendure-lab/", "name": "jay-ashok-shendure-lab", "uuid": "f9d7e470-cde0-4847-b629-2b70ae4e31cf", "display_title": "Jay Ashok Shendure, UW", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.f9d7e470-cde0-4847-b629-2b70ae4e31cf"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "accession": "4DNFILSICU64", "file_type_detailed": "reads (fastq)", "status": "released", "uuid": "e35d6dbe-8c41-4df5-8bcb-e781920729d4", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFILSICU64.fastq.gz", "@id": "/files-fastq/4DNFILSICU64/", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experimental_lab": "Jay Ashok Shendure, UW", "experiment_type": "sci-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "sci-Hi-C on five human cell lines - analyzed using topic modeling", "condition": "H1-ESC", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "Jay Ashok Shendure, UW"}, "quality_metric": {"Sequence length": "250", "@id": "/quality-metrics-fastqc/fb53b7f5-73ff-4d37-8779-18248a4c927c/", "overall_quality_status": "PASS", "uuid": "fb53b7f5-73ff-4d37-8779-18248a4c927c", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 107300246, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIBQM8JCD/fastqc_report.html", "display_title": "QualityMetricFastqc from 2018-02-12", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@type": ["ExperimentHiC", "Experiment", "Item"], "reference_files": [{"file_size": 864, "@id": "/files-reference/4DNFIUSK42KP/", "display_title": "4DNFIUSK42KP.txt", "file_type_detailed": "barcodes (txt)", "accession": "4DNFIUSK42KP", "@type": ["FileReference", "File", "Item"], "file_classification": "ancillary file", "uuid": "c8047497-0004-4f12-9387-26bd018903ee", "status": "released", "md5sum": "fc187be5c3da1f502ddfa26559dcbee9", "file_type": "barcodes", "href": "/files-reference/4DNFIUSK42KP/@@download/4DNFIUSK42KP.txt", "contributing_labs": [{"name": "william-noble-lab", "status": "current", "uuid": "a0812d8f-a4cc-4dbe-bd22-76e6e573b5ed", "@id": "/labs/william-noble-lab/", "@type": ["Lab", "Item"], "display_title": "William Noble, UW", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.a0812d8f-a4cc-4dbe-bd22-76e6e573b5ed"]}}], "file_format": {"@type": ["FileFormat", "Item"], "file_format": "txt", "@id": "/file-formats/txt/", "display_title": "txt", "status": "released", "uuid": "0cd4e777-a596-4927-95c8-b07716121aa3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "@id": "/labs/jay-ashok-shendure-lab/", "name": "jay-ashok-shendure-lab", "display_title": "Jay Ashok Shendure, UW", "status": "current", "uuid": "f9d7e470-cde0-4847-b629-2b70ae4e31cf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.f9d7e470-cde0-4847-b629-2b70ae4e31cf"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_size": 864, "@id": "/files-reference/4DNFINE9JUAI/", "display_title": "4DNFINE9JUAI.txt", "file_type_detailed": "barcodes (txt)", "accession": "4DNFINE9JUAI", "@type": ["FileReference", "File", "Item"], "file_classification": "ancillary file", "uuid": "cfb717e5-101a-4f12-afcc-d8b06b48ee6e", "status": "released", "md5sum": "f5f398961f15b57fca8118d7a11735af", "file_type": "barcodes", "href": "/files-reference/4DNFINE9JUAI/@@download/4DNFINE9JUAI.txt", "contributing_labs": [{"name": "william-noble-lab", "status": "current", "uuid": "a0812d8f-a4cc-4dbe-bd22-76e6e573b5ed", "@id": "/labs/william-noble-lab/", "@type": ["Lab", "Item"], "display_title": "William Noble, UW", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.a0812d8f-a4cc-4dbe-bd22-76e6e573b5ed"]}}], "file_format": {"@type": ["FileFormat", "Item"], "file_format": "txt", "@id": "/file-formats/txt/", "display_title": "txt", "status": "released", "uuid": "0cd4e777-a596-4927-95c8-b07716121aa3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "@id": "/labs/jay-ashok-shendure-lab/", "name": "jay-ashok-shendure-lab", "display_title": "Jay Ashok Shendure, UW", "status": "current", "uuid": "f9d7e470-cde0-4847-b629-2b70ae4e31cf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.f9d7e470-cde0-4847-b629-2b70ae4e31cf"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "biosample": {"treatments_summary": "None", "@type": ["Biosample", "Item"], "status": "released", "display_title": "4DNBSOB39EE9", "biosample_category": ["H1-hESC", "Human stem cell"], "accession": "4DNBSOB39EE9", "uuid": "fa226997-c9c4-45b2-9f52-fe05a2954551", "biosample_type": "stem cells", "modifications_summary": "None", "biosource_summary": "H1-hESC (Tier 1)", "@id": "/biosamples/4DNBSOB39EE9/", "biosource": [{"@type": ["Biosource", "Item"], "@id": "/biosources/4DNSRV3SKQ8M/", "cell_line_tier": "Tier 1", "uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "status": "released", "biosource_type": "stem cell derived cell line", "accession": "4DNSRV3SKQ8M", "cell_line": {"uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "@type": ["OntologyTerm", "Item"], "preferred_name": "H1-hESC", "synonyms": ["H1"], "term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "status": "released", "display_title": "H1-hESC", "term_name": "H1-hESC", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/GO:0005623/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000000/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"preferred_name": "stem cell", "term_name": "stem cell", "synonyms": ["animal stem cell"], "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "term_id": "CL:0000034", "@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/CL:0000034/", "display_title": "stem cell", "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "display_title": "H. sapiens", "name": "human", "status": "released", "scientific_name": "Homo sapiens", "@type": ["Organism", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "modifications": [], "cell_culture_details": [{"status": "released", "display_title": "BiosampleCellCulture from 2018-01-30", "@id": "/biosample-cell-cultures/19335a9d-c68f-4b34-a754-352b38df06a9/", "uuid": "19335a9d-c68f-4b34-a754-352b38df06a9", "@type": ["BiosampleCellCulture", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "treatments": [], "badges": [{"messages": ["Biosample missing doubling_number", "Biosample missing culture_duration"], "badge": {"@type": ["Badge", "Item"], "badge_classification": "Warning", "badge_icon": "/static/img/badges/biosample-icon.svg", "display_title": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "title": "Biosample Metadata Incomplete", "warning": "Biosample Metadata Incomplete", "status": "released", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "@id": "/badges/biosample-metadata-incomplete/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "tissue_organ_info": {"tissue_source": "stem cell"}}, "experiment_type": {"@type": ["ExperimentType", "Item"], "assay_subclassification": "DNA-DNA Pairwise Interactions - Single Cell", "assay_classification": "3C via Ligation", "uuid": "358540cb-e1b8-4d5a-b0ab-7c1b433a17ce", "@id": "/experiment-types/sci-hi-c/", "other_tags": ["DNA-DNA", "Single Cell", "3D", "Pairwise"], "assay_subclass_short": "Hi-C (single cell)", "display_title": "sci-Hi-C", "title": "sci-Hi-C", "experiment_category": "Sequencing", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"combined": "Enzyme: DpnII", "value": "DpnII", "field": "Enzyme"}, "digestion_enzyme": {"status": "released", "uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "@id": "/enzymes/DpnII/", "@type": ["Enzyme", "Item"], "display_title": "DpnII", "name": "DpnII", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2020-02-25T22:24:41.435520+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"display_title": "sci-Hi-C on H1-hESC (Tier 1) with DpnII - 4DNEXJD1GLV9", "accession": "4DNEXJD1GLV9", "@id": "/experiments-hi-c/4DNEXJD1GLV9/", "crosslinking_method": "3.5% Formaldehyde", "uuid": "4361c980-0d85-45ed-a2db-2a0c2de3477e", "status": "released", "files": [{"display_title": "4DNFI3D19GAJ.fastq.gz", "extra_files": [], "file_type_detailed": "reads (fastq)", "paired_end": "1", "uuid": "d4f5832a-3aa7-4925-9d8c-b0368efcdb29", "md5sum": "6f1aeaeb45db85a6e6cfc2d506c00176", "upload_key": "d4f5832a-3aa7-4925-9d8c-b0368efcdb29/4DNFI3D19GAJ.fastq.gz", "file_size": 11125002149, "status": "released", "accession": "4DNFI3D19GAJ", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFI3D19GAJ/", "href": "/files-fastq/4DNFI3D19GAJ/@@download/4DNFI3D19GAJ.fastq.gz", "file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/d4f5832a-3aa7-4925-9d8c-b0368efcdb29/4DNFI3D19GAJ.fastq.gz", "file_type": "reads", "lab": {"status": "current", "@id": "/labs/jay-ashok-shendure-lab/", "name": "jay-ashok-shendure-lab", "uuid": "f9d7e470-cde0-4847-b629-2b70ae4e31cf", "display_title": "Jay Ashok Shendure, UW", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.f9d7e470-cde0-4847-b629-2b70ae4e31cf"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "accession": "4DNFI4M8ASHF", "file_type_detailed": "reads (fastq)", "status": "released", "uuid": "adb98ee6-a688-4283-8c86-e74df26cd460", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFI4M8ASHF.fastq.gz", "@id": "/files-fastq/4DNFI4M8ASHF/", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experimental_lab": "Jay Ashok Shendure, UW", "experiment_type": "sci-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "sci-Hi-C on five human cell lines - analyzed using topic modeling", "condition": "H1-ESC", "replicate_info": "Biorep 1, Techrep 2", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "Jay Ashok Shendure, UW"}, "quality_metric": {"Sequence length": "250", "@id": "/quality-metrics-fastqc/daaa56ec-d48a-488e-bd8b-9a574dcbe02a/", "overall_quality_status": "PASS", "uuid": "daaa56ec-d48a-488e-bd8b-9a574dcbe02a", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 50703317, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI3D19GAJ/fastqc_report.html", "display_title": "QualityMetricFastqc from 2018-02-12", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "4DNFI4M8ASHF.fastq.gz", "extra_files": [], "file_type_detailed": "reads (fastq)", "paired_end": "2", "uuid": "adb98ee6-a688-4283-8c86-e74df26cd460", "md5sum": "dfd5b7dc49583fc69313888aa0168a5d", "upload_key": "adb98ee6-a688-4283-8c86-e74df26cd460/4DNFI4M8ASHF.fastq.gz", "file_size": 11456340061, "status": "released", "accession": "4DNFI4M8ASHF", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFI4M8ASHF/", "href": "/files-fastq/4DNFI4M8ASHF/@@download/4DNFI4M8ASHF.fastq.gz", "file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/adb98ee6-a688-4283-8c86-e74df26cd460/4DNFI4M8ASHF.fastq.gz", "file_type": "reads", "lab": {"status": "current", "@id": "/labs/jay-ashok-shendure-lab/", "name": "jay-ashok-shendure-lab", "uuid": "f9d7e470-cde0-4847-b629-2b70ae4e31cf", "display_title": "Jay Ashok Shendure, UW", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.f9d7e470-cde0-4847-b629-2b70ae4e31cf"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "accession": "4DNFI3D19GAJ", "file_type_detailed": "reads (fastq)", "status": "released", "uuid": "d4f5832a-3aa7-4925-9d8c-b0368efcdb29", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFI3D19GAJ.fastq.gz", "@id": "/files-fastq/4DNFI3D19GAJ/", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experimental_lab": "Jay Ashok Shendure, UW", "experiment_type": "sci-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "sci-Hi-C on five human cell lines - analyzed using topic modeling", "condition": "H1-ESC", "replicate_info": "Biorep 1, Techrep 2", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "Jay Ashok Shendure, UW"}, "quality_metric": {"Sequence length": "250", "@id": "/quality-metrics-fastqc/265d64d0-740e-4c54-bfeb-629adae8f1b0/", "overall_quality_status": "PASS", "uuid": "265d64d0-740e-4c54-bfeb-629adae8f1b0", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 50703317, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI4M8ASHF/fastqc_report.html", "display_title": "QualityMetricFastqc from 2018-02-12", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "4DNFITQJC8EO.fastq.gz", "extra_files": [], "file_type_detailed": "reads (fastq)", "paired_end": "1", "uuid": "cdee76f4-afd1-4d29-ac17-6d85d8d82cc5", "md5sum": "ad80e1963523fdea6c286d39a77f4e70", "upload_key": "cdee76f4-afd1-4d29-ac17-6d85d8d82cc5/4DNFITQJC8EO.fastq.gz", "file_size": 15346053734, "status": "released", "accession": "4DNFITQJC8EO", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFITQJC8EO/", "href": "/files-fastq/4DNFITQJC8EO/@@download/4DNFITQJC8EO.fastq.gz", "file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/cdee76f4-afd1-4d29-ac17-6d85d8d82cc5/4DNFITQJC8EO.fastq.gz", "file_type": "reads", "lab": {"status": "current", "@id": "/labs/jay-ashok-shendure-lab/", "name": "jay-ashok-shendure-lab", "uuid": "f9d7e470-cde0-4847-b629-2b70ae4e31cf", "display_title": "Jay Ashok Shendure, UW", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.f9d7e470-cde0-4847-b629-2b70ae4e31cf"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "accession": "4DNFIBID1LF4", "file_type_detailed": "reads (fastq)", "status": "released", "uuid": "7180e92e-a822-4cb7-9502-e108b8749e31", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIBID1LF4.fastq.gz", "@id": "/files-fastq/4DNFIBID1LF4/", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experimental_lab": "Jay Ashok Shendure, UW", "experiment_type": "sci-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "sci-Hi-C on five human cell lines - analyzed using topic modeling", "condition": "H1-ESC", "replicate_info": "Biorep 1, Techrep 2", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "Jay Ashok Shendure, UW"}, "quality_metric": {"Sequence length": "250", "@id": "/quality-metrics-fastqc/7342989d-6bac-4595-b3e6-f302c6645e2d/", "overall_quality_status": "PASS", "uuid": "7342989d-6bac-4595-b3e6-f302c6645e2d", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 69872488, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFITQJC8EO/fastqc_report.html", "display_title": "QualityMetricFastqc from 2018-02-12", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "4DNFIBID1LF4.fastq.gz", "extra_files": [], "file_type_detailed": "reads (fastq)", "paired_end": "2", "uuid": "7180e92e-a822-4cb7-9502-e108b8749e31", "md5sum": "a9a5992f7c5aab3d990cf6d6df4623bd", "upload_key": "7180e92e-a822-4cb7-9502-e108b8749e31/4DNFIBID1LF4.fastq.gz", "file_size": 15741185338, "status": "released", "accession": "4DNFIBID1LF4", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIBID1LF4/", "href": "/files-fastq/4DNFIBID1LF4/@@download/4DNFIBID1LF4.fastq.gz", "file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/7180e92e-a822-4cb7-9502-e108b8749e31/4DNFIBID1LF4.fastq.gz", "file_type": "reads", "lab": {"status": "current", "@id": "/labs/jay-ashok-shendure-lab/", "name": "jay-ashok-shendure-lab", "uuid": "f9d7e470-cde0-4847-b629-2b70ae4e31cf", "display_title": "Jay Ashok Shendure, UW", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.f9d7e470-cde0-4847-b629-2b70ae4e31cf"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "accession": "4DNFITQJC8EO", "file_type_detailed": "reads (fastq)", "status": "released", "uuid": "cdee76f4-afd1-4d29-ac17-6d85d8d82cc5", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFITQJC8EO.fastq.gz", "@id": "/files-fastq/4DNFITQJC8EO/", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experimental_lab": "Jay Ashok Shendure, UW", "experiment_type": "sci-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "sci-Hi-C on five human cell lines - analyzed using topic modeling", "condition": "H1-ESC", "replicate_info": "Biorep 1, Techrep 2", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "Jay Ashok Shendure, UW"}, "quality_metric": {"Sequence length": "250", "@id": "/quality-metrics-fastqc/e2add693-14b5-4ba3-b4cb-1b332196165b/", "overall_quality_status": "PASS", "uuid": "e2add693-14b5-4ba3-b4cb-1b332196165b", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 69872488, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIBID1LF4/fastqc_report.html", "display_title": "QualityMetricFastqc from 2018-02-12", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@type": ["ExperimentHiC", "Experiment", "Item"], "reference_files": [{"file_size": 864, "@id": "/files-reference/4DNFIUSK42KP/", "display_title": "4DNFIUSK42KP.txt", "file_type_detailed": "barcodes (txt)", "accession": "4DNFIUSK42KP", "@type": ["FileReference", "File", "Item"], "file_classification": "ancillary file", "uuid": "c8047497-0004-4f12-9387-26bd018903ee", "status": "released", "md5sum": "fc187be5c3da1f502ddfa26559dcbee9", "file_type": "barcodes", "href": "/files-reference/4DNFIUSK42KP/@@download/4DNFIUSK42KP.txt", "contributing_labs": [{"name": "william-noble-lab", "status": "current", "uuid": "a0812d8f-a4cc-4dbe-bd22-76e6e573b5ed", "@id": "/labs/william-noble-lab/", "@type": ["Lab", "Item"], "display_title": "William Noble, UW", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.a0812d8f-a4cc-4dbe-bd22-76e6e573b5ed"]}}], "file_format": {"@type": ["FileFormat", "Item"], "file_format": "txt", "@id": "/file-formats/txt/", "display_title": "txt", "status": "released", "uuid": "0cd4e777-a596-4927-95c8-b07716121aa3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "@id": "/labs/jay-ashok-shendure-lab/", "name": "jay-ashok-shendure-lab", "display_title": "Jay Ashok Shendure, UW", "status": "current", "uuid": "f9d7e470-cde0-4847-b629-2b70ae4e31cf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.f9d7e470-cde0-4847-b629-2b70ae4e31cf"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_size": 864, "@id": "/files-reference/4DNFINE9JUAI/", "display_title": "4DNFINE9JUAI.txt", "file_type_detailed": "barcodes (txt)", "accession": "4DNFINE9JUAI", "@type": ["FileReference", "File", "Item"], "file_classification": "ancillary file", "uuid": "cfb717e5-101a-4f12-afcc-d8b06b48ee6e", "status": "released", "md5sum": "f5f398961f15b57fca8118d7a11735af", "file_type": "barcodes", "href": "/files-reference/4DNFINE9JUAI/@@download/4DNFINE9JUAI.txt", "contributing_labs": [{"name": "william-noble-lab", "status": "current", "uuid": "a0812d8f-a4cc-4dbe-bd22-76e6e573b5ed", "@id": "/labs/william-noble-lab/", "@type": ["Lab", "Item"], "display_title": "William Noble, UW", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.a0812d8f-a4cc-4dbe-bd22-76e6e573b5ed"]}}], "file_format": {"@type": ["FileFormat", "Item"], "file_format": "txt", "@id": "/file-formats/txt/", "display_title": "txt", "status": "released", "uuid": "0cd4e777-a596-4927-95c8-b07716121aa3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "@id": "/labs/jay-ashok-shendure-lab/", "name": "jay-ashok-shendure-lab", "display_title": "Jay Ashok Shendure, UW", "status": "current", "uuid": "f9d7e470-cde0-4847-b629-2b70ae4e31cf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.f9d7e470-cde0-4847-b629-2b70ae4e31cf"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "biosample": {"treatments_summary": "None", "@type": ["Biosample", "Item"], "status": "released", "display_title": "4DNBSOB39EE9", "biosample_category": ["H1-hESC", "Human stem cell"], "accession": "4DNBSOB39EE9", "uuid": "fa226997-c9c4-45b2-9f52-fe05a2954551", "biosample_type": "stem cells", "modifications_summary": "None", "biosource_summary": "H1-hESC (Tier 1)", "@id": "/biosamples/4DNBSOB39EE9/", "biosource": [{"@type": ["Biosource", "Item"], "@id": "/biosources/4DNSRV3SKQ8M/", "cell_line_tier": "Tier 1", "uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "status": "released", "biosource_type": "stem cell derived cell line", "accession": "4DNSRV3SKQ8M", "cell_line": {"uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "@type": ["OntologyTerm", "Item"], "preferred_name": "H1-hESC", "synonyms": ["H1"], "term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "status": "released", "display_title": "H1-hESC", "term_name": "H1-hESC", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/GO:0005623/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000000/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"preferred_name": "stem cell", "term_name": "stem cell", "synonyms": ["animal stem cell"], "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "term_id": "CL:0000034", "@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/CL:0000034/", "display_title": "stem cell", "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "display_title": "H. sapiens", "name": "human", "status": "released", "scientific_name": "Homo sapiens", "@type": ["Organism", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "modifications": [], "cell_culture_details": [{"status": "released", "display_title": "BiosampleCellCulture from 2018-01-30", "@id": "/biosample-cell-cultures/19335a9d-c68f-4b34-a754-352b38df06a9/", "uuid": "19335a9d-c68f-4b34-a754-352b38df06a9", "@type": ["BiosampleCellCulture", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "treatments": [], "badges": [{"messages": ["Biosample missing doubling_number", "Biosample missing culture_duration"], "badge": {"@type": ["Badge", "Item"], "badge_classification": "Warning", "badge_icon": "/static/img/badges/biosample-icon.svg", "display_title": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "title": "Biosample Metadata Incomplete", "warning": "Biosample Metadata Incomplete", "status": "released", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "@id": "/badges/biosample-metadata-incomplete/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "tissue_organ_info": {"tissue_source": "stem cell"}}, "experiment_type": {"@type": ["ExperimentType", "Item"], "assay_subclassification": "DNA-DNA Pairwise Interactions - Single Cell", "assay_classification": "3C via Ligation", "uuid": "358540cb-e1b8-4d5a-b0ab-7c1b433a17ce", "@id": "/experiment-types/sci-hi-c/", "other_tags": ["DNA-DNA", "Single Cell", "3D", "Pairwise"], "assay_subclass_short": "Hi-C (single cell)", "display_title": "sci-Hi-C", "title": "sci-Hi-C", "experiment_category": "Sequencing", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"combined": "Enzyme: DpnII", "value": "DpnII", "field": "Enzyme"}, "digestion_enzyme": {"status": "released", "uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "@id": "/enzymes/DpnII/", "@type": ["Enzyme", "Item"], "display_title": "DpnII", "name": "DpnII", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2020-02-25T22:24:41.156891+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"display_title": "sci-Hi-C on H1-hESC (Tier 1) with DpnII - 4DNEXSXHFNQU", "accession": "4DNEXSXHFNQU", "@id": "/experiments-hi-c/4DNEXSXHFNQU/", "crosslinking_method": "3.5% Formaldehyde", "uuid": "094fc06f-52f9-4366-9d81-8e2ba384c0ab", "status": "released", "files": [{"display_title": "4DNFINHJ5UBM.fastq.gz", "extra_files": [], "file_type_detailed": "reads (fastq)", "paired_end": "1", "uuid": "16c2d017-4beb-4914-a456-2c7c58c47ca7", "md5sum": "47b37aca65ffe7abcf0ecbce2a0924e0", "upload_key": "16c2d017-4beb-4914-a456-2c7c58c47ca7/4DNFINHJ5UBM.fastq.gz", "file_size": 14654634065, "status": "released", "accession": "4DNFINHJ5UBM", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFINHJ5UBM/", "href": "/files-fastq/4DNFINHJ5UBM/@@download/4DNFINHJ5UBM.fastq.gz", "file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/16c2d017-4beb-4914-a456-2c7c58c47ca7/4DNFINHJ5UBM.fastq.gz", "file_type": "reads", "lab": {"status": "current", "@id": "/labs/jay-ashok-shendure-lab/", "name": "jay-ashok-shendure-lab", "uuid": "f9d7e470-cde0-4847-b629-2b70ae4e31cf", "display_title": "Jay Ashok Shendure, UW", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.f9d7e470-cde0-4847-b629-2b70ae4e31cf"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "accession": "4DNFIG2C1HMF", "file_type_detailed": "reads (fastq)", "status": "released", "uuid": "bf24229c-d666-489e-8f9b-769fcc3e1e83", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIG2C1HMF.fastq.gz", "@id": "/files-fastq/4DNFIG2C1HMF/", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experiment_type": "sci-Hi-C", "experimental_lab": "Jay Ashok Shendure, UW", "dataset": "multiple", "condition": "multiple", "biosource_name": "multiple", "experiment_bucket": "raw file", "lab_name": "Jay Ashok Shendure, UW"}, "quality_metric": {"Sequence length": "250", "@id": "/quality-metrics-fastqc/91e5eaa5-f1a8-4c91-9ef3-49045098b680/", "overall_quality_status": "PASS", "uuid": "91e5eaa5-f1a8-4c91-9ef3-49045098b680", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 68169271, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFINHJ5UBM/fastqc_report.html", "display_title": "QualityMetricFastqc from 2018-02-12", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "4DNFIG2C1HMF.fastq.gz", "extra_files": [], "file_type_detailed": "reads (fastq)", "paired_end": "2", "uuid": "bf24229c-d666-489e-8f9b-769fcc3e1e83", "md5sum": "e5d79a2cc38199701b2eae40122e0a21", "upload_key": "bf24229c-d666-489e-8f9b-769fcc3e1e83/4DNFIG2C1HMF.fastq.gz", "file_size": 15400473700, "status": "released", "accession": "4DNFIG2C1HMF", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIG2C1HMF/", "href": "/files-fastq/4DNFIG2C1HMF/@@download/4DNFIG2C1HMF.fastq.gz", "file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/bf24229c-d666-489e-8f9b-769fcc3e1e83/4DNFIG2C1HMF.fastq.gz", "file_type": "reads", "lab": {"status": "current", "@id": "/labs/jay-ashok-shendure-lab/", "name": "jay-ashok-shendure-lab", "uuid": "f9d7e470-cde0-4847-b629-2b70ae4e31cf", "display_title": "Jay Ashok Shendure, UW", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.f9d7e470-cde0-4847-b629-2b70ae4e31cf"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "accession": "4DNFINHJ5UBM", "file_type_detailed": "reads (fastq)", "status": "released", "uuid": "16c2d017-4beb-4914-a456-2c7c58c47ca7", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFINHJ5UBM.fastq.gz", "@id": "/files-fastq/4DNFINHJ5UBM/", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experiment_type": "sci-Hi-C", "experimental_lab": "Jay Ashok Shendure, UW", "dataset": "multiple", "condition": "multiple", "biosource_name": "multiple", "experiment_bucket": "raw file", "lab_name": "Jay Ashok Shendure, UW"}, "quality_metric": {"Sequence length": "250", "@id": "/quality-metrics-fastqc/d3a83a2c-ff85-48ee-903e-0c1a7c272e5b/", "overall_quality_status": "PASS", "uuid": "d3a83a2c-ff85-48ee-903e-0c1a7c272e5b", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 68169271, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIG2C1HMF/fastqc_report.html", "display_title": "QualityMetricFastqc from 2018-02-12", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "4DNFIFR5WECM.fastq.gz", "extra_files": [], "file_type_detailed": "reads (fastq)", "paired_end": "1", "uuid": "02c89afe-6dd2-4ed1-878c-5f9e3e993e7d", "md5sum": "21c5158d7f2c340d00b0b84fa6219b49", "upload_key": "02c89afe-6dd2-4ed1-878c-5f9e3e993e7d/4DNFIFR5WECM.fastq.gz", "file_size": 15984600067, "status": "released", "accession": "4DNFIFR5WECM", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIFR5WECM/", "href": "/files-fastq/4DNFIFR5WECM/@@download/4DNFIFR5WECM.fastq.gz", "file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/02c89afe-6dd2-4ed1-878c-5f9e3e993e7d/4DNFIFR5WECM.fastq.gz", "file_type": "reads", "lab": {"status": "current", "@id": "/labs/jay-ashok-shendure-lab/", "name": "jay-ashok-shendure-lab", "uuid": "f9d7e470-cde0-4847-b629-2b70ae4e31cf", "display_title": "Jay Ashok Shendure, UW", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.f9d7e470-cde0-4847-b629-2b70ae4e31cf"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "accession": "4DNFIAFZFU2Y", "file_type_detailed": "reads (fastq)", "status": "released", "uuid": "057c2a1c-204e-4a6a-bb68-4ed26b76863d", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIAFZFU2Y.fastq.gz", "@id": "/files-fastq/4DNFIAFZFU2Y/", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experiment_type": "sci-Hi-C", "experimental_lab": "Jay Ashok Shendure, UW", "dataset": "multiple", "condition": "multiple", "biosource_name": "multiple", "experiment_bucket": "raw file", "lab_name": "Jay Ashok Shendure, UW"}, "quality_metric": {"Sequence length": "250", "@id": "/quality-metrics-fastqc/c995517a-b59a-4647-a081-da6ac26bb763/", "overall_quality_status": "PASS", "uuid": "c995517a-b59a-4647-a081-da6ac26bb763", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 73838868, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIFR5WECM/fastqc_report.html", "display_title": "QualityMetricFastqc from 2018-02-12", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "4DNFIAFZFU2Y.fastq.gz", "extra_files": [], "file_type_detailed": "reads (fastq)", "paired_end": "2", "uuid": "057c2a1c-204e-4a6a-bb68-4ed26b76863d", "md5sum": "b6843a2df4067dc4a976c36321e654ca", "upload_key": "057c2a1c-204e-4a6a-bb68-4ed26b76863d/4DNFIAFZFU2Y.fastq.gz", "file_size": 16722605790, "status": "released", "accession": "4DNFIAFZFU2Y", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIAFZFU2Y/", "href": "/files-fastq/4DNFIAFZFU2Y/@@download/4DNFIAFZFU2Y.fastq.gz", "file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/057c2a1c-204e-4a6a-bb68-4ed26b76863d/4DNFIAFZFU2Y.fastq.gz", "file_type": "reads", "lab": {"status": "current", "@id": "/labs/jay-ashok-shendure-lab/", "name": "jay-ashok-shendure-lab", "uuid": "f9d7e470-cde0-4847-b629-2b70ae4e31cf", "display_title": "Jay Ashok Shendure, UW", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.f9d7e470-cde0-4847-b629-2b70ae4e31cf"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "accession": "4DNFIFR5WECM", "file_type_detailed": "reads (fastq)", "status": "released", "uuid": "02c89afe-6dd2-4ed1-878c-5f9e3e993e7d", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIFR5WECM.fastq.gz", "@id": "/files-fastq/4DNFIFR5WECM/", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experiment_type": "sci-Hi-C", "experimental_lab": "Jay Ashok Shendure, UW", "dataset": "multiple", "condition": "multiple", "biosource_name": "multiple", "experiment_bucket": "raw file", "lab_name": "Jay Ashok Shendure, UW"}, "quality_metric": {"Sequence length": "250", "@id": "/quality-metrics-fastqc/9f1d8363-a8b9-46ba-b66f-1f0cc8285d0a/", "overall_quality_status": "PASS", "uuid": "9f1d8363-a8b9-46ba-b66f-1f0cc8285d0a", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 73838868, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIAFZFU2Y/fastqc_report.html", "display_title": "QualityMetricFastqc from 2018-02-12", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@type": ["ExperimentHiC", "Experiment", "Item"], "reference_files": [{"file_size": 1440, "@id": "/files-reference/4DNFIV2MIN6H/", "display_title": "4DNFIV2MIN6H.txt", "file_type_detailed": "barcodes (txt)", "accession": "4DNFIV2MIN6H", "@type": ["FileReference", "File", "Item"], "file_classification": "ancillary file", "uuid": "953b5fd5-a4a2-4bfd-8ee6-166c3ef5e47a", "status": "released", "md5sum": "745e9a7829e9adac7047743d799d0648", "file_type": "barcodes", "href": "/files-reference/4DNFIV2MIN6H/@@download/4DNFIV2MIN6H.txt", "file_format": {"@type": ["FileFormat", "Item"], "file_format": "txt", "@id": "/file-formats/txt/", "display_title": "txt", "status": "released", "uuid": "0cd4e777-a596-4927-95c8-b07716121aa3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "@id": "/labs/jay-ashok-shendure-lab/", "name": "jay-ashok-shendure-lab", "display_title": "Jay Ashok Shendure, UW", "status": "current", "uuid": "f9d7e470-cde0-4847-b629-2b70ae4e31cf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.f9d7e470-cde0-4847-b629-2b70ae4e31cf"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_size": 864, "@id": "/files-reference/4DNFIUSK42KP/", "display_title": "4DNFIUSK42KP.txt", "file_type_detailed": "barcodes (txt)", "accession": "4DNFIUSK42KP", "@type": ["FileReference", "File", "Item"], "file_classification": "ancillary file", "uuid": "c8047497-0004-4f12-9387-26bd018903ee", "status": "released", "md5sum": "fc187be5c3da1f502ddfa26559dcbee9", "file_type": "barcodes", "href": "/files-reference/4DNFIUSK42KP/@@download/4DNFIUSK42KP.txt", "contributing_labs": [{"name": "william-noble-lab", "status": "current", "uuid": "a0812d8f-a4cc-4dbe-bd22-76e6e573b5ed", "@id": "/labs/william-noble-lab/", "@type": ["Lab", "Item"], "display_title": "William Noble, UW", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.a0812d8f-a4cc-4dbe-bd22-76e6e573b5ed"]}}], "file_format": {"@type": ["FileFormat", "Item"], "file_format": "txt", "@id": "/file-formats/txt/", "display_title": "txt", "status": "released", "uuid": "0cd4e777-a596-4927-95c8-b07716121aa3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "@id": "/labs/jay-ashok-shendure-lab/", "name": "jay-ashok-shendure-lab", "display_title": "Jay Ashok Shendure, UW", "status": "current", "uuid": "f9d7e470-cde0-4847-b629-2b70ae4e31cf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.f9d7e470-cde0-4847-b629-2b70ae4e31cf"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_size": 864, "@id": "/files-reference/4DNFINE9JUAI/", "display_title": "4DNFINE9JUAI.txt", "file_type_detailed": "barcodes (txt)", "accession": "4DNFINE9JUAI", "@type": ["FileReference", "File", "Item"], "file_classification": "ancillary file", "uuid": "cfb717e5-101a-4f12-afcc-d8b06b48ee6e", "status": "released", "md5sum": "f5f398961f15b57fca8118d7a11735af", "file_type": "barcodes", "href": "/files-reference/4DNFINE9JUAI/@@download/4DNFINE9JUAI.txt", "contributing_labs": [{"name": "william-noble-lab", "status": "current", "uuid": "a0812d8f-a4cc-4dbe-bd22-76e6e573b5ed", "@id": "/labs/william-noble-lab/", "@type": ["Lab", "Item"], "display_title": "William Noble, UW", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.a0812d8f-a4cc-4dbe-bd22-76e6e573b5ed"]}}], "file_format": {"@type": ["FileFormat", "Item"], "file_format": "txt", "@id": "/file-formats/txt/", "display_title": "txt", "status": "released", "uuid": "0cd4e777-a596-4927-95c8-b07716121aa3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "@id": "/labs/jay-ashok-shendure-lab/", "name": "jay-ashok-shendure-lab", "display_title": "Jay Ashok Shendure, UW", "status": "current", "uuid": "f9d7e470-cde0-4847-b629-2b70ae4e31cf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.f9d7e470-cde0-4847-b629-2b70ae4e31cf"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "biosample": {"treatments_summary": "None", "@type": ["Biosample", "Item"], "status": "released", "display_title": "4DNBSP9E9RLH", "biosample_category": ["H1-hESC", "Human stem cell"], "accession": "4DNBSP9E9RLH", "uuid": "95a3e2e3-7907-4012-adc0-435dc8aa73f4", "biosample_type": "stem cells", "modifications_summary": "None", "biosource_summary": "H1-hESC (Tier 1)", "@id": "/biosamples/4DNBSP9E9RLH/", "biosource": [{"@type": ["Biosource", "Item"], "@id": "/biosources/4DNSRV3SKQ8M/", "cell_line_tier": "Tier 1", "uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "status": "released", "biosource_type": "stem cell derived cell line", "accession": "4DNSRV3SKQ8M", "cell_line": {"uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "@type": ["OntologyTerm", "Item"], "preferred_name": "H1-hESC", "synonyms": ["H1"], "term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "status": "released", "display_title": "H1-hESC", "term_name": "H1-hESC", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/GO:0005623/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000000/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"preferred_name": "stem cell", "term_name": "stem cell", "synonyms": ["animal stem cell"], "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "term_id": "CL:0000034", "@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/CL:0000034/", "display_title": "stem cell", "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "display_title": "H. sapiens", "name": "human", "status": "released", "scientific_name": "Homo sapiens", "@type": ["Organism", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "modifications": [], "cell_culture_details": [{"status": "released", "display_title": "BiosampleCellCulture from 2018-01-30", "@id": "/biosample-cell-cultures/98eb39be-1aaa-4166-b966-da441fbe1fe7/", "uuid": "98eb39be-1aaa-4166-b966-da441fbe1fe7", "@type": ["BiosampleCellCulture", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "treatments": [], "badges": [{"messages": ["Biosample missing doubling_number", "Biosample missing culture_duration"], "badge": {"@type": ["Badge", "Item"], "badge_classification": "Warning", "badge_icon": "/static/img/badges/biosample-icon.svg", "display_title": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "title": "Biosample Metadata Incomplete", "warning": "Biosample Metadata Incomplete", "status": "released", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "@id": "/badges/biosample-metadata-incomplete/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "tissue_organ_info": {"tissue_source": "stem cell"}}, "experiment_type": {"@type": ["ExperimentType", "Item"], "assay_subclassification": "DNA-DNA Pairwise Interactions - Single Cell", "assay_classification": "3C via Ligation", "uuid": "358540cb-e1b8-4d5a-b0ab-7c1b433a17ce", "@id": "/experiment-types/sci-hi-c/", "other_tags": ["DNA-DNA", "Single Cell", "3D", "Pairwise"], "assay_subclass_short": "Hi-C (single cell)", "display_title": "sci-Hi-C", "title": "sci-Hi-C", "experiment_category": "Sequencing", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"combined": "Enzyme: DpnII", "value": "DpnII", "field": "Enzyme"}, "digestion_enzyme": {"status": "released", "uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "@id": "/enzymes/DpnII/", "@type": ["Enzyme", "Item"], "display_title": "DpnII", "name": "DpnII", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2020-02-25T22:24:40.282228+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"display_title": "sci-Hi-C on H1-hESC (Tier 1) with DpnII - 4DNEXSR13BV7", "accession": "4DNEXSR13BV7", "@id": "/experiments-hi-c/4DNEXSR13BV7/", "crosslinking_method": "3.5% Formaldehyde", "uuid": "5bd7e989-9073-4777-9d2b-7e23cfd166da", "status": "released", "files": [{"display_title": "4DNFIKEJMN5T.fastq.gz", "extra_files": [], "file_type_detailed": "reads (fastq)", "paired_end": "1", "uuid": "453cbaef-c2ab-49b1-8cbb-cc6dc4cfe2da", "md5sum": "bd4a16f95da0a0868787315c3a1cb2c6", "upload_key": "453cbaef-c2ab-49b1-8cbb-cc6dc4cfe2da/4DNFIKEJMN5T.fastq.gz", "file_size": 8100214575, "status": "released", "accession": "4DNFIKEJMN5T", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIKEJMN5T/", "href": "/files-fastq/4DNFIKEJMN5T/@@download/4DNFIKEJMN5T.fastq.gz", "file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/453cbaef-c2ab-49b1-8cbb-cc6dc4cfe2da/4DNFIKEJMN5T.fastq.gz", "file_type": "reads", "lab": {"status": "current", "@id": "/labs/jay-ashok-shendure-lab/", "name": "jay-ashok-shendure-lab", "uuid": "f9d7e470-cde0-4847-b629-2b70ae4e31cf", "display_title": "Jay Ashok Shendure, UW", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.f9d7e470-cde0-4847-b629-2b70ae4e31cf"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "accession": "4DNFITOOTWTP", "file_type_detailed": "reads (fastq)", "status": "released", "uuid": "91fb2bc8-d9f1-40f1-a26e-dd52c769f4ac", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFITOOTWTP.fastq.gz", "@id": "/files-fastq/4DNFITOOTWTP/", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experiment_type": "sci-Hi-C", "experimental_lab": "Jay Ashok Shendure, UW", "dataset": "multiple", "condition": "multiple", "biosource_name": "multiple", "experiment_bucket": "raw file", "lab_name": "Jay Ashok Shendure, UW"}, "quality_metric": {"Sequence length": "250", "@id": "/quality-metrics-fastqc/102c8d05-7821-4f0e-8cfb-f485c744cba6/", "overall_quality_status": "PASS", "uuid": "102c8d05-7821-4f0e-8cfb-f485c744cba6", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 39274527, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIKEJMN5T/fastqc_report.html", "display_title": "QualityMetricFastqc from 2018-02-12", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "4DNFITOOTWTP.fastq.gz", "extra_files": [], "file_type_detailed": "reads (fastq)", "paired_end": "2", "uuid": "91fb2bc8-d9f1-40f1-a26e-dd52c769f4ac", "md5sum": "6a5805237d82271b3fe8b024de3c1050", "upload_key": "91fb2bc8-d9f1-40f1-a26e-dd52c769f4ac/4DNFITOOTWTP.fastq.gz", "file_size": 8558576567, "status": "released", "accession": "4DNFITOOTWTP", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFITOOTWTP/", "href": "/files-fastq/4DNFITOOTWTP/@@download/4DNFITOOTWTP.fastq.gz", "file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/91fb2bc8-d9f1-40f1-a26e-dd52c769f4ac/4DNFITOOTWTP.fastq.gz", "file_type": "reads", "lab": {"status": "current", "@id": "/labs/jay-ashok-shendure-lab/", "name": "jay-ashok-shendure-lab", "uuid": "f9d7e470-cde0-4847-b629-2b70ae4e31cf", "display_title": "Jay Ashok Shendure, UW", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.f9d7e470-cde0-4847-b629-2b70ae4e31cf"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "accession": "4DNFIKEJMN5T", "file_type_detailed": "reads (fastq)", "status": "released", "uuid": "453cbaef-c2ab-49b1-8cbb-cc6dc4cfe2da", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIKEJMN5T.fastq.gz", "@id": "/files-fastq/4DNFIKEJMN5T/", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experiment_type": "sci-Hi-C", "experimental_lab": "Jay Ashok Shendure, UW", "dataset": "multiple", "condition": "multiple", "biosource_name": "multiple", "experiment_bucket": "raw file", "lab_name": "Jay Ashok Shendure, UW"}, "quality_metric": {"Sequence length": "250", "@id": "/quality-metrics-fastqc/f3502aa8-c6ab-490b-b0aa-693f4dec0fcf/", "overall_quality_status": "PASS", "uuid": "f3502aa8-c6ab-490b-b0aa-693f4dec0fcf", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 39274527, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFITOOTWTP/fastqc_report.html", "display_title": "QualityMetricFastqc from 2018-02-12", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "4DNFIPFPO3X4.fastq.gz", "extra_files": [], "file_type_detailed": "reads (fastq)", "paired_end": "1", "uuid": "d8086e8c-90b1-4eff-aad6-d107775bcb65", "md5sum": "7b99c8dd55b4e58043ad0df9960a88a3", "upload_key": "d8086e8c-90b1-4eff-aad6-d107775bcb65/4DNFIPFPO3X4.fastq.gz", "file_size": 28562885138, "status": "released", "accession": "4DNFIPFPO3X4", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIPFPO3X4/", "href": "/files-fastq/4DNFIPFPO3X4/@@download/4DNFIPFPO3X4.fastq.gz", "file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/d8086e8c-90b1-4eff-aad6-d107775bcb65/4DNFIPFPO3X4.fastq.gz", "file_type": "reads", "lab": {"status": "current", "@id": "/labs/jay-ashok-shendure-lab/", "name": "jay-ashok-shendure-lab", "uuid": "f9d7e470-cde0-4847-b629-2b70ae4e31cf", "display_title": "Jay Ashok Shendure, UW", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.f9d7e470-cde0-4847-b629-2b70ae4e31cf"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "accession": "4DNFICNEYGFV", "file_type_detailed": "reads (fastq)", "status": "released", "uuid": "e7ba1e88-e82d-4978-8492-b49731e3b93e", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFICNEYGFV.fastq.gz", "@id": "/files-fastq/4DNFICNEYGFV/", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experiment_type": "sci-Hi-C", "experimental_lab": "Jay Ashok Shendure, UW", "dataset": "multiple", "condition": "multiple", "biosource_name": "multiple", "experiment_bucket": "raw file", "lab_name": "Jay Ashok Shendure, UW"}, "quality_metric": {"Sequence length": "250", "@id": "/quality-metrics-fastqc/20da49bd-5909-4a50-82c9-a8b205e68cea/", "overall_quality_status": "PASS", "uuid": "20da49bd-5909-4a50-82c9-a8b205e68cea", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 128843278, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIPFPO3X4/fastqc_report.html", "display_title": "QualityMetricFastqc from 2018-02-12", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "4DNFICNEYGFV.fastq.gz", "extra_files": [], "file_type_detailed": "reads (fastq)", "paired_end": "2", "uuid": "e7ba1e88-e82d-4978-8492-b49731e3b93e", "md5sum": "cb7aef2dc4ac468205860cf8eeb38c9f", "upload_key": "e7ba1e88-e82d-4978-8492-b49731e3b93e/4DNFICNEYGFV.fastq.gz", "file_size": 29484521829, "status": "released", "accession": "4DNFICNEYGFV", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFICNEYGFV/", "href": "/files-fastq/4DNFICNEYGFV/@@download/4DNFICNEYGFV.fastq.gz", "file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/e7ba1e88-e82d-4978-8492-b49731e3b93e/4DNFICNEYGFV.fastq.gz", "file_type": "reads", "lab": {"status": "current", "@id": "/labs/jay-ashok-shendure-lab/", "name": "jay-ashok-shendure-lab", "uuid": "f9d7e470-cde0-4847-b629-2b70ae4e31cf", "display_title": "Jay Ashok Shendure, UW", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.f9d7e470-cde0-4847-b629-2b70ae4e31cf"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "accession": "4DNFIPFPO3X4", "file_type_detailed": "reads (fastq)", "status": "released", "uuid": "d8086e8c-90b1-4eff-aad6-d107775bcb65", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIPFPO3X4.fastq.gz", "@id": "/files-fastq/4DNFIPFPO3X4/", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experiment_type": "sci-Hi-C", "experimental_lab": "Jay Ashok Shendure, UW", "dataset": "multiple", "condition": "multiple", "biosource_name": "multiple", "experiment_bucket": "raw file", "lab_name": "Jay Ashok Shendure, UW"}, "quality_metric": {"Sequence length": "250", "@id": "/quality-metrics-fastqc/acbdd815-b1a5-4eaa-88b4-093dafbebc7c/", "overall_quality_status": "PASS", "uuid": "acbdd815-b1a5-4eaa-88b4-093dafbebc7c", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 128843278, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFICNEYGFV/fastqc_report.html", "display_title": "QualityMetricFastqc from 2018-02-12", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@type": ["ExperimentHiC", "Experiment", "Item"], "reference_files": [{"file_size": 1440, "@id": "/files-reference/4DNFIV2MIN6H/", "display_title": "4DNFIV2MIN6H.txt", "file_type_detailed": "barcodes (txt)", "accession": "4DNFIV2MIN6H", "@type": ["FileReference", "File", "Item"], "file_classification": "ancillary file", "uuid": "953b5fd5-a4a2-4bfd-8ee6-166c3ef5e47a", "status": "released", "md5sum": "745e9a7829e9adac7047743d799d0648", "file_type": "barcodes", "href": "/files-reference/4DNFIV2MIN6H/@@download/4DNFIV2MIN6H.txt", "file_format": {"@type": ["FileFormat", "Item"], "file_format": "txt", "@id": "/file-formats/txt/", "display_title": "txt", "status": "released", "uuid": "0cd4e777-a596-4927-95c8-b07716121aa3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "@id": "/labs/jay-ashok-shendure-lab/", "name": "jay-ashok-shendure-lab", "display_title": "Jay Ashok Shendure, UW", "status": "current", "uuid": "f9d7e470-cde0-4847-b629-2b70ae4e31cf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.f9d7e470-cde0-4847-b629-2b70ae4e31cf"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_size": 864, "@id": "/files-reference/4DNFIUSK42KP/", "display_title": "4DNFIUSK42KP.txt", "file_type_detailed": "barcodes (txt)", "accession": "4DNFIUSK42KP", "@type": ["FileReference", "File", "Item"], "file_classification": "ancillary file", "uuid": "c8047497-0004-4f12-9387-26bd018903ee", "status": "released", "md5sum": "fc187be5c3da1f502ddfa26559dcbee9", "file_type": "barcodes", "href": "/files-reference/4DNFIUSK42KP/@@download/4DNFIUSK42KP.txt", "contributing_labs": [{"name": "william-noble-lab", "status": "current", "uuid": "a0812d8f-a4cc-4dbe-bd22-76e6e573b5ed", "@id": "/labs/william-noble-lab/", "@type": ["Lab", "Item"], "display_title": "William Noble, UW", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.a0812d8f-a4cc-4dbe-bd22-76e6e573b5ed"]}}], "file_format": {"@type": ["FileFormat", "Item"], "file_format": "txt", "@id": "/file-formats/txt/", "display_title": "txt", "status": "released", "uuid": "0cd4e777-a596-4927-95c8-b07716121aa3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "@id": "/labs/jay-ashok-shendure-lab/", "name": "jay-ashok-shendure-lab", "display_title": "Jay Ashok Shendure, UW", "status": "current", "uuid": "f9d7e470-cde0-4847-b629-2b70ae4e31cf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.f9d7e470-cde0-4847-b629-2b70ae4e31cf"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_size": 864, "@id": "/files-reference/4DNFINE9JUAI/", "display_title": "4DNFINE9JUAI.txt", "file_type_detailed": "barcodes (txt)", "accession": "4DNFINE9JUAI", "@type": ["FileReference", "File", "Item"], "file_classification": "ancillary file", "uuid": "cfb717e5-101a-4f12-afcc-d8b06b48ee6e", "status": "released", "md5sum": "f5f398961f15b57fca8118d7a11735af", "file_type": "barcodes", "href": "/files-reference/4DNFINE9JUAI/@@download/4DNFINE9JUAI.txt", "contributing_labs": [{"name": "william-noble-lab", "status": "current", "uuid": "a0812d8f-a4cc-4dbe-bd22-76e6e573b5ed", "@id": "/labs/william-noble-lab/", "@type": ["Lab", "Item"], "display_title": "William Noble, UW", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.a0812d8f-a4cc-4dbe-bd22-76e6e573b5ed"]}}], "file_format": {"@type": ["FileFormat", "Item"], "file_format": "txt", "@id": "/file-formats/txt/", "display_title": "txt", "status": "released", "uuid": "0cd4e777-a596-4927-95c8-b07716121aa3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "@id": "/labs/jay-ashok-shendure-lab/", "name": "jay-ashok-shendure-lab", "display_title": "Jay Ashok Shendure, UW", "status": "current", "uuid": "f9d7e470-cde0-4847-b629-2b70ae4e31cf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.f9d7e470-cde0-4847-b629-2b70ae4e31cf"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "biosample": {"treatments_summary": "None", "@type": ["Biosample", "Item"], "status": "released", "display_title": "4DNBSP9E9RLH", "biosample_category": ["H1-hESC", "Human stem cell"], "accession": "4DNBSP9E9RLH", "uuid": "95a3e2e3-7907-4012-adc0-435dc8aa73f4", "biosample_type": "stem cells", "modifications_summary": "None", "biosource_summary": "H1-hESC (Tier 1)", "@id": "/biosamples/4DNBSP9E9RLH/", "biosource": [{"@type": ["Biosource", "Item"], "@id": "/biosources/4DNSRV3SKQ8M/", "cell_line_tier": "Tier 1", "uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "status": "released", "biosource_type": "stem cell derived cell line", "accession": "4DNSRV3SKQ8M", "cell_line": {"uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "@type": ["OntologyTerm", "Item"], "preferred_name": "H1-hESC", "synonyms": ["H1"], "term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "status": "released", "display_title": "H1-hESC", "term_name": "H1-hESC", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/GO:0005623/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000000/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"preferred_name": "stem cell", "term_name": "stem cell", "synonyms": ["animal stem cell"], "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "term_id": "CL:0000034", "@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/CL:0000034/", "display_title": "stem cell", "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "display_title": "H. sapiens", "name": "human", "status": "released", "scientific_name": "Homo sapiens", "@type": ["Organism", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "modifications": [], "cell_culture_details": [{"status": "released", "display_title": "BiosampleCellCulture from 2018-01-30", "@id": "/biosample-cell-cultures/98eb39be-1aaa-4166-b966-da441fbe1fe7/", "uuid": "98eb39be-1aaa-4166-b966-da441fbe1fe7", "@type": ["BiosampleCellCulture", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "treatments": [], "badges": [{"messages": ["Biosample missing doubling_number", "Biosample missing culture_duration"], "badge": {"@type": ["Badge", "Item"], "badge_classification": "Warning", "badge_icon": "/static/img/badges/biosample-icon.svg", "display_title": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "title": "Biosample Metadata Incomplete", "warning": "Biosample Metadata Incomplete", "status": "released", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "@id": "/badges/biosample-metadata-incomplete/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "tissue_organ_info": {"tissue_source": "stem cell"}}, "experiment_type": {"@type": ["ExperimentType", "Item"], "assay_subclassification": "DNA-DNA Pairwise Interactions - Single Cell", "assay_classification": "3C via Ligation", "uuid": "358540cb-e1b8-4d5a-b0ab-7c1b433a17ce", "@id": "/experiment-types/sci-hi-c/", "other_tags": ["DNA-DNA", "Single Cell", "3D", "Pairwise"], "assay_subclass_short": "Hi-C (single cell)", "display_title": "sci-Hi-C", "title": "sci-Hi-C", "experiment_category": "Sequencing", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"combined": "Enzyme: DpnII", "value": "DpnII", "field": "Enzyme"}, "digestion_enzyme": {"status": "released", "uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "@id": "/enzymes/DpnII/", "@type": ["Enzyme", "Item"], "display_title": "DpnII", "name": "DpnII", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2020-02-25T22:24:40.009280+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}], "experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNESIKGI39T/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "638667d3-5751-4fe8-94a2-9071649ca20c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNESIKGI39T", "external_references": [], "produced_in_pub": {"abstract": "Single-cell Hi-C (scHi-C) interrogates genome-wide chromatin interaction in individual cells, allowing us to gain insights into 3D genome organization. However, the extremely sparse nature of scHi-C data poses a significant barrier to analysis, limiting our ability to tease out hidden biological information. In  this work, we approach this problem by applying topic modeling to scHi-C data. Topic modeling is well-suited for discovering latent topics in a collection of discrete data. For our analysis, we generate nine different single-cell combinatorial indexed Hi-C (sci-Hi-C) libraries from five human cell lines (GM12878, H1Esc, HFF, IMR90, and HAP1), consisting over 19,000 cells. We demonstrate that topic modeling is able to successfully capture cell type differences from sci-Hi-C data in the form of \"chromatin topics.\" We further show enrichment of particular compartment structures associated with locus pairs in these topics.", "journal": "PLoS computational biology", "short_attribution": "Kim HJ et al. (2020)", "date_published": "2020-09", "title": "Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data.", "authors": ["Kim HJ", "Yardimci GG", "Bonora G", "Ramani V", "Liu J", "Qiu R", "Lee C", "Hesson J", "Ware CB", "Shendure J", "Duan Z", "Noble WS"], "@id": "/publications/b8075496-ce51-42a8-8e6c-8cd15a91e353/", "url": "https://www.ncbi.nlm.nih.gov/pubmed/32946435", "ID": "PMID:32946435", "status": "current", "uuid": "b8075496-ce51-42a8-8e6c-8cd15a91e353", "display_title": "Kim HJ et al. (2020) PMID:32946435", "@type": ["Publication", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"abstract": "Single-cell Hi-C (scHi-C) interrogates genome-wide chromatin interaction in individual cells, allowing us to gain insights into 3D genome organization. However, the extremely sparse nature of scHi-C data poses a significant barrier to analysis, limiting our ability to tease out hidden biological information. In  this work, we approach this problem by applying topic modeling to scHi-C data. Topic modeling is well-suited for discovering latent topics in a collection of discrete data. For our analysis, we generate nine different single-cell combinatorial indexed Hi-C (sci-Hi-C) libraries from five human cell lines (GM12878, H1Esc, HFF, IMR90, and HAP1), consisting over 19,000 cells. We demonstrate that topic modeling is able to successfully capture cell type differences from sci-Hi-C data in the form of \"chromatin topics.\" We further show enrichment of particular compartment structures associated with locus pairs in these topics.", "date_published": "2020-09", "@id": "/publications/b8075496-ce51-42a8-8e6c-8cd15a91e353/", "ID": "PMID:32946435", "status": "current", "@type": ["Publication", "Item"], "journal": "PLoS computational biology", "authors": ["Kim HJ", "Yardimci GG", "Bonora G", "Ramani V", "Liu J", "Qiu R", "Lee C", "Hesson J", "Ware CB", "Shendure J", "Duan Z", "Noble WS"], "title": "Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data.", "display_title": "Kim HJ et al. (2020) PMID:32946435", "uuid": "b8075496-ce51-42a8-8e6c-8cd15a91e353", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 4, "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSOB39EE9/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["Biosample missing doubling_number", "Biosample missing culture_duration"], "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": "/biosamples/4DNBSP9E9RLH/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["Biosample missing doubling_number", "Biosample missing culture_duration"], "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": []}