{"lab": {"@type": ["Lab", "Item"], "@id": "/labs/peter-fraser-lab/", "status": "current", "display_title": "Peter Fraser, BABRAHAM", "title": "Peter Fraser, BABRAHAM", "correspondence": [{"contact_email": "cGV0ZXIuZnJhc2VyQGJhYnJhaGFtLmFjLnVr", "@id": "/users/0b4c67fa-696c-4498-baa6-b89e598fa666/", "display_title": "Peter Fraser"}], "uuid": "fff330e2-8d3c-48e3-b7c6-42c8b9979368", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.fff330e2-8d3c-48e3-b7c6-42c8b9979368"]}}, "award": {"@type": ["Award", "Item"], "display_title": "NEW AUTOMATED EXPERIMENTAL AND COMPUTATIONAL PIPELINE FOR HIGH COVERAGE SINGLE-CELL HI-C AND ITS INTEGRATION WITH SINGLE CELL RNA-SEQ: ENABLING 4D NUCLEOMICS AT SINGLE CELL RESOLUTION", "uuid": "3caf886c-2735-4688-8c10-52d1910efbed", "name": "1U01HL129971-01", "center_title": "NT - Fraser", "status": "current", "project": "4DN", "@id": "/awards/1U01HL129971-01/", "description": "NT: In this project we will develop new methods to investigate the three dimensional arrangement of the genome in various cell types from mouse bone marrow. The three dimensional organization of the genome, how it is physically arranged in the nucleus of cells, is recognized as an important component of genome control. The mechanisms by which genes get switched on and off in the correct cells or tissue type, and during the correct stages of development include changes in the spatial organization of the genome. We will develop a new method that can assess three dimensional genome organizations in thousands of individual cells and simultaneously measure the actual gene expression profile of a large number of those cells. We will systematically analyze the data mathematically and statistically to look for new principles of genome organization that may play unknown roles in controlling the genome in health and disease. We will also use the data to generate 3D computer models of individual chromosomes and the entire genome as it exists in the individual cell nucleus. We will then use these models to look for spatial patterns, recurring structures and variable structured regions of the genome that may be important in gene control. For these experiments we will use mouse bone marrow cells, which are an important representative of human bone marrow cells. Bone marrow is a clinically important, complex tissue containing the adult stems cells that give rise to all cells of the blood and immune system. By systematically analyzing the 3D genome conformation and gene expression profiles of these important cell types we will be providing fundamental knowledge of how these cell types function to create the blood. We will cooperate with other research groups to ensure that they have access to these powerful technologies and computer analysis packages that will accelerate a fuller understanding of how the genome is controlled. This information is vital to design new effective therapeutic strategies for the treatment of diseases of the blood and other tissues, and to understand the molecular basis of cancers for more effective treatments and prevention.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "pi": {"error": "no view permissions"}}, "badges": [{"badge": {"uuid": "24a64a84-3c33-4d76-aaf2-e5ef45eff347", "title": "Replicate Numbers", "@id": "/badges/replicate-numbers/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/replicates-orange-circle.svg", "description": "Issues with replicate numbers", "warning": "Replicate Numbers", "display_title": "Replicate Numbers", "status": "released", "badge_classification": "Warning", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "messages": ["Replicate set contains only a single biological replicate"]}], "status": "released", "aliases": ["peter-fraser-lab:ExperimentSet_1CDS1"], "dbxrefs": ["GEO:GSE94489"], "accession": "4DNES1B64O2Z", "condition": "2n DNA - serum", "description": "Replicates of in situ Hi-C using MboI on diploid 1CDS1 cells", "date_created": "2018-09-19T11:32:18.227950+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "single cell Hi-C on sorted diploid F1 2-1s", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-06-12T17:29:44.449457+00:00"}, "public_release": "2018-10-24", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-hi-c/4DNEXW6DEBGE/", "uuid": "c5776955-60c7-4ea7-b731-793d26d0274b", "accession": "4DNEXW6DEBGE", "display_title": "single cell Hi-C on F1 2-1 mESC line with MboI - 4DNEXW6DEBGE", "status": "released", "@type": ["ExperimentHiC", "Experiment", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "project_release": "2018-10-24", "contributing_labs": [{"@id": "/labs/amos-tanay-lab/", "status": "current", "display_title": "Amos Tanay, WIS", "correspondence": [{"contact_email": "YW1vcy50YW5heUB3ZWl6bWFubi5hYy5pbA==", "@id": "/users/d00c6427-89e9-4572-ac38-06ac4ed475df/", "display_title": "Amos Tanay"}], "@type": ["Lab", "Item"], "uuid": "44a45fb2-33a9-4ec4-8e44-e82bc8d40d8f", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.44a45fb2-33a9-4ec4-8e44-e82bc8d40d8f"]}}], "experiments_in_set": [{"@type": ["ExperimentHiC", "Experiment", "Item"], "@id": "/experiments-hi-c/4DNEXW6DEBGE/", "status": "released", "crosslinking_method": "2% Formaldehyde", "display_title": "single cell Hi-C on F1 2-1 mESC line with MboI - 4DNEXW6DEBGE", "accession": "4DNEXW6DEBGE", "uuid": "c5776955-60c7-4ea7-b731-793d26d0274b", "files": [{"paired_end": "1", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/44825f81-13b0-455c-95e3-163b4032df8c/4DNFIDVMEOEN.fastq.gz", "file_classification": "raw file", "upload_key": "44825f81-13b0-455c-95e3-163b4032df8c/4DNFIDVMEOEN.fastq.gz", "status": "released", "file_size": 1521210775, "href": "/files-fastq/4DNFIDVMEOEN/@@download/4DNFIDVMEOEN.fastq.gz", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIDVMEOEN", "md5sum": "9cf491859bb111dccd2c9b2c9067e30e", "file_type": "reads", "uuid": "44825f81-13b0-455c-95e3-163b4032df8c", "display_title": "4DNFIDVMEOEN.fastq.gz", "@id": "/files-fastq/4DNFIDVMEOEN/", "file_type_detailed": "reads (fastq)", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFI87DFQBZ.fastq.gz", "file_type_detailed": "reads (fastq)", "accession": "4DNFI87DFQBZ", "status": "released", "@type": ["FileFastq", "File", "Item"], "paired_end": "2", "uuid": "18f02265-6b74-4fd6-b76e-7481c323f618", "file_type": "reads", "@id": "/files-fastq/4DNFI87DFQBZ/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "contributing_labs": [{"display_title": "Amos Tanay, WIS", "status": "current", "name": "amos-tanay-lab", "@id": "/labs/amos-tanay-lab/", "@type": ["Lab", "Item"], "uuid": "44a45fb2-33a9-4ec4-8e44-e82bc8d40d8f", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.44a45fb2-33a9-4ec4-8e44-e82bc8d40d8f"]}}], "lab": {"@id": "/labs/peter-fraser-lab/", "display_title": "Peter Fraser, BABRAHAM", "name": "peter-fraser-lab", "status": "current", "uuid": "fff330e2-8d3c-48e3-b7c6-42c8b9979368", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.fff330e2-8d3c-48e3-b7c6-42c8b9979368"]}}, "quality_metric": {"Sequence length": "301", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIDVMEOEN/fastqc_report.html", "@id": "/quality-metrics-fastqc/ff952276-dc8b-4edf-a985-90fb16a544e4/", "uuid": "ff952276-dc8b-4edf-a985-90fb16a544e4", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2018-10-12", "Total Sequences": 7873615, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Peter Fraser, BABRAHAM", "experiment_type": "single cell Hi-C", "experiment_bucket": "raw file", "assay_info": "MboI", "dataset": "single cell Hi-C on sorted diploid F1 2-1s", "condition": "2n DNA - serum", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Peter Fraser, BABRAHAM"}}, {"paired_end": "2", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/18f02265-6b74-4fd6-b76e-7481c323f618/4DNFI87DFQBZ.fastq.gz", "file_classification": "raw file", "upload_key": "18f02265-6b74-4fd6-b76e-7481c323f618/4DNFI87DFQBZ.fastq.gz", "status": "released", "file_size": 1590513136, "href": "/files-fastq/4DNFI87DFQBZ/@@download/4DNFI87DFQBZ.fastq.gz", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFI87DFQBZ", "md5sum": "f5bddb79ce4e2435728103bb0e8570c5", "file_type": "reads", "uuid": "18f02265-6b74-4fd6-b76e-7481c323f618", "display_title": "4DNFI87DFQBZ.fastq.gz", "@id": "/files-fastq/4DNFI87DFQBZ/", "file_type_detailed": "reads (fastq)", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIDVMEOEN.fastq.gz", "file_type_detailed": "reads (fastq)", "accession": "4DNFIDVMEOEN", "status": "released", "@type": ["FileFastq", "File", "Item"], "paired_end": "1", "uuid": "44825f81-13b0-455c-95e3-163b4032df8c", "file_type": "reads", "@id": "/files-fastq/4DNFIDVMEOEN/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "contributing_labs": [{"display_title": "Amos Tanay, WIS", "status": "current", "name": "amos-tanay-lab", "@id": "/labs/amos-tanay-lab/", "@type": ["Lab", "Item"], "uuid": "44a45fb2-33a9-4ec4-8e44-e82bc8d40d8f", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.44a45fb2-33a9-4ec4-8e44-e82bc8d40d8f"]}}], "lab": {"@id": "/labs/peter-fraser-lab/", "display_title": "Peter Fraser, BABRAHAM", "name": "peter-fraser-lab", "status": "current", "uuid": "fff330e2-8d3c-48e3-b7c6-42c8b9979368", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.fff330e2-8d3c-48e3-b7c6-42c8b9979368"]}}, "quality_metric": {"Sequence length": "301", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI87DFQBZ/fastqc_report.html", "@id": "/quality-metrics-fastqc/ee2d7550-ac83-4e16-888c-805ee4f025db/", "uuid": "ee2d7550-ac83-4e16-888c-805ee4f025db", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2018-10-12", "Total Sequences": 7873615, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Peter Fraser, BABRAHAM", "experiment_type": "single cell Hi-C", "experiment_bucket": "raw file", "assay_info": "MboI", "dataset": "single cell Hi-C on sorted diploid F1 2-1s", "condition": "2n DNA - serum", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Peter Fraser, BABRAHAM"}}, {"paired_end": "1", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/4e951c23-c825-456a-af41-93369291b7b1/4DNFIGWYZ6RZ.fastq.gz", "file_classification": "raw file", "upload_key": "4e951c23-c825-456a-af41-93369291b7b1/4DNFIGWYZ6RZ.fastq.gz", "status": "released", "file_size": 22989315411, "href": "/files-fastq/4DNFIGWYZ6RZ/@@download/4DNFIGWYZ6RZ.fastq.gz", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIGWYZ6RZ", "md5sum": "73067debe68b0817d5758419e790d338", "file_type": "reads", "uuid": "4e951c23-c825-456a-af41-93369291b7b1", "display_title": "4DNFIGWYZ6RZ.fastq.gz", "@id": "/files-fastq/4DNFIGWYZ6RZ/", "file_type_detailed": "reads (fastq)", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIOH1LLTJ.fastq.gz", "file_type_detailed": "reads (fastq)", "accession": "4DNFIOH1LLTJ", "status": "released", "@type": ["FileFastq", "File", "Item"], "paired_end": "2", "uuid": "e4055638-b963-4da4-b463-8153897d9fb2", "file_type": "reads", "@id": "/files-fastq/4DNFIOH1LLTJ/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "contributing_labs": [{"display_title": "Amos Tanay, WIS", "status": "current", "name": "amos-tanay-lab", "@id": "/labs/amos-tanay-lab/", "@type": ["Lab", "Item"], "uuid": "44a45fb2-33a9-4ec4-8e44-e82bc8d40d8f", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.44a45fb2-33a9-4ec4-8e44-e82bc8d40d8f"]}}], "lab": {"@id": "/labs/peter-fraser-lab/", "display_title": "Peter Fraser, BABRAHAM", "name": "peter-fraser-lab", "status": "current", "uuid": "fff330e2-8d3c-48e3-b7c6-42c8b9979368", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.fff330e2-8d3c-48e3-b7c6-42c8b9979368"]}}, "quality_metric": {"Sequence length": "151", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIGWYZ6RZ/fastqc_report.html", "@id": "/quality-metrics-fastqc/11585adf-d7e8-4e98-8506-576f49bb16cd/", "uuid": "11585adf-d7e8-4e98-8506-576f49bb16cd", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2018-10-17", "Total Sequences": 183759639, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Peter Fraser, BABRAHAM", "experiment_type": "single cell Hi-C", "experiment_bucket": "raw file", "assay_info": "MboI", "dataset": "single cell Hi-C on sorted diploid F1 2-1s", "condition": "2n DNA - serum", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Peter Fraser, BABRAHAM"}}, {"paired_end": "2", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/e4055638-b963-4da4-b463-8153897d9fb2/4DNFIOH1LLTJ.fastq.gz", "file_classification": "raw file", "upload_key": "e4055638-b963-4da4-b463-8153897d9fb2/4DNFIOH1LLTJ.fastq.gz", "status": "released", "file_size": 23815846838, "href": "/files-fastq/4DNFIOH1LLTJ/@@download/4DNFIOH1LLTJ.fastq.gz", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIOH1LLTJ", "md5sum": "3ecf762954592333a3b7ea6fe95a304f", "file_type": "reads", "uuid": "e4055638-b963-4da4-b463-8153897d9fb2", "display_title": "4DNFIOH1LLTJ.fastq.gz", "@id": "/files-fastq/4DNFIOH1LLTJ/", "file_type_detailed": "reads (fastq)", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIGWYZ6RZ.fastq.gz", "file_type_detailed": "reads (fastq)", "accession": "4DNFIGWYZ6RZ", "status": "released", "@type": ["FileFastq", "File", "Item"], "paired_end": "1", "uuid": "4e951c23-c825-456a-af41-93369291b7b1", "file_type": "reads", "@id": "/files-fastq/4DNFIGWYZ6RZ/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "contributing_labs": [{"display_title": "Amos Tanay, WIS", "status": "current", "name": "amos-tanay-lab", "@id": "/labs/amos-tanay-lab/", "@type": ["Lab", "Item"], "uuid": "44a45fb2-33a9-4ec4-8e44-e82bc8d40d8f", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.44a45fb2-33a9-4ec4-8e44-e82bc8d40d8f"]}}], "lab": {"@id": "/labs/peter-fraser-lab/", "display_title": "Peter Fraser, BABRAHAM", "name": "peter-fraser-lab", "status": "current", "uuid": "fff330e2-8d3c-48e3-b7c6-42c8b9979368", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.fff330e2-8d3c-48e3-b7c6-42c8b9979368"]}}, "quality_metric": {"Sequence length": "151", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIOH1LLTJ/fastqc_report.html", "@id": "/quality-metrics-fastqc/69189a79-a427-4766-bc8d-4dc42ea9d26f/", "uuid": "69189a79-a427-4766-bc8d-4dc42ea9d26f", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2018-10-17", "Total Sequences": 183759639, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Peter Fraser, BABRAHAM", "experiment_type": "single cell Hi-C", "experiment_bucket": "raw file", "assay_info": "MboI", "dataset": "single cell Hi-C on sorted diploid F1 2-1s", "condition": "2n DNA - serum", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Peter Fraser, BABRAHAM"}}, {"paired_end": "1", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/cc5bf232-0a92-423e-aaac-72c2c86edd45/4DNFIEBLIKJR.fastq.gz", "file_classification": "raw file", "upload_key": "cc5bf232-0a92-423e-aaac-72c2c86edd45/4DNFIEBLIKJR.fastq.gz", "status": "released", "file_size": 12952426520, "href": "/files-fastq/4DNFIEBLIKJR/@@download/4DNFIEBLIKJR.fastq.gz", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIEBLIKJR", "md5sum": "620d996b479b815e50cfaa7e78c62fc1", "file_type": "reads", "uuid": "cc5bf232-0a92-423e-aaac-72c2c86edd45", "display_title": "4DNFIEBLIKJR.fastq.gz", "@id": "/files-fastq/4DNFIEBLIKJR/", "file_type_detailed": "reads (fastq)", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFITX3362X.fastq.gz", "file_type_detailed": "reads (fastq)", "accession": "4DNFITX3362X", "status": "released", "@type": ["FileFastq", "File", "Item"], "paired_end": "2", "uuid": "3dfdb336-c458-470d-943a-1806a8c2a2e5", "file_type": "reads", "@id": "/files-fastq/4DNFITX3362X/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "contributing_labs": [{"display_title": "Amos Tanay, WIS", "status": "current", "name": "amos-tanay-lab", "@id": "/labs/amos-tanay-lab/", "@type": ["Lab", "Item"], "uuid": "44a45fb2-33a9-4ec4-8e44-e82bc8d40d8f", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.44a45fb2-33a9-4ec4-8e44-e82bc8d40d8f"]}}], "lab": {"@id": "/labs/peter-fraser-lab/", "display_title": "Peter Fraser, BABRAHAM", "name": "peter-fraser-lab", "status": "current", "uuid": "fff330e2-8d3c-48e3-b7c6-42c8b9979368", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.fff330e2-8d3c-48e3-b7c6-42c8b9979368"]}}, "quality_metric": {"Sequence length": "151", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIEBLIKJR/fastqc_report.html", "@id": "/quality-metrics-fastqc/1c86df81-f680-4c91-9e34-86f66149d37c/", "uuid": "1c86df81-f680-4c91-9e34-86f66149d37c", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2018-10-12", "Total Sequences": 103636162, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Peter Fraser, BABRAHAM", "experiment_type": "single cell Hi-C", "experiment_bucket": "raw file", "assay_info": "MboI", "dataset": "single cell Hi-C on sorted diploid F1 2-1s", "condition": "2n DNA - serum", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Peter Fraser, BABRAHAM"}}, {"paired_end": "2", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/3dfdb336-c458-470d-943a-1806a8c2a2e5/4DNFITX3362X.fastq.gz", "file_classification": "raw file", "upload_key": "3dfdb336-c458-470d-943a-1806a8c2a2e5/4DNFITX3362X.fastq.gz", "status": "released", "file_size": 13480718866, "href": "/files-fastq/4DNFITX3362X/@@download/4DNFITX3362X.fastq.gz", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFITX3362X", "md5sum": "215889f571a3fd6d8dff6dacfb7e1159", "file_type": "reads", "uuid": "3dfdb336-c458-470d-943a-1806a8c2a2e5", "display_title": "4DNFITX3362X.fastq.gz", "@id": "/files-fastq/4DNFITX3362X/", "file_type_detailed": "reads (fastq)", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIEBLIKJR.fastq.gz", "file_type_detailed": "reads (fastq)", "accession": "4DNFIEBLIKJR", "status": "released", "@type": ["FileFastq", "File", "Item"], "paired_end": "1", "uuid": "cc5bf232-0a92-423e-aaac-72c2c86edd45", "file_type": "reads", "@id": "/files-fastq/4DNFIEBLIKJR/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "contributing_labs": [{"display_title": "Amos Tanay, WIS", "status": "current", "name": "amos-tanay-lab", "@id": "/labs/amos-tanay-lab/", "@type": ["Lab", "Item"], "uuid": "44a45fb2-33a9-4ec4-8e44-e82bc8d40d8f", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.44a45fb2-33a9-4ec4-8e44-e82bc8d40d8f"]}}], "lab": {"@id": "/labs/peter-fraser-lab/", "display_title": "Peter Fraser, BABRAHAM", "name": "peter-fraser-lab", "status": "current", "uuid": "fff330e2-8d3c-48e3-b7c6-42c8b9979368", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.fff330e2-8d3c-48e3-b7c6-42c8b9979368"]}}, "quality_metric": {"Sequence length": "151", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFITX3362X/fastqc_report.html", "@id": "/quality-metrics-fastqc/2e51c3ae-020c-408e-865d-d53b235888bd/", "uuid": "2e51c3ae-020c-408e-865d-d53b235888bd", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2018-10-12", "Total Sequences": 103636162, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Peter Fraser, BABRAHAM", "experiment_type": "single cell Hi-C", "experiment_bucket": "raw file", "assay_info": "MboI", "dataset": "single cell Hi-C on sorted diploid F1 2-1s", "condition": "2n DNA - serum", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Peter Fraser, BABRAHAM"}}, {"paired_end": "1", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/6bd03456-9be4-4f63-a886-9f98bd3268a9/4DNFIC3FN3YM.fastq.gz", "file_classification": "raw file", "upload_key": "6bd03456-9be4-4f63-a886-9f98bd3268a9/4DNFIC3FN3YM.fastq.gz", "status": "released", "file_size": 24973576022, "href": "/files-fastq/4DNFIC3FN3YM/@@download/4DNFIC3FN3YM.fastq.gz", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIC3FN3YM", "md5sum": "8e934942b954b5da6c67dbc9aa0b012a", "file_type": "reads", "uuid": "6bd03456-9be4-4f63-a886-9f98bd3268a9", "display_title": "4DNFIC3FN3YM.fastq.gz", "@id": "/files-fastq/4DNFIC3FN3YM/", "file_type_detailed": "reads (fastq)", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIQ6OIA98.fastq.gz", "file_type_detailed": "reads (fastq)", "accession": "4DNFIQ6OIA98", "status": "released", "@type": ["FileFastq", "File", "Item"], "paired_end": "2", "uuid": "888d71bc-61c5-4ba9-8d3b-0d77c6e77d16", "file_type": "reads", "@id": "/files-fastq/4DNFIQ6OIA98/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "contributing_labs": [{"display_title": "Amos Tanay, WIS", "status": "current", "name": "amos-tanay-lab", "@id": "/labs/amos-tanay-lab/", "@type": ["Lab", "Item"], "uuid": "44a45fb2-33a9-4ec4-8e44-e82bc8d40d8f", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.44a45fb2-33a9-4ec4-8e44-e82bc8d40d8f"]}}], "lab": {"@id": "/labs/peter-fraser-lab/", "display_title": "Peter Fraser, BABRAHAM", "name": "peter-fraser-lab", "status": "current", "uuid": "fff330e2-8d3c-48e3-b7c6-42c8b9979368", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.fff330e2-8d3c-48e3-b7c6-42c8b9979368"]}}, "quality_metric": {"Sequence length": "151", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIC3FN3YM/fastqc_report.html", "@id": "/quality-metrics-fastqc/00a91cc7-6175-4794-99c7-fd91b77ea7ae/", "uuid": "00a91cc7-6175-4794-99c7-fd91b77ea7ae", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2018-10-17", "Total Sequences": 195839294, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Peter Fraser, BABRAHAM", "experiment_type": "single cell Hi-C", "experiment_bucket": "raw file", "assay_info": "MboI", "dataset": "single cell Hi-C on sorted diploid F1 2-1s", "condition": "2n DNA - serum", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Peter Fraser, BABRAHAM"}}, {"paired_end": "2", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/888d71bc-61c5-4ba9-8d3b-0d77c6e77d16/4DNFIQ6OIA98.fastq.gz", "file_classification": "raw file", "upload_key": "888d71bc-61c5-4ba9-8d3b-0d77c6e77d16/4DNFIQ6OIA98.fastq.gz", "status": "released", "file_size": 25689987737, "href": "/files-fastq/4DNFIQ6OIA98/@@download/4DNFIQ6OIA98.fastq.gz", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIQ6OIA98", "md5sum": "a8445324de173b60024f256453623ca1", "file_type": "reads", "uuid": "888d71bc-61c5-4ba9-8d3b-0d77c6e77d16", "display_title": "4DNFIQ6OIA98.fastq.gz", "@id": "/files-fastq/4DNFIQ6OIA98/", "file_type_detailed": "reads (fastq)", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIC3FN3YM.fastq.gz", "file_type_detailed": "reads (fastq)", "accession": "4DNFIC3FN3YM", "status": "released", "@type": ["FileFastq", "File", "Item"], "paired_end": "1", "uuid": "6bd03456-9be4-4f63-a886-9f98bd3268a9", "file_type": "reads", "@id": "/files-fastq/4DNFIC3FN3YM/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "contributing_labs": [{"display_title": "Amos Tanay, WIS", "status": "current", "name": "amos-tanay-lab", "@id": "/labs/amos-tanay-lab/", "@type": ["Lab", "Item"], "uuid": "44a45fb2-33a9-4ec4-8e44-e82bc8d40d8f", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.44a45fb2-33a9-4ec4-8e44-e82bc8d40d8f"]}}], "lab": {"@id": "/labs/peter-fraser-lab/", "display_title": "Peter Fraser, BABRAHAM", "name": "peter-fraser-lab", "status": "current", "uuid": "fff330e2-8d3c-48e3-b7c6-42c8b9979368", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.fff330e2-8d3c-48e3-b7c6-42c8b9979368"]}}, "quality_metric": {"Sequence length": "151", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIQ6OIA98/fastqc_report.html", "@id": "/quality-metrics-fastqc/0de2cbff-c023-4fea-83b6-6b58f62250ab/", "uuid": "0de2cbff-c023-4fea-83b6-6b58f62250ab", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2018-10-17", "Total Sequences": 195839294, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Peter Fraser, BABRAHAM", "experiment_type": "single cell Hi-C", "experiment_bucket": "raw file", "assay_info": "MboI", "dataset": "single cell Hi-C on sorted diploid F1 2-1s", "condition": "2n DNA - serum", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Peter Fraser, BABRAHAM"}}, {"paired_end": "1", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/da8714c3-e52a-4b5d-a6bc-2476bc6a8438/4DNFI4BD4LMO.fastq.gz", "file_classification": "raw file", "upload_key": "da8714c3-e52a-4b5d-a6bc-2476bc6a8438/4DNFI4BD4LMO.fastq.gz", "status": "released", "file_size": 13719413796, "href": "/files-fastq/4DNFI4BD4LMO/@@download/4DNFI4BD4LMO.fastq.gz", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFI4BD4LMO", "md5sum": "40b4c4ad86e776c10040d8cfea3e79fd", "file_type": "reads", "uuid": "da8714c3-e52a-4b5d-a6bc-2476bc6a8438", "display_title": "4DNFI4BD4LMO.fastq.gz", "@id": "/files-fastq/4DNFI4BD4LMO/", "file_type_detailed": "reads (fastq)", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIVPRK5RS.fastq.gz", "file_type_detailed": "reads (fastq)", "accession": "4DNFIVPRK5RS", "status": "released", "@type": ["FileFastq", "File", "Item"], "paired_end": "2", "uuid": "95015a39-45f4-4a83-bfd5-4c1ab59a628a", "file_type": "reads", "@id": "/files-fastq/4DNFIVPRK5RS/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "contributing_labs": [{"display_title": "Amos Tanay, WIS", "status": "current", "name": "amos-tanay-lab", "@id": "/labs/amos-tanay-lab/", "@type": ["Lab", "Item"], "uuid": "44a45fb2-33a9-4ec4-8e44-e82bc8d40d8f", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.44a45fb2-33a9-4ec4-8e44-e82bc8d40d8f"]}}], "lab": {"@id": "/labs/peter-fraser-lab/", "display_title": "Peter Fraser, BABRAHAM", "name": "peter-fraser-lab", "status": "current", "uuid": "fff330e2-8d3c-48e3-b7c6-42c8b9979368", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.fff330e2-8d3c-48e3-b7c6-42c8b9979368"]}}, "quality_metric": {"Sequence length": "151", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI4BD4LMO/fastqc_report.html", "@id": "/quality-metrics-fastqc/c201e235-11a7-4f35-90f9-8373fd1a2092/", "uuid": "c201e235-11a7-4f35-90f9-8373fd1a2092", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2018-10-17", "Total Sequences": 111574632, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Peter Fraser, BABRAHAM", "experiment_type": "single cell Hi-C", "experiment_bucket": "raw file", "assay_info": "MboI", "dataset": "single cell Hi-C on sorted diploid F1 2-1s", "condition": "2n DNA - serum", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Peter Fraser, BABRAHAM"}}, {"paired_end": "2", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/95015a39-45f4-4a83-bfd5-4c1ab59a628a/4DNFIVPRK5RS.fastq.gz", "file_classification": "raw file", "upload_key": "95015a39-45f4-4a83-bfd5-4c1ab59a628a/4DNFIVPRK5RS.fastq.gz", "status": "released", "file_size": 14138961899, "href": "/files-fastq/4DNFIVPRK5RS/@@download/4DNFIVPRK5RS.fastq.gz", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIVPRK5RS", "md5sum": "4efc2d293d00a8a71c5d0d187429f890", "file_type": "reads", "uuid": "95015a39-45f4-4a83-bfd5-4c1ab59a628a", "display_title": "4DNFIVPRK5RS.fastq.gz", "@id": "/files-fastq/4DNFIVPRK5RS/", "file_type_detailed": "reads (fastq)", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFI4BD4LMO.fastq.gz", "file_type_detailed": "reads (fastq)", "accession": "4DNFI4BD4LMO", "status": "released", "@type": ["FileFastq", "File", "Item"], "paired_end": "1", "uuid": "da8714c3-e52a-4b5d-a6bc-2476bc6a8438", "file_type": "reads", "@id": "/files-fastq/4DNFI4BD4LMO/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "contributing_labs": [{"display_title": "Amos Tanay, WIS", "status": "current", "name": "amos-tanay-lab", "@id": "/labs/amos-tanay-lab/", "@type": ["Lab", "Item"], "uuid": "44a45fb2-33a9-4ec4-8e44-e82bc8d40d8f", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.44a45fb2-33a9-4ec4-8e44-e82bc8d40d8f"]}}], "lab": {"@id": "/labs/peter-fraser-lab/", "display_title": "Peter Fraser, BABRAHAM", "name": "peter-fraser-lab", "status": "current", "uuid": "fff330e2-8d3c-48e3-b7c6-42c8b9979368", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.fff330e2-8d3c-48e3-b7c6-42c8b9979368"]}}, "quality_metric": {"Sequence length": "151", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIVPRK5RS/fastqc_report.html", "@id": "/quality-metrics-fastqc/3b5ce3da-dd87-4730-9b9e-5b548ab6f753/", "uuid": "3b5ce3da-dd87-4730-9b9e-5b548ab6f753", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2018-10-17", "Total Sequences": 111574632, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Peter Fraser, BABRAHAM", "experiment_type": "single cell Hi-C", "experiment_bucket": "raw file", "assay_info": "MboI", "dataset": "single cell Hi-C on sorted diploid F1 2-1s", "condition": "2n DNA - serum", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Peter Fraser, BABRAHAM"}}], "biosample": {"biosample_type": "stem cells", "@id": "/biosamples/4DNBSI69FM15/", "display_title": "4DNBSI69FM15", "biosample_category": ["Mouse stem cell"], "biosource_summary": "F1 2-1 mESC line", "status": "released", "uuid": "d0767d5e-e7a9-497f-a082-9c4c98a3a633", "@type": ["Biosample", "Item"], "modifications_summary": "None", "accession": "4DNBSI69FM15", "treatments_summary": "None", "biosource": [{"@type": ["Biosource", "Item"], "status": "released", "accession": "4DNSRW5UG3MR", "uuid": "4101fd9b-449a-4dc9-913e-944e1038ddf1", "display_title": "F1 2-1 mESC line - 4DNSRW5UG3MR", "cell_line_tier": "Unclassified", "@id": "/biosources/4DNSRW5UG3MR/", "biosource_type": "stem cell derived cell line", "cell_line": {"uuid": "5a7ff7a9-a2af-4137-9229-1e4e328a58da", "term_name": "F121-CASTx129", "term_id": "4DN:0000255", "preferred_name": "F1 2-1 mESC line", "status": "released", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/4DN:0000255/", "display_title": "F1 2-1 mESC line", "slim_terms": [{"@id": "/ontology-terms/CL:0002322/", "status": "released", "display_title": "embryonic stem cell", "@type": ["OntologyTerm", "Item"], "uuid": "c57be9f1-b913-43fb-8437-e76960cfab59", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CLO:0000031/", "status": "released", "display_title": "cell line", "@type": ["OntologyTerm", "Item"], "uuid": "f9483d7e-4731-47d1-b8e0-1aac05ba2b49", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@type": ["Organism", "Item"], "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "status": "released", "display_title": "M. musculus", "name": "mouse", "@id": "/organisms/10090/", "scientific_name": "Mus musculus", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"term_id": "CL:0000034", "@id": "/ontology-terms/CL:0000034/", "synonyms": ["animal stem cell"], "term_name": "stem cell", "display_title": "stem cell", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "@type": ["OntologyTerm", "Item"], "status": "released", "preferred_name": "stem cell", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "display_title": "cell", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "display_title": "cell", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "cell_culture_details": [{"@id": "/biosample-cell-cultures/c60e73e3-3441-407c-bc77-1cf5c5153b81/", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "No", "uuid": "c60e73e3-3441-407c-bc77-1cf5c5153b81", "display_title": "BiosampleCellCulture from 2018-09-19", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "badges": [{"messages": ["Biosample missing doubling_number", "Biosample missing passage_number", "Biosample missing culture_duration", "Biosample missing morphology_image", "Biosample is a stem cell line with unknown passage number missing karyotype"], "badge": {"description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "title": "Biosample Metadata Incomplete", "badge_icon": "/static/img/badges/biosample-icon.svg", "badge_classification": "Warning", "@type": ["Badge", "Item"], "status": "released", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "display_title": "Biosample Metadata Incomplete", "warning": "Biosample Metadata Incomplete", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}}, "digestion_enzyme": {"status": "released", "name": "MboI", "display_title": "MboI", "uuid": "d8da42d0-bc20-40e5-bacf-c263b8603e03", "@id": "/enzymes/MboI/", "@type": ["Enzyme", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_type": {"assay_subclassification": "DNA-DNA Pairwise Interactions - Single Cell", "@id": "/experiment-types/single-cell-hi-c/", "assay_subclass_short": "Hi-C (single cell)", "other_tags": ["DNA-DNA", "Single Cell", "3D", "Pairwise"], "title": "single cell Hi-C", "status": "released", "display_title": "single cell Hi-C", "experiment_category": "Sequencing", "assay_classification": "3C via Ligation", "@type": ["ExperimentType", "Item"], "uuid": "d8786661-161b-40ea-988d-7d2d2d008872", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"value": "MboI", "field": "Enzyme", "combined": "Enzyme: MboI"}, "last_modified": {"date_modified": "2019-04-24T16:10:22.086981+00:00"}}], "experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNES1B64O2Z/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "8bea2d56-ee27-42d8-ae55-a29b4b7db8c1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNES1B64O2Z", "external_references": [{"ref": "GEO:GSE94489", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE94489"}], "produced_in_pub": {"display_title": "Nagano T et al. (2017) doi:10.1038/nature23001", "title": "Cell-cycle dynamics of chromosomal organization at single-cell resolution.", "uuid": "d37f9a09-4339-4e47-90d1-bde1168b4f9a", "@id": "/publications/d37f9a09-4339-4e47-90d1-bde1168b4f9a/", "ID": "doi:10.1038/nature23001", "@type": ["Publication", "Item"], "status": "current", "abstract": "Chromosomes in proliferating metazoan cells undergo marked structural metamorphoses every cell cycle, alternating between highly condensed mitotic structures that facilitate chromosome segregation, and decondensed interphase structures that accommodate transcription, gene silencing and DNA replication. Here we use single-cell Hi-C (high-resolution chromosome conformation capture) analysis to study chromosome conformations in thousands of individual cells, and  discover a continuum of cis-interaction profiles that finely position individual  cells along the cell cycle. We show that chromosomal compartments, topological-associated domains (TADs), contact insulation and long-range loops, all defined by bulk Hi-C maps, are governed by distinct cell-cycle dynamics. In particular, DNA replication correlates with a build-up of compartments and a reduction in TAD insulation, while loops are generally stable from G1 to S and G2 phase. Whole-genome three-dimensional structural models reveal a radial architecture of chromosomal compartments with distinct epigenomic signatures. Our single-cell data therefore allow re-interpretation of chromosome conformation maps through the prism of the cell cycle.", "url": "https://www.ncbi.nlm.nih.gov/pubmed/28682332", "journal": "Nature", "authors": ["Nagano T", "Lubling Y", "Varnai C", "Dudley C", "Leung W", "Baran Y", "Mendelson Cohen N", "Wingett S", "Fraser P", "Tanay A"], "short_attribution": "Nagano T et al. (2017)", "date_published": "2017-07-05", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"status": "current", "title": "Cell-cycle dynamics of chromosomal organization at single-cell resolution.", "journal": "Nature", "uuid": "d37f9a09-4339-4e47-90d1-bde1168b4f9a", "authors": ["Nagano T", "Lubling Y", "Varnai C", "Dudley C", "Leung W", "Baran Y", "Mendelson Cohen N", "Wingett S", "Fraser P", "Tanay A"], "@type": ["Publication", "Item"], "@id": "/publications/d37f9a09-4339-4e47-90d1-bde1168b4f9a/", "display_title": "Nagano T et al. (2017) doi:10.1038/nature23001", "date_published": "2017-07-05", "ID": "doi:10.1038/nature23001", "abstract": "Chromosomes in proliferating metazoan cells undergo marked structural metamorphoses every cell cycle, alternating between highly condensed mitotic structures that facilitate chromosome segregation, and decondensed interphase structures that accommodate transcription, gene silencing and DNA replication. Here we use single-cell Hi-C (high-resolution chromosome conformation capture) analysis to study chromosome conformations in thousands of individual cells, and  discover a continuum of cis-interaction profiles that finely position individual  cells along the cell cycle. We show that chromosomal compartments, topological-associated domains (TADs), contact insulation and long-range loops, all defined by bulk Hi-C maps, are governed by distinct cell-cycle dynamics. In particular, DNA replication correlates with a build-up of compartments and a reduction in TAD insulation, while loops are generally stable from G1 to S and G2 phase. Whole-genome three-dimensional structural models reveal a radial architecture of chromosomal compartments with distinct epigenomic signatures. Our single-cell data therefore allow re-interpretation of chromosome conformation maps through the prism of the cell cycle.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 1, "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSI69FM15/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["Biosample missing doubling_number", "Biosample missing passage_number", "Biosample missing culture_duration", "Biosample missing morphology_image", "Biosample is a stem cell line with unknown passage number missing karyotype"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}, {"parent": "/experiment-set-replicates/4DNES1B64O2Z/", "embedded_path": "badges", "item": {"messages": ["Replicate set contains only a single biological replicate"], "badge": {"commendation": null, "warning": "Replicate Numbers", "uuid": "24a64a84-3c33-4d76-aaf2-e5ef45eff347", "@id": "/badges/replicate-numbers/", "badge_icon": "/static/img/badges/replicates-orange-circle.svg", "description": "Issues with replicate numbers"}}}]}, "validation-errors": []}