{"lab": {"status": "current", "correspondence": [{"contact_email": "am9iLmRla2tlckB1bWFzc21lZC5lZHU=", "@id": "/users/83b5073a-069b-4162-9b30-6f42d5551e34/", "display_title": "Job Dekker"}], "@id": "/labs/job-dekker-lab/", "@type": ["Lab", "Item"], "title": "Job Dekker, UMMS", "display_title": "Job Dekker, UMMS", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "award": {"@type": ["Award", "Item"], "center_title": "NOFIC - Dekker", "project": "4DN", "description": "NOFIC: The spatial organization of the genome impinges on all genomic processes, including gene regulation, maintenance of genome stability and chromosome transmission to daughter cells. A detailed understanding of the spatial arrangement of the human genome, referred to as the 4D nucleome, and the biological and physical principles that drive chromosome folding requires combining approaches from the fields of molecular and cell biology, imaging, genetics and genomics with approaches from physics, computational biology, and computer simulation. We have assembled a highly interdisciplinary center with the goal of generating extensively validated maps of the 4D nucleome, its physical and dynamic properties and its role in regulating the activity of the genome. First, the center will further optimize and extensively validate a suite of genome-wide molecular methodologies, based on chromosome conformation capture (3C) that can probe the folding of chromosomes at the scale of single nucleosomes, chromatin fibers, chromosomes and the entire nucleus, across cell populations and in single cells. Given that chromosome and nuclear organization is tightly linked to biological state of the cell, the center will map the 4D nucleome for four key biological states representing different conformations during the cell cycle (interphase and mitosis), and during cell differentiation (pluripotent and differentiated states). We will obtain complementary data regarding the structure and dynamics of chromatin, at different length scales and in single cells using extensive high-throughput imaging, live cell imaging and super resolution microscopy. Data obtained with all approaches will be analyzed, integrated and modeled using a set of methods we will further develop to gain insights into the structure, physics and dynamics of chromosome folding over different length scales. Finally, a critical component of our proposal is the biological validation and further elaboration of the chromatin interaction maps that are generated from our conformational analyses. This validation will be achieved through site-specific editing of genomic sequence and epigenetic marks, the creation of new contact points within the genome, and the identification of factors (both protein and nucleic acid) that facilitat or restrict these interactions. Effects of such perturbations in the chromosome conformation on transcription will reveal relationships between specific chromosome structural features and gene expression.", "display_title": "CENTER FOR 3D STRUCTURE AND PHYSICS OF THE GENOME", "status": "current", "uuid": "ae6c618f-7a8c-441e-a886-e30bbbe591da", "@id": "/awards/1U54DK107980-01/", "name": "1U54DK107980-01", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "study": "Cell Cycle", "badges": [{"badge": {"title": "Replicate Numbers", "badge_icon": "/static/img/badges/replicates-orange-circle.svg", "display_title": "Replicate Numbers", "badge_classification": "Warning", "warning": "Replicate Numbers", "@type": ["Badge", "Item"], "status": "released", "@id": "/badges/replicate-numbers/", "description": "Issues with replicate numbers", "uuid": "24a64a84-3c33-4d76-aaf2-e5ef45eff347", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "messages": ["Replicate set contains only a single biological replicate"]}], "status": "released", "aliases": ["dekker-lab:Experiment_Set_Mitotic-Release-Timecourse_TB-HiC-Dpn-Tasyn"], "accession": "4DNESYK6LDN6", "condition": "Before prometaphase arrest (asynchronous control)", "description": "in situ Hi-C on synchronyzed HeLa cells - Replicate 2 - Before prometaphase arrest (asynchronous control)", "study_group": "Time Course", "date_created": "2019-08-16T20:46:09.567934+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_group": "Hi-C on sync. HeLa cells", "dataset_label": "Hi-C on sync. HeLa cells - Rep2", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-01-25T05:04:43.405096+00:00"}, "public_release": "2019-11-21", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "658ced2a-ad6a-40e9-b776-4cade2ece8a1", "@id": "/experiments-hi-c/4DNEX7GLQH5A/", "accession": "4DNEX7GLQH5A", "display_title": "in situ Hi-C on HeLa-S3 with DpnII - 4DNEX7GLQH5A", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_content": [{"content": {"award": {"uuid": "ae6c618f-7a8c-441e-a886-e30bbbe591da", "@id": "/awards/1U54DK107980-01/", "status": "current", "@type": ["Award", "Item"], "display_title": "CENTER FOR 3D STRUCTURE AND PHYSICS OF THE GENOME", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "a0798bb9-6ba7-4cd2-baa1-7d575609c59b", "title": "4DNESYK6LDN6 - Processed files", "contributing_labs": [], "name": "a0798bb9-6ba7-4cd2-baa1-7d575609c59b", "@id": "/higlass-view-configs/a0798bb9-6ba7-4cd2-baa1-7d575609c59b/", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "display_title": "4DNESYK6LDN6 - Processed files", "description": "4DNESYK6LDN6 (in situ Hi-C on synchronyzed HeLa cells - Replicate 2 - Before prometaphase arrest (asynchronous control)): 4DNFIBMQ8BHU", "filetype": "HiglassViewConfig", "lab": {"status": "current", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "@id": "/labs/job-dekker-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}, "location": "tab:processed-files", "description": "auto_generated_higlass_view_config"}], "static_headers": [{"lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "In Situ Hi-C\n\n

\n In situ Hi-C is a method to detect and quantify the pairwise interactions between chromosome regions across the entire genome. It was developed in 2014 as an improvement over the dilution Hi-C method. Compared to standard dilution Hi-C, this technique reduces the frequency of random ligation because the ligation is performed in situ inside the nucleus, a constrained space, instead of in solution, where DNA fragments are floating freely. In addition, this protocol can be done more quickly in the lab and was the first to introduce the use of 4-cutter restriction enzymes as opposed to the previous 6-cutters, providing higher resolution.\n

\n

\nThe protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. The cells are then permeabilized with their nuclei intact. A 4-cutter restriction enzyme is used to digest the chromatin into multiple DNA fragments. The resulting fragments are biotinylated by end filling of the fragments ends. The fragments are then ligated and the DNA is purified and sheared. The biotinylated fragments are pulled down from the solution with streptavidin beads and a library is constructed and sequenced. Analysis of the resulting paired-end short read sequences produces a matrix that shows the number of interactions between different DNA regions.\n

\n

\nSee Rao et al., 2014 for more details.\n

\n\n
\n\n

\n Image source: Rao et al., 2014, Figure 1A\n
", "name": "item-page-headers.ExperimentType.insituhic", "award": {"status": "current", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "@type": ["Award", "Item"], "@id": "/awards/1U01CA200059-01/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Assay Description", "status": "released", "aliases": ["4dn-dcic-lab:experiment_infobox_hic"], "options": {"filetype": "html", "collapsible": false, "default_open": false, "convert_ext_links": true}, "date_created": "2018-09-07T18:19:43.777198+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2023-11-09T14:48:01.220007+00:00"}, "schema_version": "2", "@id": "/static-sections/298554ad-20e2-4449-a752-ac190123dab7/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "298554ad-20e2-4449-a752-ac190123dab7", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.56c9c683-bb11-471b-b590-c656f7dc03c1"]}, "display_title": "Assay Description", "external_references": [], "content": "In Situ Hi-C\n\n

\n In situ Hi-C is a method to detect and quantify the pairwise interactions between chromosome regions across the entire genome. It was developed in 2014 as an improvement over the dilution Hi-C method. Compared to standard dilution Hi-C, this technique reduces the frequency of random ligation because the ligation is performed in situ inside the nucleus, a constrained space, instead of in solution, where DNA fragments are floating freely. In addition, this protocol can be done more quickly in the lab and was the first to introduce the use of 4-cutter restriction enzymes as opposed to the previous 6-cutters, providing higher resolution.\n

\n

\nThe protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. The cells are then permeabilized with their nuclei intact. A 4-cutter restriction enzyme is used to digest the chromatin into multiple DNA fragments. The resulting fragments are biotinylated by end filling of the fragments ends. The fragments are then ligated and the DNA is purified and sheared. The biotinylated fragments are pulled down from the solution with streptavidin beads and a library is constructed and sequenced. Analysis of the resulting paired-end short read sequences produces a matrix that shows the number of interactions between different DNA regions.\n

\n

\nSee Rao et al., 2014 for more details.\n

\n\n
\n\n

\n Image source: Rao et al., 2014, Figure 1A\n
", "filetype": "html", "content_as_html": "
In Situ Hi-C\n

\n In situ Hi-C is a method to detect and quantify the pairwise interactions between chromosome regions across the entire genome. It was developed in 2014 as an improvement over the dilution Hi-C method. Compared to standard dilution Hi-C, this technique reduces the frequency of random ligation because the ligation is performed in situ inside the nucleus, a constrained space, instead of in solution, where DNA fragments are floating freely. In addition, this protocol can be done more quickly in the lab and was the first to introduce the use of 4-cutter restriction enzymes as opposed to the previous 6-cutters, providing higher resolution.\n

\n

\nThe protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. The cells are then permeabilized with their nuclei intact. A 4-cutter restriction enzyme is used to digest the chromatin into multiple DNA fragments. The resulting fragments are biotinylated by end filling of the fragments ends. The fragments are then ligated and the DNA is purified and sheared. The biotinylated fragments are pulled down from the solution with streptavidin beads and a library is constructed and sequenced. Analysis of the resulting paired-end short read sequences produces a matrix that shows the number of interactions between different DNA regions.\n

\n

\nSee Rao et al., 2014 for more details.\n

\n
\n\n

\nImage source: Rao et al., 2014, Figure 1A\n
"}], "processed_files": [{"accession": "4DNFI21UW2W3", "@type": ["FileProcessed", "File", "Item"], "genome_assembly": "GRCh38", "file_type_detailed": "contact list-combined (pairs)", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "display_title": "pairs", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "display_title": "4DNFI21UW2W3.pairs.gz", "md5sum": "05db0eea14b75d26aafcb5c88e3aab1f", "file_type": "contact list-combined", "file_classification": "processed file", "file_size": 839731260, "upload_key": "a0b4b9e9-5c27-480e-baad-8941514b6d41/4DNFI21UW2W3.pairs.gz", "@id": "/files-processed/4DNFI21UW2W3/", "href": "/files-processed/4DNFI21UW2W3/@@download/4DNFI21UW2W3.pairs.gz", "uuid": "a0b4b9e9-5c27-480e-baad-8941514b6d41", "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/a0b4b9e9-5c27-480e-baad-8941514b6d41/4DNFI21UW2W3.pairs.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "extra_files": [{"href": "/files-processed/4DNFI21UW2W3/@@download/4DNFI21UW2W3.pairs.gz.px2", "file_size": 12242976, "md5sum": "e333ed68fac2e33e6a51da6fe19275e0", "file_format": {"@id": "/file-formats/pairs_px2/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "display_title": "pairs_px2", "file_format": "pairs_px2", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"Total reads": 41331359, "status": "released", "display_title": "QualityMetricPairsqc from 2019-08-22", "uuid": "2fbbf52b-1788-4aa9-ac1d-803af084aa6a", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "@id": "/quality-metrics-pairsqc/2fbbf52b-1788-4aa9-ac1d-803af084aa6a/", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI21UW2W3/pairsqc_report.html", "overall_quality_status": "PASS", "quality_metric_summary": [{"title": "Filtered Reads", "value": "41331359", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "40.392", "tooltip": "Percent of filtered reads (=16.69m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "22.267", "tooltip": "Percent of filtered reads (=9.2m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "37.341", "tooltip": "Percent of filtered reads (=15.43m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"display_title": "Job Dekker, UMMS", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "name": "job-dekker-lab", "@type": ["Lab", "Item"], "@id": "/labs/job-dekker-lab/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "external_references": [], "track_and_facet_info": {"dataset": "Hi-C on sync. HeLa cells - Rep2", "condition": "Before prometaphase arrest (asynchronous control)", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "unreplicated", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "DpnII", "biosource_name": "HeLa-S3", "lab_name": "4DN DCIC, HMS"}, "last_modified": {"date_modified": "2021-04-06T20:29:42.489730+00:00"}}, {"accession": "4DNFIM6RGKPV", "@type": ["FileProcessed", "File", "Item"], "genome_assembly": "GRCh38", "file_type_detailed": "contact matrix (hic)", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/hic/", "display_title": "hic", "status": "released", "uuid": "d13d11cf-218e-4f61-bbf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "display_title": "4DNFIM6RGKPV.hic", "md5sum": "72ec777f90064cfe917e4168607c29b9", "file_type": "contact matrix", "file_classification": "processed file", "file_size": 1002617751, "upload_key": "c6582128-a930-4bcc-941e-5c0733bdd4d5/4DNFIM6RGKPV.hic", "@id": "/files-processed/4DNFIM6RGKPV/", "href": "/files-processed/4DNFIM6RGKPV/@@download/4DNFIM6RGKPV.hic", "uuid": "c6582128-a930-4bcc-941e-5c0733bdd4d5", "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/c6582128-a930-4bcc-941e-5c0733bdd4d5/4DNFIM6RGKPV.hic", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "lab": {"status": "current", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"display_title": "Job Dekker, UMMS", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "name": "job-dekker-lab", "@type": ["Lab", "Item"], "@id": "/labs/job-dekker-lab/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "external_references": [], "track_and_facet_info": {"dataset": "Hi-C on sync. HeLa cells - Rep2", "condition": "Before prometaphase arrest (asynchronous control)", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "unreplicated", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "DpnII", "biosource_name": "HeLa-S3", "lab_name": "4DN DCIC, HMS"}, "last_modified": {"date_modified": "2021-03-28T14:59:47.559940+00:00"}}, {"accession": "4DNFIBMQ8BHU", "higlass_uid": "b883bebd-2846-47dc-beb3-9ba99cca8042", "@type": ["FileProcessed", "File", "Item"], "genome_assembly": "GRCh38", "file_type_detailed": "contact matrix (mcool)", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/mcool/", "display_title": "mcool", "status": "released", "uuid": "d13d06cf-218e-4f61-ccf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "display_title": "4DNFIBMQ8BHU.mcool", "notes_to_tsv": ["WARNING - Due to a bug in the version of cooler (0.8.3) used in the current 4DN standard Hi-C processing pipeline some pixels may occur mulitple times at a single resolution with different counts being reported for each occurence. This duplication does not affect the higlass display of these files, howevver, downstream analyses using this file may encounter issues due to this pixel duplication. The counts from the duplicate pixels can be aggregated to determine the correct count value at that location. If this issue is problematic for your needs you should consider regenerating the matrices from the merged pairs file of the associated dataset using a more recent version of cooler. We are working to update the pipeline but do not yet have a predicted date for when this issue will be resolved."], "md5sum": "f3f07df54972cab07ac0f5df7b1117f9", "file_type": "contact matrix", "file_classification": "processed file", "file_size": 563963831, "upload_key": "bc6d7247-225a-4389-a252-28305371d3d1/4DNFIBMQ8BHU.mcool", "@id": "/files-processed/4DNFIBMQ8BHU/", "href": "/files-processed/4DNFIBMQ8BHU/@@download/4DNFIBMQ8BHU.mcool", "uuid": "bc6d7247-225a-4389-a252-28305371d3d1", "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/bc6d7247-225a-4389-a252-28305371d3d1/4DNFIBMQ8BHU.mcool", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric": {"status": "released", "display_title": "QualityMetricMcool from 2021-05-21", "uuid": "dc50c419-606c-445b-ac4a-9557a58df53e", "@type": ["QualityMetricMcool", "QualityMetric", "Item"], "@id": "/quality-metrics-mcool/dc50c419-606c-445b-ac4a-9557a58df53e/", "overall_quality_status": "PASS", "quality_metric_summary": [{"title": "Failed Balancing", "value": "None", "tooltip": "Resolutions where balancing failed", "numberType": "string"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"display_title": "Job Dekker, UMMS", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "name": "job-dekker-lab", "@type": ["Lab", "Item"], "@id": "/labs/job-dekker-lab/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "external_references": [], "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"@id": "/higlass-view-configs/9483b15f-6529-44a8-a7ff-475288e9f891/", "status": "released", "@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "9483b15f-6529-44a8-a7ff-475288e9f891", "display_title": "4DNFIBMQ8BHU - contact matrix for HeLa-S3 in situ Hi-C DpnII", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "track_and_facet_info": {"dataset": "Hi-C on sync. HeLa cells - Rep2", "condition": "Before prometaphase arrest (asynchronous control)", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "unreplicated", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "DpnII", "biosource_name": "HeLa-S3", "lab_name": "4DN DCIC, HMS", "track_title": "contact matrix for HeLa-S3 in situ Hi-C DpnII"}, "last_modified": {"date_modified": "2023-08-25T17:52:34.968682+00:00"}}, {"accession": "4DNFIDBVTIE8", "higlass_uid": "1ffdba0a-c4fc-4168-9fe4-f259aca74cee", "@type": ["FileProcessed", "File", "Item"], "genome_assembly": "GRCh38", "file_type_detailed": "compartments (bw)", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "display_title": "bw", "status": "released", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "display_title": "4DNFIDBVTIE8.bw", "md5sum": "248163e6b0fc31122b583a91a0d5895b", "file_type": "compartments", "file_classification": "processed file", "file_size": 212387, "upload_key": "2b83993d-81c5-4830-b2f3-2f5c7bf7f7f0/4DNFIDBVTIE8.bw", "@id": "/files-processed/4DNFIDBVTIE8/", "href": "/files-processed/4DNFIDBVTIE8/@@download/4DNFIDBVTIE8.bw", "uuid": "2b83993d-81c5-4830-b2f3-2f5c7bf7f7f0", "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/2b83993d-81c5-4830-b2f3-2f5c7bf7f7f0/4DNFIDBVTIE8.bw", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "lab": {"status": "current", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"display_title": "Job Dekker, UMMS", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "name": "job-dekker-lab", "@type": ["Lab", "Item"], "@id": "/labs/job-dekker-lab/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "external_references": [], "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"@id": "/higlass-view-configs/791ca361-056b-4617-a060-a88581ac0a01/", "status": "released", "@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "791ca361-056b-4617-a060-a88581ac0a01", "display_title": "4DNFIDBVTIE8 - compartments for HeLa-S3 in situ Hi-C DpnII", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "track_and_facet_info": {"dataset": "Hi-C on sync. HeLa cells - Rep2", "condition": "Before prometaphase arrest (asynchronous control)", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "unreplicated", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "DpnII", "biosource_name": "HeLa-S3", "lab_name": "4DN DCIC, HMS", "track_title": "compartments for HeLa-S3 in situ Hi-C DpnII"}, "last_modified": {"date_modified": "2021-03-28T14:13:23.550933+00:00"}}], "project_release": "2019-11-21", "experiments_in_set": [{"files": [{"accession": "4DNFI1K4LVSZ", "file_size": 2544577277, "md5sum": "25ddc675c4d30e40e66f7fe19499bd9c", "display_title": "4DNFI1K4LVSZ.fastq.gz", "href": "/files-fastq/4DNFI1K4LVSZ/@@download/4DNFI1K4LVSZ.fastq.gz", "paired_end": "1", "uuid": "a7d38aa3-9516-4702-a0cb-9f7c2398b663", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "a7d38aa3-9516-4702-a0cb-9f7c2398b663/4DNFI1K4LVSZ.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "restricted", "@id": "/files-fastq/4DNFI1K4LVSZ/", "dbxrefs": ["SRA:SRR9609696"], "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFI9XHCPFU.fastq.gz", "status": "restricted", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFI9XHCPFU", "file_type": "reads", "uuid": "bc236259-7aeb-4ea6-b753-8ce4b1ffecc4", "paired_end": "2", "@id": "/files-fastq/4DNFI9XHCPFU/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [{"ref": "SRA:SRR9609696", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR9609696"}], "quality_metric": {"Total Sequences": 81972204, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2019-08-20", "uuid": "0d3f3687-50b6-4c8a-9377-65c6bebe8002", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/0d3f3687-50b6-4c8a-9377-65c6bebe8002/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI1K4LVSZ/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on sync. HeLa cells - Rep2", "condition": "Before prometaphase arrest (asynchronous control)", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HeLa-S3", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFI9XHCPFU", "file_size": 2832518305, "md5sum": "d5e527bebd7646e6116aedad30ca1b81", "display_title": "4DNFI9XHCPFU.fastq.gz", "href": "/files-fastq/4DNFI9XHCPFU/@@download/4DNFI9XHCPFU.fastq.gz", "paired_end": "2", "uuid": "bc236259-7aeb-4ea6-b753-8ce4b1ffecc4", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "bc236259-7aeb-4ea6-b753-8ce4b1ffecc4/4DNFI9XHCPFU.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "restricted", "@id": "/files-fastq/4DNFI9XHCPFU/", "dbxrefs": ["SRA:SRR9609696"], "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFI1K4LVSZ.fastq.gz", "status": "restricted", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFI1K4LVSZ", "file_type": "reads", "uuid": "a7d38aa3-9516-4702-a0cb-9f7c2398b663", "paired_end": "1", "@id": "/files-fastq/4DNFI1K4LVSZ/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [{"ref": "SRA:SRR9609696", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR9609696"}], "quality_metric": {"Total Sequences": 81972204, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2019-08-20", "uuid": "af7a1af8-d26c-45a0-b65d-30c86fa35f04", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/af7a1af8-d26c-45a0-b65d-30c86fa35f04/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI9XHCPFU/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on sync. HeLa cells - Rep2", "condition": "Before prometaphase arrest (asynchronous control)", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HeLa-S3", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@type": ["ExperimentHiC", "Experiment", "Item"], "status": "released", "@id": "/experiments-hi-c/4DNEX7GLQH5A/", "uuid": "658ced2a-ad6a-40e9-b776-4cade2ece8a1", "dbxrefs": ["GEO:GSM3909723", "SRA:SRX6373090"], "display_title": "in situ Hi-C on HeLa-S3 with DpnII - 4DNEX7GLQH5A", "accession": "4DNEX7GLQH5A", "crosslinking_method": "1% Formaldehyde", "processed_files": [{"display_title": "4DNFIG5QW7HN.bam", "md5sum": "971381a58dd3114fed490038828955d3", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@type": ["FileFormat", "Item"], "display_title": "bam", "@id": "/file-formats/bam/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "0111ef99-2e3e-4339-a72d-f0ef459a76d9", "file_classification": "processed file", "upload_key": "0111ef99-2e3e-4339-a72d-f0ef459a76d9/4DNFIG5QW7HN.bam", "file_type_detailed": "alignments (bam)", "@id": "/files-processed/4DNFIG5QW7HN/", "file_type": "alignments", "@type": ["FileProcessed", "File", "Item"], "status": "restricted", "file_size": 8152132810, "accession": "4DNFIG5QW7HN", "genome_assembly": "GRCh38", "href": "/files-processed/4DNFIG5QW7HN/@@download/4DNFIG5QW7HN.bam", "last_modified": {"date_modified": "2023-04-27T21:09:48.483414+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "contributing_labs": [{"@id": "/labs/job-dekker-lab/", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "display_title": "Job Dekker, UMMS", "status": "current", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "quality_metric": {"display_title": "QualityMetricBamqc from 2020-01-16", "@id": "/quality-metrics-bamqc/29f6907e-f7f3-450c-bb2e-3c01f402c1cf/", "overall_quality_status": "PASS", "uuid": "29f6907e-f7f3-450c-bb2e-3c01f402c1cf", "@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Reads", "value": "81972204", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "15.034", "tooltip": "Percent of total reads (=12.32m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "23.92", "tooltip": "Percent of total reads (=19.61m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "10.617", "tooltip": "Percent of total reads (=8.7m)", "numberType": "percent"}, {"title": "Walks", "value": "0.008", "tooltip": "Percent of total reads (=0.01m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.205", "tooltip": "Percent of total reads (=0.17m)", "numberType": "percent"}]}, "lab": {"@type": ["Lab", "Item"], "status": "current", "name": "4dn-dcic-lab", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "DpnII", "dataset": "Hi-C on sync. HeLa cells - Rep2", "condition": "Before prometaphase arrest (asynchronous control)", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HeLa-S3", "lab_name": "4DN DCIC, HMS"}}, {"display_title": "4DNFIULRWMQD.pairs.gz", "md5sum": "05db0eea14b75d26aafcb5c88e3aab1f", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "display_title": "pairs", "@id": "/file-formats/pairs/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "63c5ad58-c082-4443-b187-5f2381c28974", "file_classification": "processed file", "upload_key": "63c5ad58-c082-4443-b187-5f2381c28974/4DNFIULRWMQD.pairs.gz", "file_type_detailed": "contact list-replicate (pairs)", "@id": "/files-processed/4DNFIULRWMQD/", "file_type": "contact list-replicate", "@type": ["FileProcessed", "File", "Item"], "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/63c5ad58-c082-4443-b187-5f2381c28974/4DNFIULRWMQD.pairs.gz", "file_size": 839731260, "accession": "4DNFIULRWMQD", "genome_assembly": "GRCh38", "href": "/files-processed/4DNFIULRWMQD/@@download/4DNFIULRWMQD.pairs.gz", "extra_files": [{"file_size": 22836431, "md5sum": "0bbefb7a73317c17ded5e5d83fc1b903", "href": "/files-processed/4DNFIULRWMQD/@@download/4DNFIULRWMQD.pairs.gz.px2", "file_format": {"status": "released", "display_title": "pairs_px2", "@type": ["FileFormat", "Item"], "file_format": "pairs_px2", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "@id": "/file-formats/pairs_px2/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "last_modified": {"date_modified": "2021-04-06T20:30:37.111153+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "contributing_labs": [{"@id": "/labs/job-dekker-lab/", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "display_title": "Job Dekker, UMMS", "status": "current", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "quality_metric": {"display_title": "QualityMetricPairsqc from 2019-08-22", "@id": "/quality-metrics-pairsqc/e3573b7b-6a81-4a3d-aeec-7dd8362a50a3/", "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIULRWMQD/pairsqc_report.html", "uuid": "e3573b7b-6a81-4a3d-aeec-7dd8362a50a3", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "status": "released", "Total reads": 41331359, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "41331359", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "40.392", "tooltip": "Percent of filtered reads (=16.69m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "22.267", "tooltip": "Percent of filtered reads (=9.2m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "37.341", "tooltip": "Percent of filtered reads (=15.43m)", "numberType": "percent"}]}, "lab": {"@type": ["Lab", "Item"], "status": "current", "name": "4dn-dcic-lab", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "DpnII", "dataset": "Hi-C on sync. HeLa cells - Rep2", "condition": "Before prometaphase arrest (asynchronous control)", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HeLa-S3", "lab_name": "4DN DCIC, HMS"}}], "biosample": {"status": "released", "uuid": "99a4f2f1-11c0-4cd4-968b-d403c6b85e71", "display_title": "4DNBSHRJ3EE4", "treatments_summary": "None", "modifications_summary": "None", "@id": "/biosamples/4DNBSHRJ3EE4/", "biosource_summary": "HeLa-S3", "accession": "4DNBSHRJ3EE4", "biosample_type": "immortalized cells", "@type": ["Biosample", "Item"], "biosample_category": ["Other"], "biosource": [{"biosource_type": "immortalized cell line", "status": "released", "accession": "4DNSRGTEEYSL", "display_title": "HeLa-S3 - 4DNSRGTEEYSL", "@id": "/biosources/4DNSRGTEEYSL/", "cell_line_tier": "Unclassified", "@type": ["Biosource", "Item"], "uuid": "a7aa4e34-de17-4336-9e0c-2844fd326a96", "tissue": {"preferred_name": "uterine cervix", "term_name": "uterine cervix", "term_id": "UBERON:0000002", "display_title": "uterine cervix", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0000002/", "synonyms": ["uterine cervix", "caudal segment of uterus", "cervix uteri", "neck of uterus", "cervical canal of uterus", "canalis cervicis uteri"], "status": "released", "uuid": "600fc714-c007-441b-b3a7-3d164ddc2689", "slim_terms": [{"display_title": "reproductive system", "@id": "/ontology-terms/UBERON:0000990/", "@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "111127bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "mesoderm", "@id": "/ontology-terms/UBERON:0000926/", "@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "111120bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "name": "human", "display_title": "H. sapiens", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"preferred_name": "HeLa-S3", "term_name": "HeLa-S3", "uuid": "840525af-614c-4559-9997-23a30e288858", "term_id": "EFO:0002791", "display_title": "HeLa-S3", "status": "released", "@id": "/ontology-terms/EFO:0002791/", "@type": ["OntologyTerm", "Item"], "slim_terms": [{"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "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": [{"display_title": "BiosampleCellCulture from 2019-08-16", "in_vitro_differentiated": "No", "@id": "/biosample-cell-cultures/51750974-c5f3-4489-a134-b64ea4d0f773/", "uuid": "51750974-c5f3-4489-a134-b64ea4d0f773", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "tissue_organ_info": {"tissue_source": "uterine cervix", "organ_system": ["reproductive system", "mesoderm"]}}, "digestion_enzyme": {"display_title": "DpnII", "uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "name": "DpnII", "@type": ["Enzyme", "Item"], "status": "released", "@id": "/enzymes/DpnII/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "GEO:GSM3909723", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3909723"}, {"ref": "SRA:SRX6373090", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRX6373090"}], "experiment_type": {"experiment_category": "Sequencing", "assay_classification": "3C via Ligation", "status": "released", "assay_subclassification": "DNA-DNA Pairwise Interactions", "assay_subclass_short": "Hi-C", "display_title": "in situ Hi-C", "uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "title": "in situ Hi-C", "@type": ["ExperimentType", "Item"], "@id": "/experiment-types/in-situ-hi-c/", "other_tags": ["DNA-DNA", "Pairwise", "3D"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"combined": "Enzyme: DpnII", "field": "Enzyme", "value": "DpnII"}, "last_modified": {"date_modified": "2023-02-02T18:31:35.792699+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experimentset_type": "replicate", "completed_processes": ["compartments_v1.2", "HiC_Pipeline_0.2.7"], "other_processed_files": [], "@id": "/experiment-set-replicates/4DNESYK6LDN6/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "3eddc670-edce-444e-8c28-f3e2331c06bb", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNESYK6LDN6", "external_references": [], "produced_in_pub": {"ID": "PMID:31685986", "journal": "Nature cell biology", "abstract": "Chromosome folding is modulated as cells progress through the cell cycle. During mitosis, condensins fold chromosomes into helical loop arrays. In interphase, the cohesin complex generates loops and topologically associating domains (TADs), while a separate process of compartmentalization drives segregation of active and inactive chromatin. We used synchronized cell cultures to determine how the mitotic chromosome conformation transforms into the interphase state. Using high-throughput chromosome conformation capture (Hi-C) analysis, chromatin binding assays and immunofluorescence, we show that, by telophase, condensin-mediated loops are lost and a transient folding intermediate is formed that is devoid of most loops. By cytokinesis, cohesin-mediated CTCF-CTCF loops and the positions of TADs emerge. Compartment boundaries are also established early, but long-range compartmentalization is a slow process and proceeds for hours after cells enter G1. Our results reveal the kinetics and order of events by which the interphase chromosome state is formed and identify telophase as a critical transition between condensin- and cohesin-driven chromosome folding.", "date_published": "2019-11-04", "uuid": "ffeab0b2-da5d-49fb-b98e-a61975dffc3e", "status": "current", "display_title": "Abramo K et al. (2019) PMID:31685986", "authors": ["Abramo K", "Valton AL", "Venev SV", "Ozadam H", "Fox AN", "Dekker J"], "short_attribution": "Abramo K et al. (2019)", "title": "A chromosome folding intermediate at the condensin-to-cohesin transition during telophase.", "@id": "/publications/ffeab0b2-da5d-49fb-b98e-a61975dffc3e/", "@type": ["Publication", "Item"], "url": "https://www.ncbi.nlm.nih.gov/pubmed/31685986", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"date_published": "2019-11-04", "status": "current", "display_title": "Abramo K et al. (2019) PMID:31685986", "@type": ["Publication", "Item"], "@id": "/publications/ffeab0b2-da5d-49fb-b98e-a61975dffc3e/", "journal": "Nature cell biology", "title": "A chromosome folding intermediate at the condensin-to-cohesin transition during telophase.", "uuid": "ffeab0b2-da5d-49fb-b98e-a61975dffc3e", "abstract": "Chromosome folding is modulated as cells progress through the cell cycle. During mitosis, condensins fold chromosomes into helical loop arrays. In interphase, the cohesin complex generates loops and topologically associating domains (TADs), while a separate process of compartmentalization drives segregation of active and inactive chromatin. We used synchronized cell cultures to determine how the mitotic chromosome conformation transforms into the interphase state. Using high-throughput chromosome conformation capture (Hi-C) analysis, chromatin binding assays and immunofluorescence, we show that, by telophase, condensin-mediated loops are lost and a transient folding intermediate is formed that is devoid of most loops. By cytokinesis, cohesin-mediated CTCF-CTCF loops and the positions of TADs emerge. Compartment boundaries are also established early, but long-range compartmentalization is a slow process and proceeds for hours after cells enter G1. Our results reveal the kinetics and order of events by which the interphase chromosome state is formed and identify telophase as a critical transition between condensin- and cohesin-driven chromosome folding.", "ID": "PMID:31685986", "authors": ["Abramo K", "Valton AL", "Venev SV", "Ozadam H", "Fox AN", "Dekker J"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 1, "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/experiment-set-replicates/4DNESYK6LDN6/", "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": []}