{"lab": {"uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@type": ["Lab", "Item"], "correspondence": [{"contact_email": "am9iLmRla2tlckB1bWFzc21lZC5lZHU=", "@id": "/users/83b5073a-069b-4162-9b30-6f42d5551e34/", "display_title": "Job Dekker"}], "display_title": "Job Dekker, UMMS", "title": "Job Dekker, UMMS", "@id": "/labs/job-dekker-lab/", "status": "current", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "award": {"@id": "/awards/3U54HG007010-05S1/", "description": "The overall aim of this proposal is to establish a comprehensive, high-quality, high-resolution catalogues of human and mouse DNasel hypersensitive sites (DHSs) spanning all major tissue lineages. Building on the prior success of the UW ENCODE center, we plan to localize DNasel hypersensitive sites, to define the locations of DNasel footprints therein, and to continue to provide relevant synergistic annotations including RNA-seq, histone modifications, and CTCF, as well as DNA methylation. The overriding focus of our production effort has been on data quality. Accordingly, samples will be rigorously screened in a pipeline fashion, with only a select set advancing to whole-genome data collection. To ensure the broadest possible coverage of both unique and non-unique genomic territories, we will employ a higher resolution, higher coverage sequencing strategy than the prior project period, significantly enhancing the information content of the data. This proposal integrates the UW-FHCRC Mouse ENCODE Center, which will be closely aligned with the human project to generate a comparative catalogue of regulatory DNA in carefully matched cells and tissues, providing an unparalleled resource. Since DNasel hypersensitive sites are generic markers of a broad spectrum of human cis-regulatory sequences, the utility of the catalogue will be greatly enhanced by the classification of DHSs into major functional categories including promoters, distal elements (enhancers, LCRs), and insulators. We plan to systematically connect distal DHSs with their cognate promoters and to perform in vivo validation of these connections using nuclease-mediated knockouts of distal DHSs in somatic cells.", "display_title": "A COMPREHENSIVE CATALOG OF DNASE I HYPERSENSITIVE SITES", "name": "3U54HG007010-05S1", "center_title": "3U54HG007010-05S1", "uuid": "43fc2984-a074-49c4-a69f-c9d3f3eadeba", "status": "current", "@type": ["Award", "Item"], "project": "ENCODE", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["dekker-lab:ExperimentSet_Encode_LNCaPcloneFGC-FA-HindIII"], "dbxrefs": ["ENCODE:ENCSR346DCU"], "accession": "4DNESNHN919R", "condition": "LNCaP clone FGC", "documents": [], "description": "HiC experiment done on LNCaP clone FGC", "study_group": "Single Time Point and Condition", "date_created": "2017-05-05T18:44:02.259043+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "Hi-C on ENCODE3 cell lines", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-01-27T03:53:06.701663+00:00"}, "public_release": "2017-07-26", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"status": "released", "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "23bacc29-3db4-4475-9077-464559a6db16", "@id": "/experiments-hi-c/4DNEXAQPT9EH/", "display_title": "Dilution Hi-C on LNCaP clone FGC with HindIII - 4DNEXAQPT9EH", "accession": "4DNEXAQPT9EH", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 1, "replicate_exp": {"status": "released", "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "398dc18c-90b4-47eb-a696-deefeb607aed", "@id": "/experiments-hi-c/4DNEXHMUQC5C/", "display_title": "Dilution Hi-C on LNCaP clone FGC with HindIII - 4DNEXHMUQC5C", "accession": "4DNEXHMUQC5C", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_content": [{"content": {"title": "4DNESNHN919R - Processed files", "@type": ["HiglassViewConfig", "UserContent", "Item"], "lab": {"@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "status": "current", "@type": ["Lab", "Item"], "display_title": "Job Dekker, UMMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "uuid": "547c3064-9720-45d4-811d-96817620e422", "description": "4DNESNHN919R (HiC experiment done on LNCaP clone FGC): 4DNFILC1IPOE, 4DNFIT299OMF, 4DNFI1H8SLX7, 4DNFI31QYTI7", "filetype": "HiglassViewConfig", "contributing_labs": [], "status": "released", "display_title": "4DNESNHN919R - Processed files", "@id": "/higlass-view-configs/547c3064-9720-45d4-811d-96817620e422/", "name": "547c3064-9720-45d4-811d-96817620e422", "award": {"status": "current", "uuid": "43fc2984-a074-49c4-a69f-c9d3f3eadeba", "display_title": "A COMPREHENSIVE CATALOG OF DNASE I HYPERSENSITIVE SITES", "@type": ["Award", "Item"], "@id": "/awards/3U54HG007010-05S1/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "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": {"display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "Dilution Hi-C\n\n

\nDilution Hi-C is a method to detect and quantify the pairwise interactions between chromosome regions across the entire genome. It was developed in 2009 and it was the first genome-wide chromosome conformation capture technique. \n

\n

\nThe protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. Then, the cells are lysed and a 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 in an extremely diluted solution in order to favor the ligation of the cross-linked fragments. Then, the DNA is purified and shreared. The biotinylated fragments are pulled down from the solution with streptavidin beads and the 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

\nAdvances in DNA sequencing depth and molecular techniques led to the development of a improved version of this technique known as in situ Hi-C that provides higher resolution, higher accuracy, and a much faster protocol. \n

\n

\nSee Lieberman-aiden et al., 2009 for more details on dilution Hi-C.\n

\n
\n\n

\n Image source: Lieberman-aiden et al., 2009, Figure 1A\n
", "name": "item-page-headers.ExperimentType.dilutionhic", "award": {"@type": ["Award", "Item"], "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "status": "current", "@id": "/awards/1U01CA200059-01/", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Assay Description", "status": "released", "aliases": ["4dn-dcic-lab:experiment_infobox_dhic"], "options": {"filetype": "html", "collapsible": false, "default_open": false}, "date_created": "2018-09-07T18:17:44.361064+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-04-22T16:25:13.985538+00:00"}, "schema_version": "2", "@id": "/static-sections/7627f4eb-9f2d-4171-9e9b-87ab800ab5cd/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "7627f4eb-9f2d-4171-9e9b-87ab800ab5cd", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.56c9c683-bb11-471b-b590-c656f7dc03c1"]}, "display_title": "Assay Description", "external_references": [], "content": "Dilution Hi-C\n\n

\nDilution Hi-C is a method to detect and quantify the pairwise interactions between chromosome regions across the entire genome. It was developed in 2009 and it was the first genome-wide chromosome conformation capture technique. \n

\n

\nThe protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. Then, the cells are lysed and a 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 in an extremely diluted solution in order to favor the ligation of the cross-linked fragments. Then, the DNA is purified and shreared. The biotinylated fragments are pulled down from the solution with streptavidin beads and the 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

\nAdvances in DNA sequencing depth and molecular techniques led to the development of a improved version of this technique known as in situ Hi-C that provides higher resolution, higher accuracy, and a much faster protocol. \n

\n

\nSee Lieberman-aiden et al., 2009 for more details on dilution Hi-C.\n

\n
\n\n

\n Image source: Lieberman-aiden et al., 2009, Figure 1A\n
", "filetype": "html", "content_as_html": "
Dilution Hi-C\n

\nDilution Hi-C is a method to detect and quantify the pairwise interactions between chromosome regions across the entire genome. It was developed in 2009 and it was the first genome-wide chromosome conformation capture technique. \n

\n

\nThe protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. Then, the cells are lysed and a 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 in an extremely diluted solution in order to favor the ligation of the cross-linked fragments. Then, the DNA is purified and shreared. The biotinylated fragments are pulled down from the solution with streptavidin beads and the 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

\nAdvances in DNA sequencing depth and molecular techniques led to the development of a improved version of this technique known as in situ Hi-C that provides higher resolution, higher accuracy, and a much faster protocol. \n

\n

\nSee Lieberman-aiden et al., 2009 for more details on dilution Hi-C.\n

\n
\n\n

\nImage source: Lieberman-aiden et al., 2009, Figure 1A\n
"}], "processed_files": [{"file_type": "contact list-combined", "uuid": "f266a254-e013-4d23-9802-d3789ff36251", "file_type_detailed": "contact list-combined (pairs)", "@type": ["FileProcessed", "File", "Item"], "file_classification": "processed file", "display_title": "4DNFIBC4JJSB.pairs.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/f266a254-e013-4d23-9802-d3789ff36251/4DNFIBC4JJSB.pairs.gz", "upload_key": "f266a254-e013-4d23-9802-d3789ff36251/4DNFIBC4JJSB.pairs.gz", "md5sum": "6384eaf40962fb26766e358821538fc6", "genome_assembly": "GRCh38", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/pairs/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNFIBC4JJSB", "href": "/files-processed/4DNFIBC4JJSB/@@download/4DNFIBC4JJSB.pairs.gz", "@id": "/files-processed/4DNFIBC4JJSB/", "file_size": 3739228728, "status": "released", "extra_files": [{"md5sum": "2bba388ba0e1d29615595c3f7eaf4a9c", "href": "/files-processed/4DNFIBC4JJSB/@@download/4DNFIBC4JJSB.pairs.gz.px2", "file_size": 25685249, "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "file_format": "pairs_px2", "display_title": "pairs_px2", "@id": "/file-formats/pairs_px2/", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"dataset": "Hi-C on ENCODE3 cell lines", "condition": "LNCaP clone FGC", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "Dilution Hi-C", "assay_info": "HindIII", "biosource_name": "LNCaP clone FGC", "lab_name": "4DN DCIC, HMS"}, "external_references": [], "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIBC4JJSB/pairsqc_report.html", "@id": "/quality-metrics-pairsqc/0eff757e-3f56-40b3-bcfb-3fc5a72f3bcd/", "overall_quality_status": "PASS", "Total reads": 195607964, "display_title": "QualityMetricPairsqc from 2018-04-26", "uuid": "0eff757e-3f56-40b3-bcfb-3fc5a72f3bcd", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "status": "released", "quality_metric_summary": [{"title": "Filtered Reads", "value": "195607964", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "14.947", "tooltip": "Percent of filtered reads (=29.24m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "26.744", "tooltip": "Percent of filtered reads (=52.31m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "58.31", "tooltip": "Percent of filtered reads (=114.06m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "status": "current", "name": "job-dekker-lab", "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"]}}], "lab": {"display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "name": "4dn-dcic-lab", "@type": ["Lab", "Item"], "status": "current", "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2022-01-10T14:30:41.249390+00:00"}}, {"file_type": "contact matrix", "uuid": "8660baeb-5be1-4ba5-93e4-66499e9a4587", "file_type_detailed": "contact matrix (hic)", "@type": ["FileProcessed", "File", "Item"], "file_classification": "processed file", "display_title": "4DNFIEBC4AF3.hic", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/8660baeb-5be1-4ba5-93e4-66499e9a4587/4DNFIEBC4AF3.hic", "upload_key": "8660baeb-5be1-4ba5-93e4-66499e9a4587/4DNFIEBC4AF3.hic", "md5sum": "fb6ca04121526ac30b1e6f3d7eda0fc6", "genome_assembly": "GRCh38", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "display_title": "hic", "uuid": "d13d11cf-218e-4f61-bbf0-91f226248b2c", "@id": "/file-formats/hic/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNFIEBC4AF3", "href": "/files-processed/4DNFIEBC4AF3/@@download/4DNFIEBC4AF3.hic", "@id": "/files-processed/4DNFIEBC4AF3/", "file_size": 3132319418, "status": "released", "extra_files": [], "track_and_facet_info": {"dataset": "Hi-C on ENCODE3 cell lines", "condition": "LNCaP clone FGC", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "Dilution Hi-C", "assay_info": "HindIII", "biosource_name": "LNCaP clone FGC", "lab_name": "4DN DCIC, HMS"}, "external_references": [], "contributing_labs": [{"uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "status": "current", "name": "job-dekker-lab", "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"]}}], "lab": {"display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "name": "4dn-dcic-lab", "@type": ["Lab", "Item"], "status": "current", "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2022-01-10T17:56:35.200304+00:00"}}, {"file_type": "contact matrix", "uuid": "dbbee0eb-d169-4562-8b5a-fafd7a317431", "file_type_detailed": "contact matrix (mcool)", "@type": ["FileProcessed", "File", "Item"], "file_classification": "processed file", "display_title": "4DNFILC1IPOE.mcool", "higlass_uid": "Z4zj8eVOQEOow16XL-4Zlw", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/dbbee0eb-d169-4562-8b5a-fafd7a317431/4DNFILC1IPOE.mcool", "upload_key": "dbbee0eb-d169-4562-8b5a-fafd7a317431/4DNFILC1IPOE.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": "fa3ab365ee906ede8e4b7af84217d110", "genome_assembly": "GRCh38", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "display_title": "mcool", "uuid": "d13d06cf-218e-4f61-ccf0-91f226248b2c", "@id": "/file-formats/mcool/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNFILC1IPOE", "href": "/files-processed/4DNFILC1IPOE/@@download/4DNFILC1IPOE.mcool", "@id": "/files-processed/4DNFILC1IPOE/", "file_size": 3138832150, "status": "released", "extra_files": [], "track_and_facet_info": {"dataset": "Hi-C on ENCODE3 cell lines", "condition": "LNCaP clone FGC", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "Dilution Hi-C", "assay_info": "HindIII", "biosource_name": "LNCaP clone FGC", "lab_name": "4DN DCIC, HMS", "track_title": "contact matrix for LNCaP clone FGC Dilution Hi-C HindIII"}, "external_references": [], "quality_metric": {"@id": "/quality-metrics-mcool/22eb0982-e19e-4ebb-87b1-ec3fe7c12e7b/", "overall_quality_status": "PASS", "display_title": "QualityMetricMcool from 2021-05-21", "uuid": "22eb0982-e19e-4ebb-87b1-ec3fe7c12e7b", "@type": ["QualityMetricMcool", "QualityMetric", "Item"], "status": "released", "quality_metric_summary": [{"title": "Failed Balancing", "value": "None", "tooltip": "Resolutions where balancing failed", "numberType": "string"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "status": "current", "name": "job-dekker-lab", "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"]}}], "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"uuid": "2f862056-8e85-4c5e-8ca0-7a49beb524e3", "@id": "/higlass-view-configs/2f862056-8e85-4c5e-8ca0-7a49beb524e3/", "@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFILC1IPOE - contact matrix for LNCaP clone FGC Dilution Hi-C HindIII", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "lab": {"display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "name": "4dn-dcic-lab", "@type": ["Lab", "Item"], "status": "current", "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-08-25T17:56:21.866807+00:00"}}, {"file_type": "boundaries", "uuid": "750b193f-42de-4e39-aa35-b08bffdbf0c9", "file_type_detailed": "boundaries (bed)", "@type": ["FileProcessed", "File", "Item"], "file_classification": "processed file", "display_title": "4DNFIT299OMF.bed.gz", "higlass_uid": "N5ifq6BaSYKZ7xaRbJtFWA", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/750b193f-42de-4e39-aa35-b08bffdbf0c9/4DNFIT299OMF.bed.gz", "upload_key": "750b193f-42de-4e39-aa35-b08bffdbf0c9/4DNFIT299OMF.bed.gz", "md5sum": "ba87265173ae6041dc72864de2f9220e", "genome_assembly": "GRCh38", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "display_title": "bed", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "@id": "/file-formats/bed/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNFIT299OMF", "href": "/files-processed/4DNFIT299OMF/@@download/4DNFIT299OMF.bed.gz", "@id": "/files-processed/4DNFIT299OMF/", "file_size": 320995, "status": "released", "extra_files": [{"use_for": "visualization", "md5sum": "c70e134925c292a10d16daeec3e61849", "href": "/files-processed/4DNFIT299OMF/@@download/4DNFIT299OMF.beddb", "file_format": {"uuid": "76dc8c06-67d8-487b-8fc8-d841752a0b60", "file_format": "beddb", "display_title": "beddb", "@id": "/file-formats/beddb/", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"dataset": "Hi-C on ENCODE3 cell lines", "condition": "LNCaP clone FGC", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "Dilution Hi-C", "assay_info": "HindIII", "biosource_name": "LNCaP clone FGC", "lab_name": "4DN DCIC, HMS", "track_title": "boundaries for LNCaP clone FGC Dilution Hi-C HindIII"}, "external_references": [], "contributing_labs": [{"uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "status": "current", "name": "job-dekker-lab", "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"]}}], "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"uuid": "253bda21-6be3-4b2c-a240-3ab9781eebc4", "@id": "/higlass-view-configs/253bda21-6be3-4b2c-a240-3ab9781eebc4/", "@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFIT299OMF - boundaries for LNCaP clone FGC Dilution Hi-C HindIII", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "lab": {"display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "name": "4dn-dcic-lab", "@type": ["Lab", "Item"], "status": "current", "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-04-06T20:10:45.739544+00:00"}}, {"file_type": "insulation score-diamond", "uuid": "e64258f1-2256-48ad-aa4b-6a1132a02953", "file_type_detailed": "insulation score-diamond (bw)", "@type": ["FileProcessed", "File", "Item"], "file_classification": "processed file", "display_title": "4DNFI1H8SLX7.bw", "higlass_uid": "5a258305-ad06-46f5-bd73-c3e50931b114", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/e64258f1-2256-48ad-aa4b-6a1132a02953/4DNFI1H8SLX7.bw", "upload_key": "e64258f1-2256-48ad-aa4b-6a1132a02953/4DNFI1H8SLX7.bw", "md5sum": "62b7554e6041fe630a3073f0d8c72bb4", "genome_assembly": "GRCh38", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNFI1H8SLX7", "href": "/files-processed/4DNFI1H8SLX7/@@download/4DNFI1H8SLX7.bw", "@id": "/files-processed/4DNFI1H8SLX7/", "file_size": 4353246, "status": "released", "track_and_facet_info": {"dataset": "Hi-C on ENCODE3 cell lines", "condition": "LNCaP clone FGC", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "Dilution Hi-C", "assay_info": "HindIII", "biosource_name": "LNCaP clone FGC", "lab_name": "4DN DCIC, HMS", "track_title": "insulation score-diamond for LNCaP clone FGC Dilution Hi-C HindIII"}, "external_references": [], "contributing_labs": [{"uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "status": "current", "name": "job-dekker-lab", "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"]}}], "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"uuid": "c37174be-a482-4211-8386-8ec7c3b49da7", "@id": "/higlass-view-configs/c37174be-a482-4211-8386-8ec7c3b49da7/", "@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFI1H8SLX7 - insulation score-diamond for LNCaP clone FGC Dilution Hi-C HindIII", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "lab": {"display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "name": "4dn-dcic-lab", "@type": ["Lab", "Item"], "status": "current", "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-03-28T14:16:51.431451+00:00"}}, {"file_type": "compartments", "uuid": "b0ce93fd-0c93-4518-b040-3a9a49af94c9", "file_type_detailed": "compartments (bw)", "@type": ["FileProcessed", "File", "Item"], "file_classification": "processed file", "display_title": "4DNFI31QYTI7.bw", "higlass_uid": "24a27ba8-e675-430d-b331-73af57df344c", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/b0ce93fd-0c93-4518-b040-3a9a49af94c9/4DNFI31QYTI7.bw", "upload_key": "b0ce93fd-0c93-4518-b040-3a9a49af94c9/4DNFI31QYTI7.bw", "md5sum": "21f8f6a353651676d9548ee2bc1452a2", "genome_assembly": "GRCh38", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNFI31QYTI7", "href": "/files-processed/4DNFI31QYTI7/@@download/4DNFI31QYTI7.bw", "@id": "/files-processed/4DNFI31QYTI7/", "file_size": 209102, "status": "released", "track_and_facet_info": {"dataset": "Hi-C on ENCODE3 cell lines", "condition": "LNCaP clone FGC", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "Dilution Hi-C", "assay_info": "HindIII", "biosource_name": "LNCaP clone FGC", "lab_name": "4DN DCIC, HMS", "track_title": "compartments for LNCaP clone FGC Dilution Hi-C HindIII"}, "external_references": [], "contributing_labs": [{"uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "status": "current", "name": "job-dekker-lab", "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"]}}], "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"uuid": "9826c404-6c5f-44b4-9647-0679d7541db8", "@id": "/higlass-view-configs/9826c404-6c5f-44b4-9647-0679d7541db8/", "@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFI31QYTI7 - compartments for LNCaP clone FGC Dilution Hi-C HindIII", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "lab": {"display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "name": "4dn-dcic-lab", "@type": ["Lab", "Item"], "status": "current", "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-03-28T14:10:22.212705+00:00"}}], "project_release": "2017-07-26", "experiments_in_set": [{"crosslinking_method": "1% Formaldehyde", "display_title": "Dilution Hi-C on LNCaP clone FGC with HindIII - 4DNEXAQPT9EH", "@type": ["ExperimentHiC", "Experiment", "Item"], "dbxrefs": ["ENCODE:ENCLB191OGC"], "status": "released", "uuid": "23bacc29-3db4-4475-9077-464559a6db16", "accession": "4DNEXAQPT9EH", "files": [{"uuid": "0fa48a39-fe9b-4d09-9d18-dea06379b607", "accession": "4DNFIZGJG2VU", "file_classification": "raw file", "display_title": "4DNFIZGJG2VU.fastq.gz", "file_size": 9009591058, "href": "/files-fastq/4DNFIZGJG2VU/@@download/4DNFIZGJG2VU.fastq.gz", "dbxrefs": ["ENCODE:ENCFF726LGW"], "paired_end": "1", "md5sum": "ff5630e38c56ede6611c12a9d41f46fa", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/0fa48a39-fe9b-4d09-9d18-dea06379b607/4DNFIZGJG2VU.fastq.gz", "@id": "/files-fastq/4DNFIZGJG2VU/", "upload_key": "0fa48a39-fe9b-4d09-9d18-dea06379b607/4DNFIZGJG2VU.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "job-dekker-lab", "display_title": "Job Dekker, UMMS", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webdev-wfoutput/4DNFIZGJG2VU/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 171250472, "uuid": "3a38b29a-4429-46ab-b7aa-b79bc462b5ba", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2017-06-30", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/3a38b29a-4429-46ab-b7aa-b79bc462b5ba/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "@id": "/files-fastq/4DNFITVNI13Q/", "paired_end": "2", "display_title": "4DNFITVNI13Q.fastq.gz", "uuid": "48d9e60a-be2e-453f-a6b2-ea497c95da67", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFITVNI13Q", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Dilution Hi-C", "experiment_bucket": "raw file", "assay_info": "HindIII", "dataset": "Hi-C on ENCODE3 cell lines", "condition": "LNCaP clone FGC", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "LNCaP clone FGC", "lab_name": "Job Dekker, UMMS"}, "external_references": [{"ref": "ENCODE:ENCFF726LGW", "uri": "https://www.encodeproject.org/ENCFF726LGW"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "48d9e60a-be2e-453f-a6b2-ea497c95da67", "accession": "4DNFITVNI13Q", "file_classification": "raw file", "display_title": "4DNFITVNI13Q.fastq.gz", "file_size": 9030797522, "href": "/files-fastq/4DNFITVNI13Q/@@download/4DNFITVNI13Q.fastq.gz", "dbxrefs": ["ENCODE:ENCFF550SKU"], "paired_end": "2", "md5sum": "753451ebc7cc2a8f0a1f0ca8dfb66bb4", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/48d9e60a-be2e-453f-a6b2-ea497c95da67/4DNFITVNI13Q.fastq.gz", "@id": "/files-fastq/4DNFITVNI13Q/", "upload_key": "48d9e60a-be2e-453f-a6b2-ea497c95da67/4DNFITVNI13Q.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "job-dekker-lab", "display_title": "Job Dekker, UMMS", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webdev-wfoutput/4DNFITVNI13Q/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 171250472, "uuid": "9c8a42d9-4165-43ea-8f1b-e139f8915545", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2017-06-30", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/9c8a42d9-4165-43ea-8f1b-e139f8915545/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "@id": "/files-fastq/4DNFIZGJG2VU/", "paired_end": "1", "display_title": "4DNFIZGJG2VU.fastq.gz", "uuid": "0fa48a39-fe9b-4d09-9d18-dea06379b607", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIZGJG2VU", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Dilution Hi-C", "experiment_bucket": "raw file", "assay_info": "HindIII", "dataset": "Hi-C on ENCODE3 cell lines", "condition": "LNCaP clone FGC", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "LNCaP clone FGC", "lab_name": "Job Dekker, UMMS"}, "external_references": [{"ref": "ENCODE:ENCFF550SKU", "uri": "https://www.encodeproject.org/ENCFF550SKU"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-hi-c/4DNEXAQPT9EH/", "biosample": {"display_title": "4DNBS4ANA3P9", "biosample_category": ["Other"], "uuid": "e1864e77-92ea-4148-86f9-404656777e6c", "modifications_summary": "None", "biosample_type": "immortalized cells", "accession": "4DNBS4ANA3P9", "@id": "/biosamples/4DNBS4ANA3P9/", "treatments_summary": "None", "status": "released", "biosource_summary": "LNCaP clone FGC", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "1def5d96-712e-4c76-a27f-c260d2a2b313", "@id": "/biosources/4DNSR4OQOB67/", "biosource_type": "immortalized cell line", "cell_line_tier": "Unclassified", "@type": ["Biosource", "Item"], "display_title": "LNCaP clone FGC - 4DNSR4OQOB67", "accession": "4DNSR4OQOB67", "status": "released", "cell_line": {"term_id": "EFO:0005726", "@id": "/ontology-terms/EFO:0005726/", "term_name": "LNCaP clone FGC", "preferred_name": "LNCaP clone FGC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "LNCaP clone FGC", "synonyms": ["CRL-1740", "LNCaP-FGC", "LNCaP clone FGC cell", "LNCaP_FGC"], "uuid": "cdc0ee56-c960-4165-b5a3-1fafe67f2856", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@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"]}}, "tissue": {"synonyms": ["male prostate", "prostate"], "status": "released", "term_name": "prostate gland", "@type": ["OntologyTerm", "Item"], "preferred_name": "prostate gland", "@id": "/ontology-terms/UBERON:0002367/", "uuid": "111176bc-8535-4448-903e-854af460a233", "display_title": "prostate gland", "term_id": "UBERON:0002367", "slim_terms": [{"uuid": "111176bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0002367/", "status": "released", "display_title": "prostate gland", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "111121bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0000925/", "status": "released", "display_title": "endoderm", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "111127bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0000990/", "status": "released", "display_title": "reproductive system", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "111120bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0000926/", "status": "released", "display_title": "mesoderm", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "modifications": [], "treatments": [], "badges": [{"messages": ["Biosample missing doubling_number", "Biosample missing morphology_image"], "badge": {"warning": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-icon.svg", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "title": "Biosample Metadata Incomplete", "badge_classification": "Warning", "status": "released", "display_title": "Biosample Metadata Incomplete", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "prostate gland", "organ_system": ["prostate gland", "endoderm", "reproductive system", "mesoderm"]}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/fcdc9f3b-fa50-4214-8b5d-6fcf6591a47b/", "display_title": "BiosampleCellCulture from 2017-05-05", "uuid": "fcdc9f3b-fa50-4214-8b5d-6fcf6591a47b", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFI27BD7Z9.bam", "upload_key": "08c2fe81-f521-47fb-85f6-06094ba66d5c/4DNFI27BD7Z9.bam", "href": "/files-processed/4DNFI27BD7Z9/@@download/4DNFI27BD7Z9.bam", "accession": "4DNFI27BD7Z9", "md5sum": "4862e991bea85fe1b0830740b10471a0", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI27BD7Z9/", "file_size": 22132305298, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/08c2fe81-f521-47fb-85f6-06094ba66d5c/4DNFI27BD7Z9.bam", "file_type_detailed": "alignments (bam)", "uuid": "08c2fe81-f521-47fb-85f6-06094ba66d5c", "status": "released", "quality_metric": {"status": "released", "uuid": "f03c67e7-3ae2-41ab-9d0d-02f99d951326", "@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "display_title": "QualityMetricBamqc from 2019-12-21", "overall_quality_status": "PASS", "@id": "/quality-metrics-bamqc/f03c67e7-3ae2-41ab-9d0d-02f99d951326/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Reads", "value": "171250472", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "15.283", "tooltip": "Percent of total reads (=26.17m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "17.039", "tooltip": "Percent of total reads (=29.18m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "3.259", "tooltip": "Percent of total reads (=5.58m)", "numberType": "percent"}, {"title": "Walks", "value": "0.002", "tooltip": "Percent of total reads (=0.0m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.418", "tooltip": "Percent of total reads (=0.72m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "extra_files": [], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2022-01-10T09:31:59.964333+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Dilution Hi-C", "experiment_bucket": "processed file", "assay_info": "HindIII", "dataset": "Hi-C on ENCODE3 cell lines", "condition": "LNCaP clone FGC", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "LNCaP clone FGC", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "contact list-replicate", "genome_assembly": "GRCh38", "display_title": "4DNFISPRKYIO.pairs.gz", "upload_key": "e3cdedb6-8133-4cd2-897e-c19e912a4501/4DNFISPRKYIO.pairs.gz", "href": "/files-processed/4DNFISPRKYIO/@@download/4DNFISPRKYIO.pairs.gz", "accession": "4DNFISPRKYIO", "md5sum": "7ef336cd407e30c137e2ba858ad8510a", "file_format": {"display_title": "pairs", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFISPRKYIO/", "file_size": 2186773529, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/e3cdedb6-8133-4cd2-897e-c19e912a4501/4DNFISPRKYIO.pairs.gz", "file_type_detailed": "contact list-replicate (pairs)", "uuid": "e3cdedb6-8133-4cd2-897e-c19e912a4501", "status": "released", "quality_metric": {"status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFISPRKYIO/pairsqc_report.html", "uuid": "a5fbd4f3-d2d2-45e3-9957-138194d06d32", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "Total reads": 110316058, "display_title": "QualityMetricPairsqc from 2018-02-15", "overall_quality_status": "PASS", "@id": "/quality-metrics-pairsqc/a5fbd4f3-d2d2-45e3-9957-138194d06d32/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "110316058", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "14.516", "tooltip": "Percent of filtered reads (=16.01m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "30.138", "tooltip": "Percent of filtered reads (=33.25m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "55.346", "tooltip": "Percent of filtered reads (=61.06m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "extra_files": [{"md5sum": "526629218368b2673c0c7fc45767aebd", "file_size": 27657516, "href": "/files-processed/4DNFISPRKYIO/@@download/4DNFISPRKYIO.pairs.gz.px2", "file_format": {"display_title": "pairs_px2", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "file_format": "pairs_px2", "status": "released", "@id": "/file-formats/pairs_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2022-01-10T16:35:03.905743+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Dilution Hi-C", "experiment_bucket": "processed file", "assay_info": "HindIII", "dataset": "Hi-C on ENCODE3 cell lines", "condition": "LNCaP clone FGC", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "LNCaP clone FGC", "lab_name": "4DN DCIC, HMS"}}], "digestion_enzyme": {"@type": ["Enzyme", "Item"], "name": "HindIII", "@id": "/enzymes/HindIII/", "display_title": "HindIII", "status": "released", "uuid": "2ace2f00-c913-4bac-a6ef-0b316bc2108e", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"uuid": "832b7989-69ab-4bb6-97b9-195d5dd965ea", "status": "released", "assay_classification": "3C via Ligation", "title": "Dilution Hi-C", "assay_subclassification": "DNA-DNA Pairwise Interactions", "experiment_category": "Sequencing", "other_tags": ["DNA-DNA", "Pairwise", "3D"], "assay_subclass_short": "Hi-C", "display_title": "Dilution Hi-C", "@id": "/experiment-types/dilution-hi-c/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "ENCODE:ENCLB191OGC", "uri": "https://www.encodeproject.org/ENCLB191OGC"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Enzyme", "combined": "Enzyme: HindIII", "value": "HindIII"}, "last_modified": {"date_modified": "2019-04-24T17:00:35.393943+00:00"}}, {"crosslinking_method": "1% Formaldehyde", "display_title": "Dilution Hi-C on LNCaP clone FGC with HindIII - 4DNEXHMUQC5C", "@type": ["ExperimentHiC", "Experiment", "Item"], "dbxrefs": ["ENCODE:ENCLB473XWD"], "status": "released", "uuid": "398dc18c-90b4-47eb-a696-deefeb607aed", "accession": "4DNEXHMUQC5C", "files": [{"uuid": "a70a4818-4507-4f2d-a37d-5cd79a75276a", "accession": "4DNFIW7NRRN3", "file_classification": "raw file", "display_title": "4DNFIW7NRRN3.fastq.gz", "file_size": 4570358149, "href": "/files-fastq/4DNFIW7NRRN3/@@download/4DNFIW7NRRN3.fastq.gz", "dbxrefs": ["ENCODE:ENCFF950CQX"], "paired_end": "1", "md5sum": "0c883ad6f3ac775bcc6de0d855fe1f81", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/a70a4818-4507-4f2d-a37d-5cd79a75276a/4DNFIW7NRRN3.fastq.gz", "@id": "/files-fastq/4DNFIW7NRRN3/", "upload_key": "a70a4818-4507-4f2d-a37d-5cd79a75276a/4DNFIW7NRRN3.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "job-dekker-lab", "display_title": "Job Dekker, UMMS", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webdev-wfoutput/4DNFIW7NRRN3/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 135238721, "uuid": "81eee7e5-bc19-4870-b56c-adb85786efe1", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2017-06-30", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/81eee7e5-bc19-4870-b56c-adb85786efe1/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "@id": "/files-fastq/4DNFIEN6IM4S/", "paired_end": "2", "display_title": "4DNFIEN6IM4S.fastq.gz", "uuid": "ecc1ccb6-f5f4-40a2-accc-059e38c44baa", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIEN6IM4S", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Dilution Hi-C", "experiment_bucket": "raw file", "assay_info": "HindIII", "dataset": "Hi-C on ENCODE3 cell lines", "condition": "LNCaP clone FGC", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "LNCaP clone FGC", "lab_name": "Job Dekker, UMMS"}, "external_references": [{"ref": "ENCODE:ENCFF950CQX", "uri": "https://www.encodeproject.org/ENCFF950CQX"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "ecc1ccb6-f5f4-40a2-accc-059e38c44baa", "accession": "4DNFIEN6IM4S", "file_classification": "raw file", "display_title": "4DNFIEN6IM4S.fastq.gz", "file_size": 4827578660, "href": "/files-fastq/4DNFIEN6IM4S/@@download/4DNFIEN6IM4S.fastq.gz", "dbxrefs": ["ENCODE:ENCFF411TZJ"], "paired_end": "2", "md5sum": "53584a00070f8a76efbf3b836da78cda", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/ecc1ccb6-f5f4-40a2-accc-059e38c44baa/4DNFIEN6IM4S.fastq.gz", "@id": "/files-fastq/4DNFIEN6IM4S/", "upload_key": "ecc1ccb6-f5f4-40a2-accc-059e38c44baa/4DNFIEN6IM4S.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "job-dekker-lab", "display_title": "Job Dekker, UMMS", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webdev-wfoutput/4DNFIEN6IM4S/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 135238721, "uuid": "e7967851-e897-4827-9411-5516d8b8711b", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2017-06-30", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/e7967851-e897-4827-9411-5516d8b8711b/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "@id": "/files-fastq/4DNFIW7NRRN3/", "paired_end": "1", "display_title": "4DNFIW7NRRN3.fastq.gz", "uuid": "a70a4818-4507-4f2d-a37d-5cd79a75276a", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIW7NRRN3", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Dilution Hi-C", "experiment_bucket": "raw file", "assay_info": "HindIII", "dataset": "Hi-C on ENCODE3 cell lines", "condition": "LNCaP clone FGC", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "LNCaP clone FGC", "lab_name": "Job Dekker, UMMS"}, "external_references": [{"ref": "ENCODE:ENCFF411TZJ", "uri": "https://www.encodeproject.org/ENCFF411TZJ"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-hi-c/4DNEXHMUQC5C/", "biosample": {"display_title": "4DNBSJC6JJZW", "biosample_category": ["Other"], "uuid": "c63416d6-1638-427b-879a-0c58338e87dc", "modifications_summary": "None", "biosample_type": "immortalized cells", "accession": "4DNBSJC6JJZW", "@id": "/biosamples/4DNBSJC6JJZW/", "treatments_summary": "None", "status": "released", "biosource_summary": "LNCaP clone FGC", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "1def5d96-712e-4c76-a27f-c260d2a2b313", "@id": "/biosources/4DNSR4OQOB67/", "biosource_type": "immortalized cell line", "cell_line_tier": "Unclassified", "@type": ["Biosource", "Item"], "display_title": "LNCaP clone FGC - 4DNSR4OQOB67", "accession": "4DNSR4OQOB67", "status": "released", "cell_line": {"term_id": "EFO:0005726", "@id": "/ontology-terms/EFO:0005726/", "term_name": "LNCaP clone FGC", "preferred_name": "LNCaP clone FGC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "LNCaP clone FGC", "synonyms": ["CRL-1740", "LNCaP-FGC", "LNCaP clone FGC cell", "LNCaP_FGC"], "uuid": "cdc0ee56-c960-4165-b5a3-1fafe67f2856", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@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"]}}, "tissue": {"synonyms": ["male prostate", "prostate"], "status": "released", "term_name": "prostate gland", "@type": ["OntologyTerm", "Item"], "preferred_name": "prostate gland", "@id": "/ontology-terms/UBERON:0002367/", "uuid": "111176bc-8535-4448-903e-854af460a233", "display_title": "prostate gland", "term_id": "UBERON:0002367", "slim_terms": [{"uuid": "111176bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0002367/", "status": "released", "display_title": "prostate gland", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "111121bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0000925/", "status": "released", "display_title": "endoderm", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "111127bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0000990/", "status": "released", "display_title": "reproductive system", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "111120bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0000926/", "status": "released", "display_title": "mesoderm", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "modifications": [], "treatments": [], "badges": [{"messages": ["Biosample missing doubling_number", "Biosample missing morphology_image"], "badge": {"warning": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-icon.svg", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "title": "Biosample Metadata Incomplete", "badge_classification": "Warning", "status": "released", "display_title": "Biosample Metadata Incomplete", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "prostate gland", "organ_system": ["prostate gland", "endoderm", "reproductive system", "mesoderm"]}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/7f191833-8a3b-487d-93fc-b15846986e53/", "display_title": "BiosampleCellCulture from 2017-05-05", "uuid": "7f191833-8a3b-487d-93fc-b15846986e53", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFI3DTOIAY.bam", "upload_key": "33b15d9f-8546-490f-82ab-16b4e6da5bed/4DNFI3DTOIAY.bam", "href": "/files-processed/4DNFI3DTOIAY/@@download/4DNFI3DTOIAY.bam", "accession": "4DNFI3DTOIAY", "md5sum": "928cb405574056c917af1ae2cccefd58", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI3DTOIAY/", "file_size": 12630807906, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/33b15d9f-8546-490f-82ab-16b4e6da5bed/4DNFI3DTOIAY.bam", "file_type_detailed": "alignments (bam)", "uuid": "33b15d9f-8546-490f-82ab-16b4e6da5bed", "status": "released", "quality_metric": {"status": "released", "uuid": "7c3cbe28-bef3-4ea2-b874-3c78b9a203a5", "@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "display_title": "QualityMetricBamqc from 2019-12-21", "overall_quality_status": "PASS", "@id": "/quality-metrics-bamqc/7c3cbe28-bef3-4ea2-b874-3c78b9a203a5/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Reads", "value": "135238721", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "17.691", "tooltip": "Percent of total reads (=23.93m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "15.788", "tooltip": "Percent of total reads (=21.35m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "3.451", "tooltip": "Percent of total reads (=4.67m)", "numberType": "percent"}, {"title": "Walks", "value": "0.002", "tooltip": "Percent of total reads (=0.0m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.468", "tooltip": "Percent of total reads (=0.63m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "extra_files": [], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2022-01-10T09:32:21.990115+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Dilution Hi-C", "experiment_bucket": "processed file", "assay_info": "HindIII", "dataset": "Hi-C on ENCODE3 cell lines", "condition": "LNCaP clone FGC", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "LNCaP clone FGC", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "contact list-replicate", "genome_assembly": "GRCh38", "display_title": "4DNFI197IG9Y.pairs.gz", "upload_key": "f60ef28c-f3c7-452a-b567-4cb0dbc47a61/4DNFI197IG9Y.pairs.gz", "href": "/files-processed/4DNFI197IG9Y/@@download/4DNFI197IG9Y.pairs.gz", "accession": "4DNFI197IG9Y", "md5sum": "2b0dc4f231ebdaa6ed307fbf84d1849b", "file_format": {"display_title": "pairs", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI197IG9Y/", "file_size": 1712454120, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/f60ef28c-f3c7-452a-b567-4cb0dbc47a61/4DNFI197IG9Y.pairs.gz", "file_type_detailed": "contact list-replicate (pairs)", "uuid": "f60ef28c-f3c7-452a-b567-4cb0dbc47a61", "status": "released", "quality_metric": {"status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI197IG9Y/pairsqc_report.html", "uuid": "75b161b8-cc37-4f58-9592-8e94eccaa385", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "Total reads": 85291906, "display_title": "QualityMetricPairsqc from 2018-02-15", "overall_quality_status": "PASS", "@id": "/quality-metrics-pairsqc/75b161b8-cc37-4f58-9592-8e94eccaa385/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "85291906", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "15.504", "tooltip": "Percent of filtered reads (=13.22m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "22.353", "tooltip": "Percent of filtered reads (=19.07m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "62.143", "tooltip": "Percent of filtered reads (=53.0m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "extra_files": [{"md5sum": "8d1c3ce08c0dd503f68fcb05a063d474", "file_size": 26903244, "href": "/files-processed/4DNFI197IG9Y/@@download/4DNFI197IG9Y.pairs.gz.px2", "file_format": {"display_title": "pairs_px2", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "file_format": "pairs_px2", "status": "released", "@id": "/file-formats/pairs_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2022-01-10T16:35:35.031658+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Dilution Hi-C", "experiment_bucket": "processed file", "assay_info": "HindIII", "dataset": "Hi-C on ENCODE3 cell lines", "condition": "LNCaP clone FGC", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "LNCaP clone FGC", "lab_name": "4DN DCIC, HMS"}}], "digestion_enzyme": {"@type": ["Enzyme", "Item"], "name": "HindIII", "@id": "/enzymes/HindIII/", "display_title": "HindIII", "status": "released", "uuid": "2ace2f00-c913-4bac-a6ef-0b316bc2108e", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"uuid": "832b7989-69ab-4bb6-97b9-195d5dd965ea", "status": "released", "assay_classification": "3C via Ligation", "title": "Dilution Hi-C", "assay_subclassification": "DNA-DNA Pairwise Interactions", "experiment_category": "Sequencing", "other_tags": ["DNA-DNA", "Pairwise", "3D"], "assay_subclass_short": "Hi-C", "display_title": "Dilution Hi-C", "@id": "/experiment-types/dilution-hi-c/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "ENCODE:ENCLB473XWD", "uri": "https://www.encodeproject.org/ENCLB473XWD"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Enzyme", "combined": "Enzyme: HindIII", "value": "HindIII"}, "last_modified": {"date_modified": "2019-04-24T17:00:33.845175+00:00"}}], "experimentset_type": "replicate", "completed_processes": ["compartments_v1.2", "insulation_scores_and_boundaries_v1", "HiC_Pipeline_0.2.6"], "alternate_accessions": [], "other_processed_files": [], "@id": "/experiment-set-replicates/4DNESNHN919R/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "5f605a56-21f8-4c0b-8c29-ef68b31c3e19", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNESNHN919R", "external_references": [{"ref": "ENCODE:ENCSR346DCU", "uri": "https://www.encodeproject.org/ENCSR346DCU"}], "pubs_using": [], "publications_of_set": [], "number_of_experiments": 2, "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBS4ANA3P9/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["Biosample missing doubling_number", "Biosample missing morphology_image"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}, {"parent": "/biosamples/4DNBSJC6JJZW/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["Biosample missing doubling_number", "Biosample missing morphology_image"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}]}, "validation-errors": []}