{"lab": {"uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "title": "Job Dekker, UMMS", "correspondence": [{"contact_email": "am9iLmRla2tlckB1bWFzc21lZC5lZHU=", "@id": "/users/83b5073a-069b-4162-9b30-6f42d5551e34/", "display_title": "Job Dekker"}], "display_title": "Job Dekker, UMMS", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/job-dekker-lab/", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "tags": ["matrix_project", "not-deep_data"], "award": {"name": "1U54DK107980-01", "@id": "/awards/1U54DK107980-01/", "uuid": "ae6c618f-7a8c-441e-a886-e30bbbe591da", "center_title": "NOFIC - Dekker", "status": "current", "project": "4DN", "display_title": "CENTER FOR 3D STRUCTURE AND PHYSICS OF THE GENOME", "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.", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "pi": {"error": "no view permissions"}}, "study": "Experimental Protocol Variations", "badges": [{"badge": {"warning": "Replicate Numbers", "@type": ["Badge", "Item"], "@id": "/badges/replicate-numbers/", "badge_icon": "/static/img/badges/replicates-orange-circle.svg", "description": "Issues with replicate numbers", "badge_classification": "Warning", "display_title": "Replicate Numbers", "uuid": "24a64a84-3c33-4d76-aaf2-e5ef45eff347", "status": "released", "title": "Replicate Numbers", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "messages": ["Replicate set contains only a single biological replicate"]}], "status": "released", "aliases": ["dekker-lab:ExperimentSetReplicate_U54_U54-HelaS3-G1-DSG-MNase-08072018-R1-T1"], "accession": "4DNESGCCOT7T", "condition": "Formaldehyde+DSG, G1 phase", "description": "Micro-C on HeLa-S3 (G1 phase) with 1% Formaldehyde and 3mM DSG crosslinking", "study_group": "Single Time Point and Condition", "date_created": "2020-06-27T18:56:17.640891+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "Micro-C on HeLa cells - protocol variations", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-01-25T04:50:05.986321+00:00"}, "public_release": "2021-01-04", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"accession": "4DNEX9TYL3XW", "status": "released", "@type": ["ExperimentHiC", "Experiment", "Item"], "display_title": "Micro-C on HeLa-S3 with MNase - 4DNEX9TYL3XW", "uuid": "d25687e8-811c-4921-8ee1-2591beb3f28e", "@id": "/experiments-hi-c/4DNEX9TYL3XW/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_content": [{"content": {"title": "4DNESGCCOT7T - Processed files", "description": "4DNESGCCOT7T (Micro-C on HeLa-S3 (G1 phase) with 1% Formaldehyde and 3mM DSG crosslinking): 4DNFI5T9D5WW", "@id": "/higlass-view-configs/f87c039f-9a72-4e1d-b609-bf5ed2b23c19/", "name": "f87c039f-9a72-4e1d-b609-bf5ed2b23c19", "contributing_labs": [], "award": {"uuid": "ae6c618f-7a8c-441e-a886-e30bbbe591da", "@type": ["Award", "Item"], "@id": "/awards/1U54DK107980-01/", "status": "current", "display_title": "CENTER FOR 3D STRUCTURE AND PHYSICS OF THE GENOME", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "status": "released", "filetype": "HiglassViewConfig", "uuid": "f87c039f-9a72-4e1d-b609-bf5ed2b23c19", "display_title": "4DNESGCCOT7T - Processed files", "@type": ["HiglassViewConfig", "UserContent", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}, "location": "tab:processed-files", "description": "auto_generated_higlass_view_config"}], "processed_files": [{"file_size": 4339470747, "uuid": "c2fbd73b-815b-4283-af84-8342de3b6551", "href": "/files-processed/4DNFIYIFFAYM/@@download/4DNFIYIFFAYM.pairs.gz", "@id": "/files-processed/4DNFIYIFFAYM/", "file_type": "contact list-combined", "upload_key": "c2fbd73b-815b-4283-af84-8342de3b6551/4DNFIYIFFAYM.pairs.gz", "file_type_detailed": "contact list-combined (pairs)", "genome_assembly": "GRCh38", "file_format": {"display_title": "pairs", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/c2fbd73b-815b-4283-af84-8342de3b6551/4DNFIYIFFAYM.pairs.gz", "display_title": "4DNFIYIFFAYM.pairs.gz", "file_classification": "processed file", "md5sum": "e212ef9a716f32ef2da001f8483f066a", "accession": "4DNFIYIFFAYM", "@type": ["FileProcessed", "File", "Item"], "status": "released", "contributing_labs": [{"@id": "/labs/job-dekker-lab/", "status": "current", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "name": "4dn-dcic-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "extra_files": [{"file_size": 12687096, "md5sum": "59daa1e9eaf5a6384ec9d2c633f00073", "href": "/files-processed/4DNFIYIFFAYM/@@download/4DNFIYIFFAYM.pairs.gz.px2", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "display_title": "pairs_px2", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs_px2/", "file_format": "pairs_px2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIYIFFAYM/pairsqc_report.html", "status": "released", "Total reads": 238106260, "display_title": "QualityMetricPairsqc from 2020-06-30", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "uuid": "8f18bc3f-9ae1-46c1-aec8-215a33ddac52", "@id": "/quality-metrics-pairsqc/8f18bc3f-9ae1-46c1-aec8-215a33ddac52/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "238106260", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "21.996", "tooltip": "Percent of filtered reads (=52.37m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "69.327", "tooltip": "Percent of filtered reads (=165.07m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "8.677", "tooltip": "Percent of filtered reads (=20.66m)", "numberType": "percent"}]}, "external_references": [], "last_modified": {"date_modified": "2021-04-06T20:16:03.717336+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "Micro-C on HeLa cells - protocol variations", "condition": "Formaldehyde+DSG, G1 phase", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "unreplicated", "experiment_bucket": "processed file", "experiment_type": "Micro-C", "assay_info": "MNase", "biosource_name": "HeLa-S3", "lab_name": "4DN DCIC, HMS"}}, {"file_size": 1361383227, "uuid": "7a865a6f-9c88-4209-9b79-d2f66ee673d5", "href": "/files-processed/4DNFIWLGIO3R/@@download/4DNFIWLGIO3R.hic", "@id": "/files-processed/4DNFIWLGIO3R/", "file_type": "contact matrix", "upload_key": "7a865a6f-9c88-4209-9b79-d2f66ee673d5/4DNFIWLGIO3R.hic", "file_type_detailed": "contact matrix (hic)", "genome_assembly": "GRCh38", "file_format": {"display_title": "hic", "@id": "/file-formats/hic/", "@type": ["FileFormat", "Item"], "uuid": "d13d11cf-218e-4f61-bbf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/7a865a6f-9c88-4209-9b79-d2f66ee673d5/4DNFIWLGIO3R.hic", "display_title": "4DNFIWLGIO3R.hic", "file_classification": "processed file", "md5sum": "d0b3bcdfcea7faa8fa656b91ea482238", "accession": "4DNFIWLGIO3R", "@type": ["FileProcessed", "File", "Item"], "status": "released", "contributing_labs": [{"@id": "/labs/job-dekker-lab/", "status": "current", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "name": "4dn-dcic-lab", "status": "current", "@type": ["Lab", "Item"], "@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": [], "last_modified": {"date_modified": "2021-03-28T14:26:59.796694+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "Micro-C on HeLa cells - protocol variations", "condition": "Formaldehyde+DSG, G1 phase", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "unreplicated", "experiment_bucket": "processed file", "experiment_type": "Micro-C", "assay_info": "MNase", "biosource_name": "HeLa-S3", "lab_name": "4DN DCIC, HMS"}}, {"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."], "file_size": 833544112, "uuid": "8c4ad910-f220-4a10-9e1b-fd567c4b871e", "href": "/files-processed/4DNFI5T9D5WW/@@download/4DNFI5T9D5WW.mcool", "@id": "/files-processed/4DNFI5T9D5WW/", "file_type": "contact matrix", "upload_key": "8c4ad910-f220-4a10-9e1b-fd567c4b871e/4DNFI5T9D5WW.mcool", "file_type_detailed": "contact matrix (mcool)", "genome_assembly": "GRCh38", "higlass_uid": "75d3f331-68ca-4fa0-b7de-c80eb114a957", "file_format": {"display_title": "mcool", "@id": "/file-formats/mcool/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-ccf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/8c4ad910-f220-4a10-9e1b-fd567c4b871e/4DNFI5T9D5WW.mcool", "display_title": "4DNFI5T9D5WW.mcool", "file_classification": "processed file", "md5sum": "c21687eea86102187fed80f820ab2588", "accession": "4DNFI5T9D5WW", "@type": ["FileProcessed", "File", "Item"], "status": "released", "contributing_labs": [{"@id": "/labs/job-dekker-lab/", "status": "current", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "name": "4dn-dcic-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "quality_metric": {"status": "released", "display_title": "QualityMetricMcool from 2021-05-21", "@type": ["QualityMetricMcool", "QualityMetric", "Item"], "overall_quality_status": "PASS", "uuid": "e5c186ca-7d3f-4f50-8ade-c9a1a4f05f4f", "@id": "/quality-metrics-mcool/e5c186ca-7d3f-4f50-8ade-c9a1a4f05f4f/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Failed Balancing", "value": "None", "tooltip": "Resolutions where balancing failed", "numberType": "string"}]}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "7ec85f80-88c6-428e-bc25-ae2a42076165", "status": "released", "display_title": "4DNFI5T9D5WW - contact matrix for HeLa-S3 Micro-C MNase", "@id": "/higlass-view-configs/7ec85f80-88c6-428e-bc25-ae2a42076165/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "external_references": [], "last_modified": {"date_modified": "2023-08-25T17:50:03.189929+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "Micro-C on HeLa cells - protocol variations", "condition": "Formaldehyde+DSG, G1 phase", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "unreplicated", "experiment_bucket": "processed file", "experiment_type": "Micro-C", "assay_info": "MNase", "biosource_name": "HeLa-S3", "lab_name": "4DN DCIC, HMS", "track_title": "contact matrix for HeLa-S3 Micro-C MNase"}}, {"file_size": 252796, "uuid": "8a8e7875-859b-42c5-b236-46b0dd7db306", "href": "/files-processed/4DNFID5G47VP/@@download/4DNFID5G47VP.bed.gz", "@id": "/files-processed/4DNFID5G47VP/", "file_type": "boundaries", "upload_key": "8a8e7875-859b-42c5-b236-46b0dd7db306/4DNFID5G47VP.bed.gz", "file_type_detailed": "boundaries (bed)", "genome_assembly": "GRCh38", "higlass_uid": "FG9X5f2LQLqFNPJ8a08rKQ", "file_format": {"display_title": "bed", "@id": "/file-formats/bed/", "@type": ["FileFormat", "Item"], "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/8a8e7875-859b-42c5-b236-46b0dd7db306/4DNFID5G47VP.bed.gz", "display_title": "4DNFID5G47VP.bed.gz", "file_classification": "processed file", "md5sum": "221e731938b33610e3ad5aef723e1905", "accession": "4DNFID5G47VP", "@type": ["FileProcessed", "File", "Item"], "status": "released", "contributing_labs": [{"@id": "/labs/job-dekker-lab/", "status": "current", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "name": "4dn-dcic-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "extra_files": [{"md5sum": "9499f47f391aa0dad9fa0517a29ba5b9", "use_for": "visualization", "href": "/files-processed/4DNFID5G47VP/@@download/4DNFID5G47VP.beddb", "file_format": {"status": "released", "uuid": "76dc8c06-67d8-487b-8fc8-d841752a0b60", "display_title": "beddb", "@type": ["FileFormat", "Item"], "@id": "/file-formats/beddb/", "file_format": "beddb", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "523cdeec-9291-4e17-bf02-013c68dfa608", "status": "released", "display_title": "4DNFID5G47VP - boundaries for HeLa-S3 Micro-C MNase", "@id": "/higlass-view-configs/523cdeec-9291-4e17-bf02-013c68dfa608/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "external_references": [], "last_modified": {"date_modified": "2021-05-10T23:49:56.600090+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "Micro-C on HeLa cells - protocol variations", "condition": "Formaldehyde+DSG, G1 phase", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "unreplicated", "experiment_bucket": "processed file", "experiment_type": "Micro-C", "assay_info": "MNase", "biosource_name": "HeLa-S3", "lab_name": "4DN DCIC, HMS", "track_title": "boundaries for HeLa-S3 Micro-C MNase"}}, {"file_size": 8551755, "uuid": "d263c113-6b02-4a58-980b-ba638d41ce32", "href": "/files-processed/4DNFIXBQOAZE/@@download/4DNFIXBQOAZE.bw", "@id": "/files-processed/4DNFIXBQOAZE/", "file_type": "insulation score-diamond", "upload_key": "d263c113-6b02-4a58-980b-ba638d41ce32/4DNFIXBQOAZE.bw", "file_type_detailed": "insulation score-diamond (bw)", "genome_assembly": "GRCh38", "higlass_uid": "b1dd87e1-f9a7-4d99-a451-d0a69594cc6a", "file_format": {"display_title": "bw", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/d263c113-6b02-4a58-980b-ba638d41ce32/4DNFIXBQOAZE.bw", "display_title": "4DNFIXBQOAZE.bw", "file_classification": "processed file", "md5sum": "9b112ec7ee0ea16caba4f16f11818b8f", "accession": "4DNFIXBQOAZE", "@type": ["FileProcessed", "File", "Item"], "status": "released", "contributing_labs": [{"@id": "/labs/job-dekker-lab/", "status": "current", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "name": "4dn-dcic-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "83b6638d-ec20-4173-bf0b-d6e0b2b824d3", "status": "released", "display_title": "4DNFIXBQOAZE - insulation score-diamond for HeLa-S3 Micro-C MNase", "@id": "/higlass-view-configs/83b6638d-ec20-4173-bf0b-d6e0b2b824d3/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "external_references": [], "last_modified": {"date_modified": "2021-03-28T14:06:07.916288+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "Micro-C on HeLa cells - protocol variations", "condition": "Formaldehyde+DSG, G1 phase", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "unreplicated", "experiment_bucket": "processed file", "experiment_type": "Micro-C", "assay_info": "MNase", "biosource_name": "HeLa-S3", "lab_name": "4DN DCIC, HMS", "track_title": "insulation score-diamond for HeLa-S3 Micro-C MNase"}}, {"file_size": 214078, "uuid": "60edd844-800b-4e8e-b162-c15eb02b4812", "href": "/files-processed/4DNFI3XHIBT9/@@download/4DNFI3XHIBT9.bw", "@id": "/files-processed/4DNFI3XHIBT9/", "file_type": "compartments", "upload_key": "60edd844-800b-4e8e-b162-c15eb02b4812/4DNFI3XHIBT9.bw", "file_type_detailed": "compartments (bw)", "genome_assembly": "GRCh38", "higlass_uid": "34f7d64d-36e2-4b18-a8d9-c14bac830a12", "file_format": {"display_title": "bw", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/60edd844-800b-4e8e-b162-c15eb02b4812/4DNFI3XHIBT9.bw", "display_title": "4DNFI3XHIBT9.bw", "file_classification": "processed file", "md5sum": "342be3dc1d6e86b97f6da7a0343b9767", "accession": "4DNFI3XHIBT9", "@type": ["FileProcessed", "File", "Item"], "status": "released", "contributing_labs": [{"@id": "/labs/job-dekker-lab/", "status": "current", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "name": "4dn-dcic-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "17802736-c9da-4ebb-990b-beda51533397", "status": "released", "display_title": "4DNFI3XHIBT9 - compartments for HeLa-S3 Micro-C MNase", "@id": "/higlass-view-configs/17802736-c9da-4ebb-990b-beda51533397/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "external_references": [], "last_modified": {"date_modified": "2021-03-28T14:05:53.233893+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "Micro-C on HeLa cells - protocol variations", "condition": "Formaldehyde+DSG, G1 phase", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "unreplicated", "experiment_bucket": "processed file", "experiment_type": "Micro-C", "assay_info": "MNase", "biosource_name": "HeLa-S3", "lab_name": "4DN DCIC, HMS", "track_title": "compartments for HeLa-S3 Micro-C MNase"}}], "project_release": "2020-08-11", "experiments_in_set": [{"@type": ["ExperimentHiC", "Experiment", "Item"], "@id": "/experiments-hi-c/4DNEX9TYL3XW/", "status": "released", "dbxrefs": ["GEO:GSM5057493", "SRA:SRX9995909"], "crosslinking_method": "1% Formaldehyde and 3mM DSG", "files": [{"upload_key": "40c0db55-3660-4b82-a709-1f5c9fb83d43/4DNFISZH6PSU.fastq.gz", "file_type_detailed": "reads (fastq)", "paired_end": "1", "display_title": "4DNFISZH6PSU.fastq.gz", "@id": "/files-fastq/4DNFISZH6PSU/", "file_size": 11114110717, "accession": "4DNFISZH6PSU", "href": "/files-fastq/4DNFISZH6PSU/@@download/4DNFISZH6PSU.fastq.gz", "@type": ["FileFastq", "File", "Item"], "uuid": "40c0db55-3660-4b82-a709-1f5c9fb83d43", "file_classification": "raw file", "md5sum": "519f0db347cf059c2b815c2ab5d724bc", "status": "restricted", "file_type": "reads", "dbxrefs": ["SRA:SRR13601677"], "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "53143fb6-b384-4037-a5a2-80c8733dfbac", "display_title": "4DNFI2UQCQC6.fastq.gz", "accession": "4DNFI2UQCQC6", "status": "restricted", "file_type_detailed": "reads (fastq)", "@id": "/files-fastq/4DNFI2UQCQC6/", "file_type": "reads", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric": {"Total Sequences": 354369746, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFISZH6PSU/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/cc9cbc67-fba7-434a-8d99-95c281c1caff/", "uuid": "cc9cbc67-fba7-434a-8d99-95c281c1caff", "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-27", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "SRA:SRR13601677", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR13601677"}], "lab": {"name": "job-dekker-lab", "@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "raw file", "assay_info": "MNase", "dataset": "Micro-C on HeLa cells - protocol variations", "condition": "Formaldehyde+DSG, G1 phase", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HeLa-S3", "lab_name": "Job Dekker, UMMS"}}, {"upload_key": "53143fb6-b384-4037-a5a2-80c8733dfbac/4DNFI2UQCQC6.fastq.gz", "file_type_detailed": "reads (fastq)", "paired_end": "2", "display_title": "4DNFI2UQCQC6.fastq.gz", "@id": "/files-fastq/4DNFI2UQCQC6/", "file_size": 12337045638, "accession": "4DNFI2UQCQC6", "href": "/files-fastq/4DNFI2UQCQC6/@@download/4DNFI2UQCQC6.fastq.gz", "@type": ["FileFastq", "File", "Item"], "uuid": "53143fb6-b384-4037-a5a2-80c8733dfbac", "file_classification": "raw file", "md5sum": "5a0e3e234552ba537f484f72c9a3b5d3", "status": "restricted", "file_type": "reads", "dbxrefs": ["SRA:SRR13601677"], "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "40c0db55-3660-4b82-a709-1f5c9fb83d43", "display_title": "4DNFISZH6PSU.fastq.gz", "accession": "4DNFISZH6PSU", "status": "restricted", "file_type_detailed": "reads (fastq)", "@id": "/files-fastq/4DNFISZH6PSU/", "file_type": "reads", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric": {"Total Sequences": 354369746, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI2UQCQC6/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/44913f29-8948-4387-b2f7-23e6d2e4295c/", "uuid": "44913f29-8948-4387-b2f7-23e6d2e4295c", "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-27", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "SRA:SRR13601677", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR13601677"}], "lab": {"name": "job-dekker-lab", "@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "raw file", "assay_info": "MNase", "dataset": "Micro-C on HeLa cells - protocol variations", "condition": "Formaldehyde+DSG, G1 phase", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HeLa-S3", "lab_name": "Job Dekker, UMMS"}}], "accession": "4DNEX9TYL3XW", "display_title": "Micro-C on HeLa-S3 with MNase - 4DNEX9TYL3XW", "uuid": "d25687e8-811c-4921-8ee1-2591beb3f28e", "biosample": {"status": "released", "modifications_summary": "None", "biosample_category": ["Other"], "biosample_type": "immortalized cells", "@id": "/biosamples/4DNBS15992MC/", "treatments_summary": "Thymidine treatment (2.0 mM, 24.0h at 37.0\u00b0C) and Nocodazole treatment (2e-05 percent, 12.0h at 37.0\u00b0C) and Nocodazole washout (9h at 37\u00b0C)", "biosource_summary": "HeLa-S3", "accession": "4DNBS15992MC", "@type": ["Biosample", "Item"], "display_title": "4DNBS15992MC", "uuid": "4fe9e590-b56e-492e-8bf7-2502f47b2ac8", "cell_culture_details": [{"@type": ["BiosampleCellCulture", "Item"], "status": "released", "@id": "/biosample-cell-cultures/72bde839-c47e-40a6-a50d-324d4e733a34/", "uuid": "72bde839-c47e-40a6-a50d-324d4e733a34", "in_vitro_differentiated": "No", "display_title": "BiosampleCellCulture from 2020-06-27", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "biosource": [{"uuid": "a7aa4e34-de17-4336-9e0c-2844fd326a96", "display_title": "HeLa-S3 - 4DNSRGTEEYSL", "@id": "/biosources/4DNSRGTEEYSL/", "accession": "4DNSRGTEEYSL", "@type": ["Biosource", "Item"], "cell_line_tier": "Unclassified", "status": "released", "biosource_type": "immortalized cell line", "tissue": {"uuid": "600fc714-c007-441b-b3a7-3d164ddc2689", "@id": "/ontology-terms/UBERON:0000002/", "synonyms": ["uterine cervix", "caudal segment of uterus", "cervix uteri", "neck of uterus", "cervical canal of uterus", "canalis cervicis uteri"], "preferred_name": "uterine cervix", "@type": ["OntologyTerm", "Item"], "term_name": "uterine cervix", "term_id": "UBERON:0000002", "status": "released", "display_title": "uterine cervix", "slim_terms": [{"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0000990/", "display_title": "reproductive system", "status": "released", "uuid": "111127bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0000926/", "display_title": "mesoderm", "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": {"display_title": "H. sapiens", "name": "human", "@id": "/organisms/9606/", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"@type": ["OntologyTerm", "Item"], "display_title": "HeLa-S3", "term_id": "EFO:0002791", "status": "released", "uuid": "840525af-614c-4559-9997-23a30e288858", "term_name": "HeLa-S3", "@id": "/ontology-terms/EFO:0002791/", "preferred_name": "HeLa-S3", "slim_terms": [{"status": "current", "@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "treatments": [{"uuid": "0e70a01b-ae68-43b5-ad22-1e4f31a38f72", "duration": 24.0, "@type": ["TreatmentAgent", "Treatment", "Item"], "concentration": 2.0, "temperature": 37.0, "status": "released", "description": "synchronize cells to S phase", "display_title": "Thymidine treatment (2.0 mM, 24.0h at 37.0\u00b0C)", "treatment_type": "Chemical", "duration_units": "hour", "@id": "/treatments-agent/0e70a01b-ae68-43b5-ad22-1e4f31a38f72/", "concentration_units": "mM", "chemical": "Thymidine", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "0f7d2225-c5f1-42fc-879c-bcb3c8f30f51", "duration": 12.0, "@type": ["TreatmentAgent", "Treatment", "Item"], "concentration": 2e-05, "temperature": 37.0, "status": "released", "description": "synchronize cells to prometaphase (after thymidine)", "display_title": "Nocodazole treatment (2e-05 percent, 12.0h at 37.0\u00b0C)", "treatment_type": "Chemical", "duration_units": "hour", "@id": "/treatments-agent/0f7d2225-c5f1-42fc-879c-bcb3c8f30f51/", "concentration_units": "percent", "chemical": "Nocodazole", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "2c85e225-94d3-4f06-a1e6-1049e58d9890", "duration": 9, "@type": ["TreatmentAgent", "Treatment", "Item"], "concentration": 0, "temperature": 37, "status": "released", "description": "9 h washout of nocodazole", "display_title": "Nocodazole washout (9h at 37\u00b0C)", "treatment_type": "Chemical", "duration_units": "hour", "@id": "/treatments-agent/2c85e225-94d3-4f06-a1e6-1049e58d9890/", "concentration_units": "percent", "chemical": "Nocodazole", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "tissue_organ_info": {"organ_system": ["reproductive system", "mesoderm"], "tissue_source": "uterine cervix"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"href": "/files-processed/4DNFICDPNVK7/@@download/4DNFICDPNVK7.bam", "file_type_detailed": "alignments (bam)", "uuid": "ab4ec23b-484d-46e8-9e7b-c9349121f585", "@id": "/files-processed/4DNFICDPNVK7/", "status": "restricted", "display_title": "4DNFICDPNVK7.bam", "genome_assembly": "GRCh38", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFICDPNVK7", "file_type": "alignments", "file_classification": "processed file", "upload_key": "ab4ec23b-484d-46e8-9e7b-c9349121f585/4DNFICDPNVK7.bam", "file_size": 32595116915, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "3c92e96825a814d7476befcf6752da7e", "quality_metric": {"uuid": "4c3d4ea5-844c-4d35-913d-a0609e27f3a9", "overall_quality_status": "PASS", "status": "released", "@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "@id": "/quality-metrics-bamqc/4c3d4ea5-844c-4d35-913d-a0609e27f3a9/", "display_title": "QualityMetricBamqc from 2020-06-30", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Reads", "value": "354369746", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "3.952", "tooltip": "Percent of total reads (=14.0m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "18.912", "tooltip": "Percent of total reads (=67.02m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "9.939", "tooltip": "Percent of total reads (=35.22m)", "numberType": "percent"}, {"title": "Walks", "value": "0.006", "tooltip": "Percent of total reads (=0.02m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.055", "tooltip": "Percent of total reads (=0.19m)", "numberType": "percent"}]}, "lab": {"@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "name": "4dn-dcic-lab", "display_title": "4DN DCIC, HMS", "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/job-dekker-lab/", "name": "job-dekker-lab", "display_title": "Job Dekker, UMMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "external_references": [], "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "processed file", "assay_info": "MNase", "dataset": "Micro-C on HeLa cells - protocol variations", "condition": "Formaldehyde+DSG, G1 phase", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HeLa-S3", "lab_name": "4DN DCIC, HMS"}, "last_modified": {"date_modified": "2023-04-27T21:01:24.919892+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"href": "/files-processed/4DNFIH2FLZ43/@@download/4DNFIH2FLZ43.pairs.gz", "file_type_detailed": "contact list-replicate (pairs)", "uuid": "1fea6b94-943d-4cf5-9160-e208f90a3658", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/1fea6b94-943d-4cf5-9160-e208f90a3658/4DNFIH2FLZ43.pairs.gz", "@id": "/files-processed/4DNFIH2FLZ43/", "status": "released", "display_title": "4DNFIH2FLZ43.pairs.gz", "genome_assembly": "GRCh38", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIH2FLZ43", "file_type": "contact list-replicate", "file_classification": "processed file", "upload_key": "1fea6b94-943d-4cf5-9160-e208f90a3658/4DNFIH2FLZ43.pairs.gz", "file_size": 4339470747, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/pairs/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "e212ef9a716f32ef2da001f8483f066a", "quality_metric": {"uuid": "0c56a68e-ecbe-43ec-a7b4-149963620110", "overall_quality_status": "PASS", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIH2FLZ43/pairsqc_report.html", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "Total reads": 238106260, "@id": "/quality-metrics-pairsqc/0c56a68e-ecbe-43ec-a7b4-149963620110/", "display_title": "QualityMetricPairsqc from 2020-06-30", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "238106260", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "21.996", "tooltip": "Percent of filtered reads (=52.37m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "69.327", "tooltip": "Percent of filtered reads (=165.07m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "8.677", "tooltip": "Percent of filtered reads (=20.66m)", "numberType": "percent"}]}, "lab": {"@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "name": "4dn-dcic-lab", "display_title": "4DN DCIC, HMS", "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "extra_files": [{"href": "/files-processed/4DNFIH2FLZ43/@@download/4DNFIH2FLZ43.pairs.gz.px2", "file_size": 23611097, "md5sum": "673b9e4435514afc16c3c3810b1fc3d8", "file_format": {"file_format": "pairs_px2", "display_title": "pairs_px2", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "@id": "/file-formats/pairs_px2/", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "contributing_labs": [{"uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/job-dekker-lab/", "name": "job-dekker-lab", "display_title": "Job Dekker, UMMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "external_references": [], "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "processed file", "assay_info": "MNase", "dataset": "Micro-C on HeLa cells - protocol variations", "condition": "Formaldehyde+DSG, G1 phase", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HeLa-S3", "lab_name": "4DN DCIC, HMS"}, "last_modified": {"date_modified": "2021-04-06T20:17:05.440963+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "digestion_enzyme": {"uuid": "e781b59c-ef3d-4ae4-9a94-4a34190bc6d2", "display_title": "MNase", "@type": ["Enzyme", "Item"], "name": "MNase", "@id": "/enzymes/MNase/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"uuid": "bc7899cf-8352-4360-b9be-efc3c7e3a574", "@type": ["ExperimentType", "Item"], "assay_subclass_short": "Hi-C", "@id": "/experiment-types/micro-c/", "assay_subclassification": "DNA-DNA Pairwise Interactions", "display_title": "Micro-C", "title": "Micro-C", "status": "released", "other_tags": ["DNA-DNA", "Pairwise", "3D"], "experiment_category": "Sequencing", "assay_classification": "3C via Ligation", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"value": "MNase", "combined": "Enzyme: MNase", "field": "Enzyme"}, "last_modified": {"date_modified": "2022-06-29T15:15:49.332259+00:00"}, "external_references": [{"ref": "GEO:GSM5057493", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5057493"}, {"ref": "SRA:SRX9995909", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRX9995909"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experimentset_type": "replicate", "completed_processes": ["insulation_scores_and_boundaries_v1", "HiC_Pipeline_0.2.7", "compartments_v1.2"], "other_processed_files": [{"type": "supplementary", "files": [{"file_type_detailed": "compartments (compressed_txt)", "display_title": "4DNFI4IEOINA.txt.gz", "href": "/files-processed/4DNFI4IEOINA/@@download/4DNFI4IEOINA.txt.gz", "uuid": "8ec896ea-77a5-4abc-b250-35bde2f3cd59", "accession": "4DNFI4IEOINA", "file_type": "compartments", "status": "released", "md5sum": "fb267e7622725bb2ed18187c9ec2acc0", "@id": "/files-processed/4DNFI4IEOINA/", "@type": ["FileProcessed", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/8ec896ea-77a5-4abc-b250-35bde2f3cd59/4DNFI4IEOINA.txt.gz", "genome_assembly": "GRCh38", "file_format": {"uuid": "dba26778-f40a-4561-a552-65539702ded4", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "display_title": "compressed_txt", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "file_size": 1048974, "lab": {"@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "status": "current", "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"]}}, "track_and_facet_info": {"dataset": "Micro-C on HeLa cells - protocol variations", "condition": "Formaldehyde+DSG, G1 phase", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "unreplicated", "experiment_bucket": "Compartment and insulation calls - Dekker Lab", "experiment_type": "Micro-C", "assay_info": "MNase", "biosource_name": "HeLa-S3", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-12-16T07:05:58.970018+00:00"}}, {"file_type_detailed": "compartments (bw)", "display_title": "4DNFIZ37YAX9.bw", "href": "/files-processed/4DNFIZ37YAX9/@@download/4DNFIZ37YAX9.bw", "uuid": "e0351ec0-c64c-45fe-8aab-9ca80dfbef59", "accession": "4DNFIZ37YAX9", "file_type": "compartments", "higlass_uid": "4d9a9aa0-e426-42e7-ae0d-fc1ef14939fd", "status": "released", "md5sum": "2c7ebf3986e82985cedeb597b9feeb5e", "@id": "/files-processed/4DNFIZ37YAX9/", "@type": ["FileProcessed", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/e0351ec0-c64c-45fe-8aab-9ca80dfbef59/4DNFIZ37YAX9.bw", "genome_assembly": "GRCh38", "file_format": {"uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "display_title": "bw", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "file_size": 321494, "lab": {"@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "status": "current", "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"]}}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"uuid": "c3f1d90b-e717-42fd-939b-ab3866c4c235", "status": "released", "@id": "/higlass-view-configs/c3f1d90b-e717-42fd-939b-ab3866c4c235/", "display_title": "4DNFIZ37YAX9 - compartments for HeLa-S3 Micro-C MNase", "@type": ["HiglassViewConfig", "UserContent", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "track_and_facet_info": {"dataset": "Micro-C on HeLa cells - protocol variations", "condition": "Formaldehyde+DSG, G1 phase", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "unreplicated", "experiment_bucket": "Compartment and insulation calls - Dekker Lab", "experiment_type": "Micro-C", "assay_info": "MNase", "biosource_name": "HeLa-S3", "lab_name": "Job Dekker, UMMS", "track_title": "compartments for HeLa-S3 Micro-C MNase"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-12-16T07:04:07.460577+00:00"}}, {"file_type_detailed": "insulation score (compressed_txt)", "display_title": "4DNFIMBA54WI.txt.gz", "href": "/files-processed/4DNFIMBA54WI/@@download/4DNFIMBA54WI.txt.gz", "uuid": "ea67e271-6476-4d3b-b3a9-22f6061eb984", "accession": "4DNFIMBA54WI", "file_type": "insulation score", "status": "released", "md5sum": "be025437dbc63ba4afca3bb50d0be29e", "@id": "/files-processed/4DNFIMBA54WI/", "@type": ["FileProcessed", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/ea67e271-6476-4d3b-b3a9-22f6061eb984/4DNFIMBA54WI.txt.gz", "genome_assembly": "GRCh38", "file_format": {"uuid": "dba26778-f40a-4561-a552-65539702ded4", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "display_title": "compressed_txt", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "file_size": 4920531, "lab": {"@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "status": "current", "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"]}}, "track_and_facet_info": {"dataset": "Micro-C on HeLa cells - protocol variations", "condition": "Formaldehyde+DSG, G1 phase", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "unreplicated", "experiment_bucket": "Compartment and insulation calls - Dekker Lab", "experiment_type": "Micro-C", "assay_info": "MNase", "biosource_name": "HeLa-S3", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-12-16T07:02:52.795007+00:00"}}], "title": "Compartment and insulation calls - Dekker Lab", "description": "These files are provided by the Dekker Lab. Note that they are derived from lab-generated processed files and not from the files in the 'Processed Files' tab that were generated by the standardized 4DN-DCIC pipeline.", "higlass_view_config": {"@id": "/higlass-view-configs/59601b31-32fc-43e5-9ca8-dcf8c503cf9b/", "description": "Supplementary Files (Compartment and insulation calls - Dekker Lab) for 4DNESGCCOT7T (Micro-C on HeLa-S3 (G1 phase) with 1% Formaldehyde and 3mM DSG crosslinking): 4DNFIZ37YAX9", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "display_title": "4DNESGCCOT7T - Compartment and insulation calls - Dekker Lab", "uuid": "59601b31-32fc-43e5-9ca8-dcf8c503cf9b", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}, "last_modified": {"date_modified": "2021-01-25T06:03:34.647400+00:00"}}}], "@id": "/experiment-set-replicates/4DNESGCCOT7T/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "35cb9028-a8bf-48ad-838c-bde77afc4065", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNESGCCOT7T", "external_references": [], "produced_in_pub": {"abstract": "Chromosome conformation capture (3C) assays are used to map chromatin interactions genome-wide. Chromatin interaction maps provide insights into the spatial organization of chromosomes and the mechanisms by which they fold. Hi-C and Micro-C are widely used 3C protocols that differ in key experimental parameters including cross-linking chemistry and chromatin fragmentation strategy. To understand how the choice of experimental protocol determines the ability to detect and quantify aspects of chromosome folding we have performed a  systematic evaluation of 3C experimental parameters. We identified optimal protocol variants for either loop or compartment detection, optimizing fragment size and cross-linking chemistry. We used this knowledge to develop a greatly improved Hi-C protocol (Hi-C 3.0) that can detect both loops and compartments relatively effectively. In addition to providing benchmarked protocols, this work produced ultra-deep chromatin interaction maps using Micro-C, conventional Hi-C and Hi-C 3.0 for key cell lines used by the 4D Nucleome project.", "display_title": "Akgol Oksuz B et al. (2021) PMID:34480151", "journal": "Nature methods", "authors": ["Akgol Oksuz B", "Yang L", "Abraham S", "Venev SV", "Krietenstein N", "Parsi KM", "Ozadam H", "Oomen ME", "Nand A", "Mao H", "Genga RMJ", "Maehr R", "Rando OJ", "Mirny LA", "Gibcus JH", "Dekker J"], "title": "Systematic evaluation of chromosome conformation capture assays.", "date_published": "2021-09", "@type": ["Publication", "Item"], "short_attribution": "Akgol Oksuz B et al. (2021)", "url": "https://www.ncbi.nlm.nih.gov/pubmed/34480151", "ID": "PMID:34480151", "status": "current", "@id": "/publications/dfc530f1-82c0-4ddc-8f95-6f40417f87a0/", "uuid": "dfc530f1-82c0-4ddc-8f95-6f40417f87a0", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"uuid": "dfc530f1-82c0-4ddc-8f95-6f40417f87a0", "@type": ["Publication", "Item"], "@id": "/publications/dfc530f1-82c0-4ddc-8f95-6f40417f87a0/", "abstract": "Chromosome conformation capture (3C) assays are used to map chromatin interactions genome-wide. Chromatin interaction maps provide insights into the spatial organization of chromosomes and the mechanisms by which they fold. Hi-C and Micro-C are widely used 3C protocols that differ in key experimental parameters including cross-linking chemistry and chromatin fragmentation strategy. To understand how the choice of experimental protocol determines the ability to detect and quantify aspects of chromosome folding we have performed a  systematic evaluation of 3C experimental parameters. We identified optimal protocol variants for either loop or compartment detection, optimizing fragment size and cross-linking chemistry. We used this knowledge to develop a greatly improved Hi-C protocol (Hi-C 3.0) that can detect both loops and compartments relatively effectively. In addition to providing benchmarked protocols, this work produced ultra-deep chromatin interaction maps using Micro-C, conventional Hi-C and Hi-C 3.0 for key cell lines used by the 4D Nucleome project.", "journal": "Nature methods", "date_published": "2021-09", "status": "current", "display_title": "Akgol Oksuz B et al. (2021) PMID:34480151", "authors": ["Akgol Oksuz B", "Yang L", "Abraham S", "Venev SV", "Krietenstein N", "Parsi KM", "Ozadam H", "Oomen ME", "Nand A", "Mao H", "Genga RMJ", "Maehr R", "Rando OJ", "Mirny LA", "Gibcus JH", "Dekker J"], "ID": "PMID:34480151", "title": "Systematic evaluation of chromosome conformation capture assays.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 1, "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/experiment-set-replicates/4DNESGCCOT7T/", "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": []}