{"lab": {"@id": "/labs/job-dekker-lab/", "@type": ["Lab", "Item"], "title": "Job Dekker, UMMS", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "correspondence": [{"contact_email": "am9iLmRla2tlckB1bWFzc21lZC5lZHU=", "@id": "/users/83b5073a-069b-4162-9b30-6f42d5551e34/", "display_title": "Job Dekker"}], "status": "current", "display_title": "Job Dekker, UMMS", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "award": {"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.", "center_title": "3U54HG007010-05S1", "@id": "/awards/3U54HG007010-05S1/", "project": "ENCODE", "uuid": "43fc2984-a074-49c4-a69f-c9d3f3eadeba", "status": "current", "display_title": "A COMPREHENSIVE CATALOG OF DNASE I HYPERSENSITIVE SITES", "name": "3U54HG007010-05S1", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "files": [{"file_classification": "raw file", "status": "released", "href": "/files-fastq/4DNFID5IDQV4/@@download/4DNFID5IDQV4.fastq.gz", "uuid": "0600b406-e099-4318-84a8-64d2b7293d86", "file_type_detailed": "reads (fastq)", "upload_key": "0600b406-e099-4318-84a8-64d2b7293d86/4DNFID5IDQV4.fastq.gz", "paired_end": "1", "dbxrefs": ["ENCODE:ENCFF846FHX", "SRA:SRR6212956"], "file_type": "reads", "accession": "4DNFID5IDQV4", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFID5IDQV4/", "file_size": 11169841301, "display_title": "4DNFID5IDQV4.fastq.gz", "quality_metric": {"display_title": "QualityMetricFastqc from 2018-10-11", "Total Sequences": 363269068, "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFID5IDQV4/fastqc_report.html", "Sequence length": "50", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/4a44f462-e33c-4707-993d-532e2a625a58/", "uuid": "4a44f462-e33c-4707-993d-532e2a625a58", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"accession": "4DNFIUWQ3N6T", "display_title": "4DNFIUWQ3N6T.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "paired_end": "2", "@id": "/files-fastq/4DNFIUWQ3N6T/", "uuid": "f8394d7c-90b4-4527-9585-f7a6912e61ea", "@type": ["FileFastq", "File", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "ENCODE:ENCFF846FHX", "uri": "https://www.encodeproject.org/ENCFF846FHX"}, {"ref": "SRA:SRR6212956", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR6212956"}]}, {"file_classification": "raw file", "status": "released", "href": "/files-fastq/4DNFIUWQ3N6T/@@download/4DNFIUWQ3N6T.fastq.gz", "uuid": "f8394d7c-90b4-4527-9585-f7a6912e61ea", "file_type_detailed": "reads (fastq)", "upload_key": "f8394d7c-90b4-4527-9585-f7a6912e61ea/4DNFIUWQ3N6T.fastq.gz", "paired_end": "2", "dbxrefs": ["ENCODE:ENCFF616FUR", "SRA:SRR6212956"], "file_type": "reads", "accession": "4DNFIUWQ3N6T", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIUWQ3N6T/", "file_size": 11826769073, "display_title": "4DNFIUWQ3N6T.fastq.gz", "quality_metric": {"display_title": "QualityMetricFastqc from 2018-10-11", "Total Sequences": 363269068, "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIUWQ3N6T/fastqc_report.html", "Sequence length": "50", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/5ada15c1-b3e3-4b75-98e1-473369f47e29/", "uuid": "5ada15c1-b3e3-4b75-98e1-473369f47e29", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"accession": "4DNFID5IDQV4", "display_title": "4DNFID5IDQV4.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "paired_end": "1", "@id": "/files-fastq/4DNFID5IDQV4/", "uuid": "0600b406-e099-4318-84a8-64d2b7293d86", "@type": ["FileFastq", "File", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "ENCODE:ENCFF616FUR", "uri": "https://www.encodeproject.org/ENCFF616FUR"}, {"ref": "SRA:SRR6212956", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR6212956"}]}, {"file_classification": "raw file", "status": "released", "href": "/files-fastq/4DNFISA2ZJDE/@@download/4DNFISA2ZJDE.fastq.gz", "uuid": "220c55f1-ac24-4bbd-a035-48e7020142fb", "file_type_detailed": "reads (fastq)", "upload_key": "220c55f1-ac24-4bbd-a035-48e7020142fb/4DNFISA2ZJDE.fastq.gz", "paired_end": "1", "dbxrefs": ["ENCODE:ENCFF973IEP", "SRA:SRR6212957"], "file_type": "reads", "accession": "4DNFISA2ZJDE", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFISA2ZJDE/", "file_size": 11028687598, "display_title": "4DNFISA2ZJDE.fastq.gz", "quality_metric": {"display_title": "QualityMetricFastqc from 2018-10-11", "Total Sequences": 351195291, "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFISA2ZJDE/fastqc_report.html", "Sequence length": "50", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/ce42f527-ba32-4414-8e92-f6fd572a5715/", "uuid": "ce42f527-ba32-4414-8e92-f6fd572a5715", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"accession": "4DNFIE16SG9E", "display_title": "4DNFIE16SG9E.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "paired_end": "2", "@id": "/files-fastq/4DNFIE16SG9E/", "uuid": "aa9def91-06db-4068-bb31-b621fbe73eb5", "@type": ["FileFastq", "File", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "ENCODE:ENCFF973IEP", "uri": "https://www.encodeproject.org/ENCFF973IEP"}, {"ref": "SRA:SRR6212957", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR6212957"}]}, {"file_classification": "raw file", "status": "released", "href": "/files-fastq/4DNFIE16SG9E/@@download/4DNFIE16SG9E.fastq.gz", "uuid": "aa9def91-06db-4068-bb31-b621fbe73eb5", "file_type_detailed": "reads (fastq)", "upload_key": "aa9def91-06db-4068-bb31-b621fbe73eb5/4DNFIE16SG9E.fastq.gz", "paired_end": "2", "dbxrefs": ["ENCODE:ENCFF602QHH", "SRA:SRR6212957"], "file_type": "reads", "accession": "4DNFIE16SG9E", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIE16SG9E/", "file_size": 11641071694, "display_title": "4DNFIE16SG9E.fastq.gz", "quality_metric": {"display_title": "QualityMetricFastqc from 2018-10-11", "Total Sequences": 351195291, "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIE16SG9E/fastqc_report.html", "Sequence length": "50", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/2cdb41ce-c122-4c5a-ac30-43de7cef4286/", "uuid": "2cdb41ce-c122-4c5a-ac30-43de7cef4286", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"accession": "4DNFISA2ZJDE", "display_title": "4DNFISA2ZJDE.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "paired_end": "1", "@id": "/files-fastq/4DNFISA2ZJDE/", "uuid": "220c55f1-ac24-4bbd-a035-48e7020142fb", "@type": ["FileFastq", "File", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "ENCODE:ENCFF602QHH", "uri": "https://www.encodeproject.org/ENCFF602QHH"}, {"ref": "SRA:SRR6212957", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR6212957"}]}, {"file_classification": "raw file", "status": "released", "href": "/files-fastq/4DNFIHUGK8CD/@@download/4DNFIHUGK8CD.fastq.gz", "uuid": "93e85204-5cd2-41eb-864c-efe024877ccc", "file_type_detailed": "reads (fastq)", "upload_key": "93e85204-5cd2-41eb-864c-efe024877ccc/4DNFIHUGK8CD.fastq.gz", "paired_end": "1", "dbxrefs": ["ENCODE:ENCFF385SWQ", "SRA:SRR6212958"], "file_type": "reads", "accession": "4DNFIHUGK8CD", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIHUGK8CD/", "file_size": 11066065445, "display_title": "4DNFIHUGK8CD.fastq.gz", "quality_metric": {"display_title": "QualityMetricFastqc from 2018-10-11", "Total Sequences": 352467404, "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIHUGK8CD/fastqc_report.html", "Sequence length": "50", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/adc7b7da-8f8c-4b3a-9581-7c50e9f626d4/", "uuid": "adc7b7da-8f8c-4b3a-9581-7c50e9f626d4", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"accession": "4DNFIHUTJTKD", "display_title": "4DNFIHUTJTKD.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "paired_end": "2", "@id": "/files-fastq/4DNFIHUTJTKD/", "uuid": "2806626b-853b-4692-b465-f1ae34087072", "@type": ["FileFastq", "File", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "ENCODE:ENCFF385SWQ", "uri": "https://www.encodeproject.org/ENCFF385SWQ"}, {"ref": "SRA:SRR6212958", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR6212958"}]}, {"file_classification": "raw file", "status": "released", "href": "/files-fastq/4DNFIHUTJTKD/@@download/4DNFIHUTJTKD.fastq.gz", "uuid": "2806626b-853b-4692-b465-f1ae34087072", "file_type_detailed": "reads (fastq)", "upload_key": "2806626b-853b-4692-b465-f1ae34087072/4DNFIHUTJTKD.fastq.gz", "paired_end": "2", "dbxrefs": ["ENCODE:ENCFF424TRG", "SRA:SRR6212958"], "file_type": "reads", "accession": "4DNFIHUTJTKD", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIHUTJTKD/", "file_size": 11673153334, "display_title": "4DNFIHUTJTKD.fastq.gz", "quality_metric": {"display_title": "QualityMetricFastqc from 2018-10-11", "Total Sequences": 352467404, "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIHUTJTKD/fastqc_report.html", "Sequence length": "50", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/845d9aab-6b60-402b-99ed-3016752a4447/", "uuid": "845d9aab-6b60-402b-99ed-3016752a4447", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"accession": "4DNFIHUGK8CD", "display_title": "4DNFIHUGK8CD.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "paired_end": "1", "@id": "/files-fastq/4DNFIHUGK8CD/", "uuid": "93e85204-5cd2-41eb-864c-efe024877ccc", "@type": ["FileFastq", "File", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "ENCODE:ENCFF424TRG", "uri": "https://www.encodeproject.org/ENCFF424TRG"}, {"ref": "SRA:SRR6212958", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR6212958"}]}, {"file_classification": "raw file", "status": "released", "href": "/files-fastq/4DNFILBCZV38/@@download/4DNFILBCZV38.fastq.gz", "uuid": "63173b3a-1850-4141-bedb-a205071108cc", "file_type_detailed": "reads (fastq)", "upload_key": "63173b3a-1850-4141-bedb-a205071108cc/4DNFILBCZV38.fastq.gz", "paired_end": "1", "dbxrefs": ["ENCODE:ENCFF932XVZ", "SRA:SRR6212959"], "file_type": "reads", "accession": "4DNFILBCZV38", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFILBCZV38/", "file_size": 11020132333, "display_title": "4DNFILBCZV38.fastq.gz", "quality_metric": {"display_title": "QualityMetricFastqc from 2018-10-11", "Total Sequences": 350536419, "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFILBCZV38/fastqc_report.html", "Sequence length": "50", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/ce2e1566-58a3-4e90-97b0-dc7d370e2f64/", "uuid": "ce2e1566-58a3-4e90-97b0-dc7d370e2f64", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"accession": "4DNFIVRQ1HAC", "display_title": "4DNFIVRQ1HAC.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "paired_end": "2", "@id": "/files-fastq/4DNFIVRQ1HAC/", "uuid": "3009fc0b-b037-4b91-975f-89570e74ae16", "@type": ["FileFastq", "File", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "ENCODE:ENCFF932XVZ", "uri": "https://www.encodeproject.org/ENCFF932XVZ"}, {"ref": "SRA:SRR6212959", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR6212959"}]}, {"file_classification": "raw file", "status": "released", "href": "/files-fastq/4DNFIVRQ1HAC/@@download/4DNFIVRQ1HAC.fastq.gz", "uuid": "3009fc0b-b037-4b91-975f-89570e74ae16", "file_type_detailed": "reads (fastq)", "upload_key": "3009fc0b-b037-4b91-975f-89570e74ae16/4DNFIVRQ1HAC.fastq.gz", "paired_end": "2", "dbxrefs": ["ENCODE:ENCFF024QBA", "SRA:SRR6212959"], "file_type": "reads", "accession": "4DNFIVRQ1HAC", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIVRQ1HAC/", "file_size": 11599704169, "display_title": "4DNFIVRQ1HAC.fastq.gz", "quality_metric": {"display_title": "QualityMetricFastqc from 2018-10-11", "Total Sequences": 350536419, "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIVRQ1HAC/fastqc_report.html", "Sequence length": "50", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/7d387187-badb-49bf-995b-0505fe6ac57f/", "uuid": "7d387187-badb-49bf-995b-0505fe6ac57f", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"accession": "4DNFILBCZV38", "display_title": "4DNFILBCZV38.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "paired_end": "1", "@id": "/files-fastq/4DNFILBCZV38/", "uuid": "63173b3a-1850-4141-bedb-a205071108cc", "@type": ["FileFastq", "File", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "ENCODE:ENCFF024QBA", "uri": "https://www.encodeproject.org/ENCFF024QBA"}, {"ref": "SRA:SRR6212959", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR6212959"}]}, {"file_classification": "raw file", "status": "released", "href": "/files-fastq/4DNFIXQMNSX9/@@download/4DNFIXQMNSX9.fastq.gz", "uuid": "c937a95d-5a92-4d1c-be3d-a3f527e964a9", "file_type_detailed": "reads (fastq)", "upload_key": "c937a95d-5a92-4d1c-be3d-a3f527e964a9/4DNFIXQMNSX9.fastq.gz", "paired_end": "1", "dbxrefs": ["ENCODE:ENCFF181XUK", "SRA:SRR6212960"], "file_type": "reads", "accession": "4DNFIXQMNSX9", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIXQMNSX9/", "file_size": 11123144533, "display_title": "4DNFIXQMNSX9.fastq.gz", "quality_metric": {"display_title": "QualityMetricFastqc from 2018-10-11", "Total Sequences": 354199404, "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIXQMNSX9/fastqc_report.html", "Sequence length": "50", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/007718e6-9be2-4617-93f1-dbd126e90e20/", "uuid": "007718e6-9be2-4617-93f1-dbd126e90e20", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"accession": "4DNFIDHVW46D", "display_title": "4DNFIDHVW46D.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "paired_end": "2", "@id": "/files-fastq/4DNFIDHVW46D/", "uuid": "859abf98-9316-4f61-b320-5c6eb304cd38", "@type": ["FileFastq", "File", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "ENCODE:ENCFF181XUK", "uri": "https://www.encodeproject.org/ENCFF181XUK"}, {"ref": "SRA:SRR6212960", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR6212960"}]}, {"file_classification": "raw file", "status": "released", "href": "/files-fastq/4DNFIDHVW46D/@@download/4DNFIDHVW46D.fastq.gz", "uuid": "859abf98-9316-4f61-b320-5c6eb304cd38", "file_type_detailed": "reads (fastq)", "upload_key": "859abf98-9316-4f61-b320-5c6eb304cd38/4DNFIDHVW46D.fastq.gz", "paired_end": "2", "dbxrefs": ["ENCODE:ENCFF574TXX", "SRA:SRR6212960"], "file_type": "reads", "accession": "4DNFIDHVW46D", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIDHVW46D/", "file_size": 11700351996, "display_title": "4DNFIDHVW46D.fastq.gz", "quality_metric": {"display_title": "QualityMetricFastqc from 2018-10-11", "Total Sequences": 354199404, "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIDHVW46D/fastqc_report.html", "Sequence length": "50", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/49ca1c3c-7bf9-462c-bf78-37dce35805db/", "uuid": "49ca1c3c-7bf9-462c-bf78-37dce35805db", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"accession": "4DNFIXQMNSX9", "display_title": "4DNFIXQMNSX9.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "paired_end": "1", "@id": "/files-fastq/4DNFIXQMNSX9/", "uuid": "c937a95d-5a92-4d1c-be3d-a3f527e964a9", "@type": ["FileFastq", "File", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "ENCODE:ENCFF574TXX", "uri": "https://www.encodeproject.org/ENCFF574TXX"}, {"ref": "SRA:SRR6212960", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR6212960"}]}, {"file_classification": "raw file", "status": "released", "href": "/files-fastq/4DNFIEAVG6S9/@@download/4DNFIEAVG6S9.fastq.gz", "uuid": "bd81a6c8-2e50-4057-8256-1ab3f66f7a62", "file_type_detailed": "reads (fastq)", "upload_key": "bd81a6c8-2e50-4057-8256-1ab3f66f7a62/4DNFIEAVG6S9.fastq.gz", "paired_end": "1", "file_type": "reads", "accession": "4DNFIEAVG6S9", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIEAVG6S9/", "file_size": 11468674886, "display_title": "4DNFIEAVG6S9.fastq.gz", "quality_metric": {"display_title": "QualityMetricFastqc from 2018-10-11", "Total Sequences": 364662881, "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIEAVG6S9/fastqc_report.html", "Sequence length": "50", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/98b636b6-3b01-4618-ac2d-8cca93cc1660/", "uuid": "98b636b6-3b01-4618-ac2d-8cca93cc1660", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"accession": "4DNFIBL3IF1C", "display_title": "4DNFIBL3IF1C.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "paired_end": "2", "@id": "/files-fastq/4DNFIBL3IF1C/", "uuid": "4fdb8a9c-d5b5-4c63-8bf3-8bc055b89a11", "@type": ["FileFastq", "File", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": []}, {"file_classification": "raw file", "status": "released", "href": "/files-fastq/4DNFIBL3IF1C/@@download/4DNFIBL3IF1C.fastq.gz", "uuid": "4fdb8a9c-d5b5-4c63-8bf3-8bc055b89a11", "file_type_detailed": "reads (fastq)", "upload_key": "4fdb8a9c-d5b5-4c63-8bf3-8bc055b89a11/4DNFIBL3IF1C.fastq.gz", "paired_end": "2", "file_type": "reads", "accession": "4DNFIBL3IF1C", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIBL3IF1C/", "file_size": 12132995572, "display_title": "4DNFIBL3IF1C.fastq.gz", "quality_metric": {"display_title": "QualityMetricFastqc from 2018-10-11", "Total Sequences": 364662881, "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIBL3IF1C/fastqc_report.html", "Sequence length": "50", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/224e463d-2cc4-4087-8d92-38d02af5a3f6/", "uuid": "224e463d-2cc4-4087-8d92-38d02af5a3f6", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"accession": "4DNFIEAVG6S9", "display_title": "4DNFIEAVG6S9.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "paired_end": "1", "@id": "/files-fastq/4DNFIEAVG6S9/", "uuid": "bd81a6c8-2e50-4057-8256-1ab3f66f7a62", "@type": ["FileFastq", "File", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": []}], "status": "released", "aliases": ["dekker-lab:Experiment_Encode_ENCODE-HepG2-DpnII-2-ENCLB625TGE"], "dbxrefs": ["ENCODE:ENCLB625TGE"], "protocol": {"status": "released", "uuid": "d53fc13f-ae11-425d-a399-8ef12f6d8fc8", "@id": "/protocols/d53fc13f-ae11-425d-a399-8ef12f6d8fc8/", "@type": ["Protocol", "Item"], "display_title": "in situ Hi-C 2.0", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNEXFPG8JQ4", "biosample": {"modifications_summary": "None", "@id": "/biosamples/4DNBSQDIFNVO/", "accession": "4DNBSQDIFNVO", "treatments_summary": "None", "biosource_summary": "HepG2", "display_title": "4DNBSQDIFNVO", "uuid": "85d43df0-095e-4195-be77-c2139ae04516", "@type": ["Biosample", "Item"], "status": "released", "biosample_type": "immortalized cells", "biosource": [{"lab": {"uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "status": "current", "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"]}}, "url": "https://www.atcc.org/Products/All/HB-8065.aspx", "award": {"uuid": "43fc2984-a074-49c4-a69f-c9d3f3eadeba", "status": "current", "@type": ["Award", "Item"], "@id": "/awards/3U54HG007010-05S1/", "display_title": "A COMPREHENSIVE CATALOG OF DNASE I HYPERSENSITIVE SITES", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"status": "released", "term_id": "UBERON:0002107", "uuid": "111182bc-8535-4448-903e-854af460a233", "display_title": "liver", "@id": "/ontology-terms/UBERON:0002107/", "@type": ["OntologyTerm", "Item"], "preferred_name": "liver", "slim_terms": [{"status": "released", "display_title": "endocrine system", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0000949/", "uuid": "111126bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "liver", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0002107/", "uuid": "111182bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "endoderm", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0000925/", "uuid": "111121bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "digestive system", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0001007/", "uuid": "111129bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "synonyms": ["jecur", "iecur", "Entire liver"], "term_name": "liver", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["dekker-lab:Biosource_HepG2"], "accession": "4DNSRETMV7QH", "cell_line": {"@id": "/ontology-terms/EFO:0001187/", "status": "released", "uuid": "3ac8a63a-bd02-45ef-bd0f-5afe390f4767", "display_title": "HepG2", "@type": ["OntologyTerm", "Item"], "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "synonyms": ["Hep-G2", "HepG2 cell"], "term_name": "HepG2", "term_id": "EFO:0001187", "preferred_name": "HepG2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"@type": ["IndividualHuman", "Individual", "Item"], "@id": "/individuals-human/4DNINAUVG48J/", "uuid": "67092c27-345e-4655-a41a-19f6d8edc36a", "status": "released", "display_title": "4DNINAUVG48J", "protected_data": false, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "description": "Homo sapiens HepG2 cell line", "date_created": "2018-10-04T19:33:54.306716+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-06-05T13:04:26.639262+00:00"}, "biosource_type": "immortalized cell line", "cell_line_tier": "Unclassified", "public_release": "2018-10-16", "schema_version": "2", "project_release": "2018-10-16", "contributing_labs": [{"@id": "/labs/john-stamatoyannopoulos-lab/", "display_title": "John Stamatoyannopoulos, UW", "uuid": "73a39ac7-ffbc-46f5-aed6-b3cd4933f589", "@type": ["Lab", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.73a39ac7-ffbc-46f5-aed6-b3cd4933f589"]}}], "@id": "/biosources/4DNSRETMV7QH/", "@type": ["Biosource", "Item"], "uuid": "4b606af8-2725-459f-b306-d0263fa1fd06", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "HepG2 - 4DNSRETMV7QH", "external_references": [], "biosource_name": "HepG2", "biosource_category": ["Other"], "organism": {"uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "@id": "/organisms/9606/", "status": "released", "@type": ["Organism", "Item"], "display_title": "H. sapiens", "name": "human", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "badges": [{"messages": ["Biosample missing doubling_number", "Biosample missing passage_number", "Biosample missing morphology_image"], "badge": {"warning": "Biosample Metadata Incomplete", "badge_classification": "Warning", "title": "Biosample Metadata Incomplete", "display_title": "Biosample Metadata Incomplete", "badge_icon": "/static/img/badges/biosample-icon.svg", "@id": "/badges/biosample-metadata-incomplete/", "@type": ["Badge", "Item"], "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "description": "HiC experiment done on HepG2", "sop_mapping": {"has_sop": "No"}, "date_created": "2018-10-04T19:42:12.174318+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-04-24T16:09:58.709742+00:00"}, "ligation_time": 240.0, "biotin_removed": "Yes", "digestion_time": 960.0, "public_release": "2018-10-16", "schema_version": "2", "tagging_method": "biotin-dATP", "experiment_type": {"display_title": "in situ Hi-C", "experiment_category": "Sequencing", "uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "status": "released", "title": "in situ Hi-C", "@id": "/experiment-types/in-situ-hi-c/", "@type": ["ExperimentType", "Item"], "assay_subclass_short": "Hi-C", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "ligation_volume": 1.2, "processed_files": [{"accession": "4DNFI5FJ4V1B", "file_size": 199979012723, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/a4e6a275-fea0-4dbb-920a-ab7c852ea658/4DNFI5FJ4V1B.bam", "display_title": "4DNFI5FJ4V1B.bam", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "file_format": "bam", "status": "released", "@id": "/file-formats/bam/", "@type": ["FileFormat", "Item"], "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "href": "/files-processed/4DNFI5FJ4V1B/@@download/4DNFI5FJ4V1B.bam", "status": "released", "@id": "/files-processed/4DNFI5FJ4V1B/", "@type": ["FileProcessed", "File", "Item"], "file_type": "alignments", "file_type_detailed": "alignments (bam)", "uuid": "a4e6a275-fea0-4dbb-920a-ab7c852ea658", "file_classification": "processed file", "upload_key": "a4e6a275-fea0-4dbb-920a-ab7c852ea658/4DNFI5FJ4V1B.bam", "quality_metric": {"uuid": "6ff3fafc-ea4b-40ed-a43d-efcaf072af59", "overall_quality_status": "PASS", "@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "@id": "/quality-metrics-bamqc/6ff3fafc-ea4b-40ed-a43d-efcaf072af59/", "display_title": "QualityMetricBamqc from 2019-12-21", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Reads", "value": "2136330467", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "14.098", "tooltip": "Percent of total reads (=301.17m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "22.802", "tooltip": "Percent of total reads (=487.13m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "10.218", "tooltip": "Percent of total reads (=218.28m)", "numberType": "percent"}, {"title": "Walks", "value": "0.01", "tooltip": "Percent of total reads (=0.21m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.45", "tooltip": "Percent of total reads (=9.61m)", "numberType": "percent"}]}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "DpnII", "dataset": "Hi-C on ENCODE3 cell lines", "condition": "HepG2", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HepG2", "lab_name": "4DN DCIC, HMS"}}, {"accession": "4DNFIMA6DZHF", "file_size": 22606084963, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/8bec0b05-5051-48b8-b740-4a9a11b68125/4DNFIMA6DZHF.pairs.gz", "display_title": "4DNFIMA6DZHF.pairs.gz", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "pairs", "status": "released", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "href": "/files-processed/4DNFIMA6DZHF/@@download/4DNFIMA6DZHF.pairs.gz", "status": "released", "@id": "/files-processed/4DNFIMA6DZHF/", "@type": ["FileProcessed", "File", "Item"], "file_type": "contact list-replicate", "file_type_detailed": "contact list-replicate (pairs)", "uuid": "8bec0b05-5051-48b8-b740-4a9a11b68125", "file_classification": "processed file", "upload_key": "8bec0b05-5051-48b8-b740-4a9a11b68125/4DNFIMA6DZHF.pairs.gz", "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIMA6DZHF/pairsqc_report.html", "uuid": "6067aabf-7dac-4bf6-b599-b315996e5fbf", "overall_quality_status": "PASS", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "@id": "/quality-metrics-pairsqc/6067aabf-7dac-4bf6-b599-b315996e5fbf/", "Total reads": 1129530731, "display_title": "QualityMetricPairsqc from 2018-10-23", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "1129530731", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "38.497", "tooltip": "Percent of filtered reads (=434.84m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "28.052", "tooltip": "Percent of filtered reads (=316.85m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "33.451", "tooltip": "Percent of filtered reads (=377.84m)", "numberType": "percent"}]}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "DpnII", "dataset": "Hi-C on ENCODE3 cell lines", "condition": "HepG2", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HepG2", "lab_name": "4DN DCIC, HMS"}}], "project_release": "2018-10-16", "digestion_enzyme": {"name": "DpnII", "uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "display_title": "DpnII", "status": "released", "@id": "/enzymes/DpnII/", "@type": ["Enzyme", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "crosslinking_time": 10.0, "biosample_quantity": 24000000.0, "crosslinking_method": "1% Formaldehyde", "fragment_size_range": "180-300", "fragmentation_method": "sonication", "ligation_temperature": 16.0, "average_fragment_size": 200, "digestion_temperature": 37.0, "biosample_quantity_units": "cells", "crosslinking_temperature": 23.0, "library_preparation_date": "2016-12-01", "fragment_size_selection_method": "SPRI beads", "@id": "/experiments-hi-c/4DNEXFPG8JQ4/", "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "116554de-6f33-4861-827d-3b1ce01d416d", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "in situ Hi-C on HepG2 with DpnII - 4DNEXFPG8JQ4", "external_references": [{"ref": "ENCODE:ENCLB625TGE", "uri": "https://www.encodeproject.org/ENCLB625TGE"}], "experiment_sets": [{"experimentset_type": "replicate", "uuid": "75fc9da2-572b-4ff6-b0e2-48ba48a8cd98", "accession": "4DNESC2DEQIJ", "display_title": "4DNESC2DEQIJ", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "@id": "/experiment-set-replicates/4DNESC2DEQIJ/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "publications_of_exp": [], "experiment_categorizer": {"field": "Enzyme", "value": "DpnII", "combined": "Enzyme: DpnII"}, "experiment_summary": "in situ Hi-C on HepG2 with DpnII", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSQDIFNVO/", "embedded_path": "biosample.badges", "item": {"messages": ["Biosample missing doubling_number", "Biosample missing passage_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": []}