{"lab": {"display_title": "Francois Spitz, PASTEUR", "correspondence": [{"contact_email": "ZnNwaXR6QHVjaGljYWdvLmVkdQ==", "@id": "/users/fbcf7895-3eba-4844-950f-855c02be74a2/", "display_title": "Francois Spitz"}], "@type": ["Lab", "Item"], "uuid": "06d4f485-ccf2-4332-b226-d8a05e5497db", "@id": "/labs/francois-spitz-lab/", "title": "Francois Spitz, PASTEUR", "status": "current", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.06d4f485-ccf2-4332-b226-d8a05e5497db"]}}, "award": {"center_title": "External", "display_title": "EXTERNAL AWARD", "@type": ["Award", "Item"], "name": "external-award", "center": "External", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "project": "External", "description": "Funding source is from outside 4DN.", "@id": "/awards/external-award/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "files": [{"accession": "4DNFIYOEZMYJ", "upload_key": "aeaa7f19-a9e3-4124-b2de-53a774a4411a/4DNFIYOEZMYJ.fastq.gz", "file_size": 788667671, "display_title": "4DNFIYOEZMYJ.fastq.gz", "@id": "/files-fastq/4DNFIYOEZMYJ/", "href": "/files-fastq/4DNFIYOEZMYJ/@@download/4DNFIYOEZMYJ.fastq.gz", "file_classification": "raw file", "paired_end": "1", "dbxrefs": ["SRA:SRR5168118"], "status": "released", "file_type_detailed": "reads (fastq)", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "uuid": "aeaa7f19-a9e3-4124-b2de-53a774a4411a", "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "@id": "/quality-metrics-fastqc/91d32b94-7a17-41e2-8824-009ce89cd560/", "display_title": "QualityMetricFastqc from 2018-11-26", "Total Sequences": 18063305, "overall_quality_status": "PASS", "Sequence length": "54", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIYOEZMYJ/fastqc_report.html", "uuid": "91d32b94-7a17-41e2-8824-009ce89cd560", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "status": "released", "uuid": "91cb107a-1f44-46e6-a318-0e514214cccc", "display_title": "4DNFIW7P1D7C.fastq.gz", "@id": "/files-fastq/4DNFIW7P1D7C/", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "file_type": "reads", "accession": "4DNFIW7P1D7C", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRR5168118", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5168118"}]}, {"accession": "4DNFIW7P1D7C", "upload_key": "91cb107a-1f44-46e6-a318-0e514214cccc/4DNFIW7P1D7C.fastq.gz", "file_size": 803255341, "display_title": "4DNFIW7P1D7C.fastq.gz", "@id": "/files-fastq/4DNFIW7P1D7C/", "href": "/files-fastq/4DNFIW7P1D7C/@@download/4DNFIW7P1D7C.fastq.gz", "file_classification": "raw file", "paired_end": "2", "dbxrefs": ["SRA:SRR5168118"], "status": "released", "file_type_detailed": "reads (fastq)", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "uuid": "91cb107a-1f44-46e6-a318-0e514214cccc", "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "@id": "/quality-metrics-fastqc/6e986658-c24b-41da-b2da-d7b1975a932a/", "display_title": "QualityMetricFastqc from 2018-11-26", "Total Sequences": 18063305, "overall_quality_status": "PASS", "Sequence length": "54", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIW7P1D7C/fastqc_report.html", "uuid": "6e986658-c24b-41da-b2da-d7b1975a932a", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "status": "released", "uuid": "aeaa7f19-a9e3-4124-b2de-53a774a4411a", "display_title": "4DNFIYOEZMYJ.fastq.gz", "@id": "/files-fastq/4DNFIYOEZMYJ/", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "file_type": "reads", "accession": "4DNFIYOEZMYJ", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRR5168118", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5168118"}]}, {"accession": "4DNFI25GV4GG", "upload_key": "eec6e034-3c38-4cb1-8677-e7419a9b3649/4DNFI25GV4GG.fastq.gz", "file_size": 738186481, "display_title": "4DNFI25GV4GG.fastq.gz", "@id": "/files-fastq/4DNFI25GV4GG/", "href": "/files-fastq/4DNFI25GV4GG/@@download/4DNFI25GV4GG.fastq.gz", "file_classification": "raw file", "paired_end": "1", "dbxrefs": ["SRA:SRR5168119"], "status": "released", "file_type_detailed": "reads (fastq)", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "uuid": "eec6e034-3c38-4cb1-8677-e7419a9b3649", "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "@id": "/quality-metrics-fastqc/db487830-72d6-4591-88e1-ba5a008fe9ef/", "display_title": "QualityMetricFastqc from 2018-11-26", "Total Sequences": 17119117, "overall_quality_status": "PASS", "Sequence length": "54", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI25GV4GG/fastqc_report.html", "uuid": "db487830-72d6-4591-88e1-ba5a008fe9ef", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "status": "released", "uuid": "059b6ec1-4f7e-4c08-a987-825153e73305", "display_title": "4DNFIEGUH2D3.fastq.gz", "@id": "/files-fastq/4DNFIEGUH2D3/", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "file_type": "reads", "accession": "4DNFIEGUH2D3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRR5168119", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5168119"}]}, {"accession": "4DNFIEGUH2D3", "upload_key": "059b6ec1-4f7e-4c08-a987-825153e73305/4DNFIEGUH2D3.fastq.gz", "file_size": 752524939, "display_title": "4DNFIEGUH2D3.fastq.gz", "@id": "/files-fastq/4DNFIEGUH2D3/", "href": "/files-fastq/4DNFIEGUH2D3/@@download/4DNFIEGUH2D3.fastq.gz", "file_classification": "raw file", "paired_end": "2", "dbxrefs": ["SRA:SRR5168119"], "status": "released", "file_type_detailed": "reads (fastq)", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "uuid": "059b6ec1-4f7e-4c08-a987-825153e73305", "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "@id": "/quality-metrics-fastqc/dd4126ba-e57e-4263-81cc-009a81b98e1c/", "display_title": "QualityMetricFastqc from 2018-11-26", "Total Sequences": 17119117, "overall_quality_status": "PASS", "Sequence length": "54", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIEGUH2D3/fastqc_report.html", "uuid": "dd4126ba-e57e-4263-81cc-009a81b98e1c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "status": "released", "uuid": "eec6e034-3c38-4cb1-8677-e7419a9b3649", "display_title": "4DNFI25GV4GG.fastq.gz", "@id": "/files-fastq/4DNFI25GV4GG/", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "file_type": "reads", "accession": "4DNFI25GV4GG", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRR5168119", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5168119"}]}, {"accession": "4DNFIEJ14ERM", "upload_key": "32bc291d-97e2-4a44-966c-eeba35d2d02a/4DNFIEJ14ERM.fastq.gz", "file_size": 741331396, "display_title": "4DNFIEJ14ERM.fastq.gz", "@id": "/files-fastq/4DNFIEJ14ERM/", "href": "/files-fastq/4DNFIEJ14ERM/@@download/4DNFIEJ14ERM.fastq.gz", "file_classification": "raw file", "paired_end": "1", "dbxrefs": ["SRA:SRR5168120"], "status": "released", "file_type_detailed": "reads (fastq)", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "uuid": "32bc291d-97e2-4a44-966c-eeba35d2d02a", "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "@id": "/quality-metrics-fastqc/76bf6a40-1ba3-46c0-a05e-9f511c1f79c6/", "display_title": "QualityMetricFastqc from 2018-11-26", "Total Sequences": 17129688, "overall_quality_status": "PASS", "Sequence length": "54", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIEJ14ERM/fastqc_report.html", "uuid": "76bf6a40-1ba3-46c0-a05e-9f511c1f79c6", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "status": "released", "uuid": "a517aed5-756c-4392-be02-2616f050c38b", "display_title": "4DNFILKGGY46.fastq.gz", "@id": "/files-fastq/4DNFILKGGY46/", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "file_type": "reads", "accession": "4DNFILKGGY46", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRR5168120", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5168120"}]}, {"accession": "4DNFILKGGY46", "upload_key": "a517aed5-756c-4392-be02-2616f050c38b/4DNFILKGGY46.fastq.gz", "file_size": 754526818, "display_title": "4DNFILKGGY46.fastq.gz", "@id": "/files-fastq/4DNFILKGGY46/", "href": "/files-fastq/4DNFILKGGY46/@@download/4DNFILKGGY46.fastq.gz", "file_classification": "raw file", "paired_end": "2", "dbxrefs": ["SRA:SRR5168120"], "status": "released", "file_type_detailed": "reads (fastq)", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "uuid": "a517aed5-756c-4392-be02-2616f050c38b", "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "@id": "/quality-metrics-fastqc/edefd180-6a58-4a69-9991-694b30239435/", "display_title": "QualityMetricFastqc from 2018-11-26", "Total Sequences": 17129688, "overall_quality_status": "PASS", "Sequence length": "54", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFILKGGY46/fastqc_report.html", "uuid": "edefd180-6a58-4a69-9991-694b30239435", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "status": "released", "uuid": "32bc291d-97e2-4a44-966c-eeba35d2d02a", "display_title": "4DNFIEJ14ERM.fastq.gz", "@id": "/files-fastq/4DNFIEJ14ERM/", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "file_type": "reads", "accession": "4DNFIEJ14ERM", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRR5168120", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5168120"}]}, {"accession": "4DNFI3G7RTCO", "upload_key": "bdb4e457-fd22-44a5-ba1f-2824dacb316b/4DNFI3G7RTCO.fastq.gz", "file_size": 752753583, "display_title": "4DNFI3G7RTCO.fastq.gz", "@id": "/files-fastq/4DNFI3G7RTCO/", "href": "/files-fastq/4DNFI3G7RTCO/@@download/4DNFI3G7RTCO.fastq.gz", "file_classification": "raw file", "paired_end": "1", "dbxrefs": ["SRA:SRR5168121"], "status": "released", "file_type_detailed": "reads (fastq)", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "uuid": "bdb4e457-fd22-44a5-ba1f-2824dacb316b", "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "@id": "/quality-metrics-fastqc/8b410601-2186-47e5-b008-0e9deebeb9a2/", "display_title": "QualityMetricFastqc from 2018-11-26", "Total Sequences": 17299807, "overall_quality_status": "PASS", "Sequence length": "54", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI3G7RTCO/fastqc_report.html", "uuid": "8b410601-2186-47e5-b008-0e9deebeb9a2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "status": "released", "uuid": "1509dad3-f718-4e25-86a5-80402a7de0af", "display_title": "4DNFIRUVF51T.fastq.gz", "@id": "/files-fastq/4DNFIRUVF51T/", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "file_type": "reads", "accession": "4DNFIRUVF51T", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRR5168121", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5168121"}]}, {"accession": "4DNFIRUVF51T", "upload_key": "1509dad3-f718-4e25-86a5-80402a7de0af/4DNFIRUVF51T.fastq.gz", "file_size": 766048980, "display_title": "4DNFIRUVF51T.fastq.gz", "@id": "/files-fastq/4DNFIRUVF51T/", "href": "/files-fastq/4DNFIRUVF51T/@@download/4DNFIRUVF51T.fastq.gz", "file_classification": "raw file", "paired_end": "2", "dbxrefs": ["SRA:SRR5168121"], "status": "released", "file_type_detailed": "reads (fastq)", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "uuid": "1509dad3-f718-4e25-86a5-80402a7de0af", "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "@id": "/quality-metrics-fastqc/32985ba6-352a-41bc-a021-81c36f52e14a/", "display_title": "QualityMetricFastqc from 2018-11-26", "Total Sequences": 17299807, "overall_quality_status": "PASS", "Sequence length": "54", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIRUVF51T/fastqc_report.html", "uuid": "32985ba6-352a-41bc-a021-81c36f52e14a", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "status": "released", "uuid": "bdb4e457-fd22-44a5-ba1f-2824dacb316b", "display_title": "4DNFI3G7RTCO.fastq.gz", "@id": "/files-fastq/4DNFI3G7RTCO/", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "file_type": "reads", "accession": "4DNFI3G7RTCO", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRR5168121", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5168121"}]}, {"accession": "4DNFIVVJUYDQ", "upload_key": "57100049-3d01-4029-a11f-13396ec4808a/4DNFIVVJUYDQ.fastq.gz", "file_size": 755626389, "display_title": "4DNFIVVJUYDQ.fastq.gz", "@id": "/files-fastq/4DNFIVVJUYDQ/", "href": "/files-fastq/4DNFIVVJUYDQ/@@download/4DNFIVVJUYDQ.fastq.gz", "file_classification": "raw file", "paired_end": "1", "dbxrefs": ["SRA:SRR5168122"], "status": "released", "file_type_detailed": "reads (fastq)", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "uuid": "57100049-3d01-4029-a11f-13396ec4808a", "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "@id": "/quality-metrics-fastqc/051254cc-aa45-4412-8b59-60564ce676d4/", "display_title": "QualityMetricFastqc from 2018-11-26", "Total Sequences": 17244613, "overall_quality_status": "PASS", "Sequence length": "54", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIVVJUYDQ/fastqc_report.html", "uuid": "051254cc-aa45-4412-8b59-60564ce676d4", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "status": "released", "uuid": "ef1c6eee-4726-4418-b52d-a8b1c0404c89", "display_title": "4DNFIF8OU4IR.fastq.gz", "@id": "/files-fastq/4DNFIF8OU4IR/", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "file_type": "reads", "accession": "4DNFIF8OU4IR", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRR5168122", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5168122"}]}, {"accession": "4DNFIF8OU4IR", "upload_key": "ef1c6eee-4726-4418-b52d-a8b1c0404c89/4DNFIF8OU4IR.fastq.gz", "file_size": 770303696, "display_title": "4DNFIF8OU4IR.fastq.gz", "@id": "/files-fastq/4DNFIF8OU4IR/", "href": "/files-fastq/4DNFIF8OU4IR/@@download/4DNFIF8OU4IR.fastq.gz", "file_classification": "raw file", "paired_end": "2", "dbxrefs": ["SRA:SRR5168122"], "status": "released", "file_type_detailed": "reads (fastq)", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "uuid": "ef1c6eee-4726-4418-b52d-a8b1c0404c89", "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "@id": "/quality-metrics-fastqc/bfea6a93-e647-4f29-a9fb-4ed55078ea96/", "display_title": "QualityMetricFastqc from 2018-11-26", "Total Sequences": 17244613, "overall_quality_status": "PASS", "Sequence length": "54", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIF8OU4IR/fastqc_report.html", "uuid": "bfea6a93-e647-4f29-a9fb-4ed55078ea96", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "status": "released", "uuid": "57100049-3d01-4029-a11f-13396ec4808a", "display_title": "4DNFIVVJUYDQ.fastq.gz", "@id": "/files-fastq/4DNFIVVJUYDQ/", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "file_type": "reads", "accession": "4DNFIVVJUYDQ", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRR5168122", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5168122"}]}, {"accession": "4DNFITISJRAM", "upload_key": "31adbc1f-79ad-427a-a181-508e283bbabd/4DNFITISJRAM.fastq.gz", "file_size": 740750917, "display_title": "4DNFITISJRAM.fastq.gz", "@id": "/files-fastq/4DNFITISJRAM/", "href": "/files-fastq/4DNFITISJRAM/@@download/4DNFITISJRAM.fastq.gz", "file_classification": "raw file", "paired_end": "1", "dbxrefs": ["SRA:SRR5168123"], "status": "released", "file_type_detailed": "reads (fastq)", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "uuid": "31adbc1f-79ad-427a-a181-508e283bbabd", "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "@id": "/quality-metrics-fastqc/b9e0cf85-ba25-439b-aa8d-759094f66c0d/", "display_title": "QualityMetricFastqc from 2018-11-26", "Total Sequences": 17154342, "overall_quality_status": "PASS", "Sequence length": "54", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFITISJRAM/fastqc_report.html", "uuid": "b9e0cf85-ba25-439b-aa8d-759094f66c0d", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "status": "released", "uuid": "3fe85382-e1a0-4799-87b3-8598c4d0c3cf", "display_title": "4DNFISGA855B.fastq.gz", "@id": "/files-fastq/4DNFISGA855B/", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "file_type": "reads", "accession": "4DNFISGA855B", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRR5168123", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5168123"}]}, {"accession": "4DNFISGA855B", "upload_key": "3fe85382-e1a0-4799-87b3-8598c4d0c3cf/4DNFISGA855B.fastq.gz", "file_size": 753449791, "display_title": "4DNFISGA855B.fastq.gz", "@id": "/files-fastq/4DNFISGA855B/", "href": "/files-fastq/4DNFISGA855B/@@download/4DNFISGA855B.fastq.gz", "file_classification": "raw file", "paired_end": "2", "dbxrefs": ["SRA:SRR5168123"], "status": "released", "file_type_detailed": "reads (fastq)", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "uuid": "3fe85382-e1a0-4799-87b3-8598c4d0c3cf", "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "@id": "/quality-metrics-fastqc/3c400558-477c-4c7b-97dc-e3e01ab2bfe9/", "display_title": "QualityMetricFastqc from 2018-11-26", "Total Sequences": 17154342, "overall_quality_status": "PASS", "Sequence length": "54", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFISGA855B/fastqc_report.html", "uuid": "3c400558-477c-4c7b-97dc-e3e01ab2bfe9", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "status": "released", "uuid": "31adbc1f-79ad-427a-a181-508e283bbabd", "display_title": "4DNFITISJRAM.fastq.gz", "@id": "/files-fastq/4DNFITISJRAM/", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "file_type": "reads", "accession": "4DNFITISJRAM", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRR5168123", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5168123"}]}, {"accession": "4DNFICTPBDVT", "upload_key": "610b10a7-fab3-4d06-be7b-76bffa7d0c84/4DNFICTPBDVT.fastq.gz", "file_size": 715208870, "display_title": "4DNFICTPBDVT.fastq.gz", "@id": "/files-fastq/4DNFICTPBDVT/", "href": "/files-fastq/4DNFICTPBDVT/@@download/4DNFICTPBDVT.fastq.gz", "file_classification": "raw file", "paired_end": "1", "dbxrefs": ["SRA:SRR5168124"], "status": "released", "file_type_detailed": "reads (fastq)", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "uuid": "610b10a7-fab3-4d06-be7b-76bffa7d0c84", "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "@id": "/quality-metrics-fastqc/85b9f322-aad7-4a03-8c5c-72a9d6620937/", "display_title": "QualityMetricFastqc from 2018-11-26", "Total Sequences": 18049022, "overall_quality_status": "PASS", "Sequence length": "51", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFICTPBDVT/fastqc_report.html", "uuid": "85b9f322-aad7-4a03-8c5c-72a9d6620937", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "status": "released", "uuid": "890ad92b-372f-4dcd-89ea-2ab390202436", "display_title": "4DNFIQYCHECH.fastq.gz", "@id": "/files-fastq/4DNFIQYCHECH/", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "file_type": "reads", "accession": "4DNFIQYCHECH", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRR5168124", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5168124"}]}, {"accession": "4DNFIQYCHECH", "upload_key": "890ad92b-372f-4dcd-89ea-2ab390202436/4DNFIQYCHECH.fastq.gz", "file_size": 743218206, "display_title": "4DNFIQYCHECH.fastq.gz", "@id": "/files-fastq/4DNFIQYCHECH/", "href": "/files-fastq/4DNFIQYCHECH/@@download/4DNFIQYCHECH.fastq.gz", "file_classification": "raw file", "paired_end": "2", "dbxrefs": ["SRA:SRR5168124"], "status": "released", "file_type_detailed": "reads (fastq)", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "uuid": "890ad92b-372f-4dcd-89ea-2ab390202436", "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "@id": "/quality-metrics-fastqc/569dfdb1-d407-4987-b655-72ae3735ff9c/", "display_title": "QualityMetricFastqc from 2018-11-26", "Total Sequences": 18049022, "overall_quality_status": "PASS", "Sequence length": "51", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIQYCHECH/fastqc_report.html", "uuid": "569dfdb1-d407-4987-b655-72ae3735ff9c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "status": "released", "uuid": "610b10a7-fab3-4d06-be7b-76bffa7d0c84", "display_title": "4DNFICTPBDVT.fastq.gz", "@id": "/files-fastq/4DNFICTPBDVT/", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "file_type": "reads", "accession": "4DNFICTPBDVT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRR5168124", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5168124"}]}, {"accession": "4DNFI4OHX8ZE", "upload_key": "80d0d92b-c001-4a9f-b940-17dfe8ce3c35/4DNFI4OHX8ZE.fastq.gz", "file_size": 748888272, "display_title": "4DNFI4OHX8ZE.fastq.gz", "@id": "/files-fastq/4DNFI4OHX8ZE/", "href": "/files-fastq/4DNFI4OHX8ZE/@@download/4DNFI4OHX8ZE.fastq.gz", "file_classification": "raw file", "paired_end": "1", "dbxrefs": ["SRA:SRR5168125"], "status": "released", "file_type_detailed": "reads (fastq)", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "uuid": "80d0d92b-c001-4a9f-b940-17dfe8ce3c35", "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "@id": "/quality-metrics-fastqc/dd6bbde7-05b8-4d23-ab1c-3889c9f70bc8/", "display_title": "QualityMetricFastqc from 2018-11-26", "Total Sequences": 17283813, "overall_quality_status": "PASS", "Sequence length": "54", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI4OHX8ZE/fastqc_report.html", "uuid": "dd6bbde7-05b8-4d23-ab1c-3889c9f70bc8", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "status": "released", "uuid": "d7e987fd-6993-4fcd-a6ab-d51f68c74a3f", "display_title": "4DNFICJVI9UF.fastq.gz", "@id": "/files-fastq/4DNFICJVI9UF/", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "file_type": "reads", "accession": "4DNFICJVI9UF", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRR5168125", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5168125"}]}, {"accession": "4DNFICJVI9UF", "upload_key": "d7e987fd-6993-4fcd-a6ab-d51f68c74a3f/4DNFICJVI9UF.fastq.gz", "file_size": 759382628, "display_title": "4DNFICJVI9UF.fastq.gz", "@id": "/files-fastq/4DNFICJVI9UF/", "href": "/files-fastq/4DNFICJVI9UF/@@download/4DNFICJVI9UF.fastq.gz", "file_classification": "raw file", "paired_end": "2", "dbxrefs": ["SRA:SRR5168125"], "status": "released", "file_type_detailed": "reads (fastq)", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "uuid": "d7e987fd-6993-4fcd-a6ab-d51f68c74a3f", "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "@id": "/quality-metrics-fastqc/36a37bb1-a0cf-4124-94e6-f3f64ee0efa9/", "display_title": "QualityMetricFastqc from 2018-11-26", "Total Sequences": 17283813, "overall_quality_status": "PASS", "Sequence length": "54", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFICJVI9UF/fastqc_report.html", "uuid": "36a37bb1-a0cf-4124-94e6-f3f64ee0efa9", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "status": "released", "uuid": "80d0d92b-c001-4a9f-b940-17dfe8ce3c35", "display_title": "4DNFI4OHX8ZE.fastq.gz", "@id": "/files-fastq/4DNFI4OHX8ZE/", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "file_type": "reads", "accession": "4DNFI4OHX8ZE", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRR5168125", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5168125"}]}], "status": "released", "aliases": ["leonid-mirny-lab:29094699-TCC-WTrep1"], "dbxrefs": ["GEO:GSM2453279"], "protocol": {"@id": "/protocols/a5ee0c2d-aa4a-4a39-a84d-c022bc2b0096/", "display_title": "TCC_protocol.pdf", "@type": ["Protocol", "Item"], "status": "released", "uuid": "a5ee0c2d-aa4a-4a39-a84d-c022bc2b0096", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNEXN25ESPT", "biosample": {"display_title": "4DNBSU328LQ3", "accession": "4DNBSU328LQ3", "biosource_summary": "hepatocyte", "uuid": "92f95a5e-e8dd-43a8-a7d1-11617cfb7258", "@id": "/biosamples/4DNBSU328LQ3/", "modifications_summary": "None", "status": "released", "biosample_type": "primary cells", "@type": ["Biosample", "Item"], "treatments_summary": "mock treatment (5.0d)", "biosource": [{"lab": {"display_title": "Francois Spitz, PASTEUR", "@id": "/labs/francois-spitz-lab/", "status": "current", "uuid": "06d4f485-ccf2-4332-b226-d8a05e5497db", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.06d4f485-ccf2-4332-b226-d8a05e5497db"]}}, "award": {"uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "@type": ["Award", "Item"], "display_title": "EXTERNAL AWARD", "@id": "/awards/external-award/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"display_title": "liver", "@id": "/ontology-terms/UBERON:0002107/", "synonyms": ["jecur", "iecur", "Entire liver"], "term_id": "UBERON:0002107", "uuid": "111182bc-8535-4448-903e-854af460a233", "preferred_name": "liver", "term_name": "liver", "@type": ["OntologyTerm", "Item"], "slim_terms": [{"uuid": "111126bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "status": "released", "display_title": "endocrine system", "@id": "/ontology-terms/UBERON:0000949/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "111182bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "status": "released", "display_title": "liver", "@id": "/ontology-terms/UBERON:0002107/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "111121bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "status": "released", "display_title": "endoderm", "@id": "/ontology-terms/UBERON:0000925/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "111129bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "status": "released", "display_title": "digestive system", "@id": "/ontology-terms/UBERON:0001007/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["leonid-mirny-lab:Nipbl-flox-cre-hepatocytes"], "accession": "4DNSRMDUDYLW", "cell_line": {"uuid": "a1b0f241-64ca-47a4-b9b8-19c28b5bdedb", "preferred_name": "hepatocyte", "@id": "/ontology-terms/CL:0000182/", "@type": ["OntologyTerm", "Item"], "term_name": "hepatocyte", "display_title": "hepatocyte", "term_id": "CL:0000182", "status": "released", "slim_terms": [{"display_title": "endocrine system", "uuid": "111126bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/UBERON:0000949/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "digestive system", "uuid": "111129bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/UBERON:0001007/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "liver", "uuid": "111182bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/UBERON:0002107/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@type": ["OntologyTerm", "Item"], "status": "current", "@id": "/ontology-terms/GO:0005623/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/CL:0000000/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "endoderm", "uuid": "111121bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/UBERON:0000925/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"@type": ["IndividualMouse", "Individual", "Item"], "status": "released", "uuid": "5483ddbf-d764-43a8-9c83-049f6237c64d", "@id": "/individuals-mouse/4DNIN2BSSV7N/", "display_title": "4DNIN2BSSV7N", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "description": "hepatocytes from NIBPL KO mice", "date_created": "2018-05-10T18:35:30.544577+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-06-05T17:46:32.561882+00:00"}, "biosource_type": "primary cell", "cell_line_tier": "Unclassified", "public_release": "2018-07-06", "schema_version": "2", "project_release": "2018-07-06", "contributing_labs": [{"@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "status": "current", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "@id": "/biosources/4DNSRMDUDYLW/", "@type": ["Biosource", "Item"], "uuid": "13e689ba-3ae3-4302-817b-3818bda0862f", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "hepatocyte - 4DNSRMDUDYLW", "external_references": [], "biosource_name": "hepatocyte", "biosource_category": ["Primary Cells"], "organism": {"uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "display_title": "M. musculus", "status": "released", "name": "mouse", "@type": ["Organism", "Item"], "@id": "/organisms/10090/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "modifications": [], "treatments": [{"duration": 5.0, "treatment_type": "Chemical", "description": "mock injection", "display_title": "mock treatment (5.0d)", "duration_units": "day", "chemical": "mock", "@id": "/treatments-agent/4c6c9ee6-3176-42ed-bde2-2e514301132e/", "@type": ["TreatmentAgent", "Treatment", "Item"], "uuid": "4c6c9ee6-3176-42ed-bde2-2e514301132e", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pcr_cycles": 12, "description": "TCC on uninduced control hepatocytes, bio replicate 1", "sop_mapping": {"has_sop": "No"}, "date_created": "2018-05-10T18:36:47.746189+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-04-24T16:48:57.337259+00:00"}, "ligation_time": 240.0, "biotin_removed": "Yes", "digestion_time": 960.0, "public_release": "2018-07-06", "schema_version": "2", "tagging_method": "Iodoacetyl-PEG2-Biotin", "experiment_type": {"status": "released", "assay_subclass_short": "Hi-C", "title": "TCC", "display_title": "TCC", "@type": ["ExperimentType", "Item"], "experiment_category": "Sequencing", "@id": "/experiment-types/tcc/", "uuid": "e95e3626-aadc-464b-9ef0-0cdbea689744", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "ligation_volume": 5.0, "processed_files": [{"file_size": 17132844692, "display_title": "4DNFIN92AY28.bam", "file_type": "alignments", "href": "/files-processed/4DNFIN92AY28/@@download/4DNFIN92AY28.bam", "@type": ["FileProcessed", "File", "Item"], "file_format": {"@id": "/file-formats/bam/", "status": "released", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "05073cdb-2612-4e34-a756-a8cc2f4cbe9d", "status": "released", "accession": "4DNFIN92AY28", "@id": "/files-processed/4DNFIN92AY28/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/05073cdb-2612-4e34-a756-a8cc2f4cbe9d/4DNFIN92AY28.bam", "file_classification": "processed file", "file_type_detailed": "alignments (bam)", "upload_key": "05073cdb-2612-4e34-a756-a8cc2f4cbe9d/4DNFIN92AY28.bam", "quality_metric": {"display_title": "QualityMetricBamqc from 2020-01-17", "overall_quality_status": "PASS", "@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "@id": "/quality-metrics-bamqc/1bb18980-a545-4586-a6d9-3b3f6e06b799/", "uuid": "1bb18980-a545-4586-a6d9-3b3f6e06b799", "status": "released", "quality_metric_summary": [{"title": "Total Reads", "value": "139343707", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "20.075", "tooltip": "Percent of total reads (=27.97m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "18.358", "tooltip": "Percent of total reads (=25.58m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "8.279", "tooltip": "Percent of total reads (=11.54m)", "numberType": "percent"}, {"title": "Walks", "value": "0.679", "tooltip": "Percent of total reads (=0.95m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.085", "tooltip": "Percent of total reads (=0.12m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Francois Spitz, PASTEUR", "experiment_type": "TCC", "experiment_bucket": "processed file", "assay_info": "HindIII", "dataset": "TCC on hepatocytes +/- NIPBL", "condition": "uninduced control", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "hepatocyte", "lab_name": "4DN DCIC, HMS"}, "external_references": []}, {"file_size": 1126693324, "display_title": "4DNFIT3MMU1S.pairs.gz", "file_type": "contact list-replicate", "href": "/files-processed/4DNFIT3MMU1S/@@download/4DNFIT3MMU1S.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "file_format": {"@id": "/file-formats/pairs/", "status": "released", "file_format": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "pairs", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "a7148ecc-b808-4e2b-9a61-32a5af8cb6d8", "status": "released", "accession": "4DNFIT3MMU1S", "@id": "/files-processed/4DNFIT3MMU1S/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/a7148ecc-b808-4e2b-9a61-32a5af8cb6d8/4DNFIT3MMU1S.pairs.gz", "file_classification": "processed file", "file_type_detailed": "contact list-replicate (pairs)", "upload_key": "a7148ecc-b808-4e2b-9a61-32a5af8cb6d8/4DNFIT3MMU1S.pairs.gz", "quality_metric": {"display_title": "QualityMetricPairsqc from 2018-11-28", "overall_quality_status": "PASS", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "@id": "/quality-metrics-pairsqc/baaf39b3-33e9-4b00-80f1-0b913476200f/", "uuid": "baaf39b3-33e9-4b00-80f1-0b913476200f", "status": "released", "Total reads": 73308190, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIT3MMU1S/pairsqc_report.html", "quality_metric_summary": [{"title": "Filtered Reads", "value": "73308190", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "50.356", "tooltip": "Percent of filtered reads (=36.92m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "30.001", "tooltip": "Percent of filtered reads (=21.99m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "19.642", "tooltip": "Percent of filtered reads (=14.4m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Francois Spitz, PASTEUR", "experiment_type": "TCC", "experiment_bucket": "processed file", "assay_info": "HindIII", "dataset": "TCC on hepatocytes +/- NIPBL", "condition": "uninduced control", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "hepatocyte", "lab_name": "4DN DCIC, HMS"}, "external_references": []}], "project_release": "2018-07-06", "digestion_enzyme": {"status": "released", "name": "HindIII", "uuid": "2ace2f00-c913-4bac-a6ef-0b316bc2108e", "display_title": "HindIII", "@type": ["Enzyme", "Item"], "@id": "/enzymes/HindIII/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "correspondence": [{"contact_email": "bGVvbmlkQG1pdC5lZHU=", "@id": "/users/f520d12a-e4c4-4774-a230-08d6dc4f5ef1/", "display_title": "Leonid Mirny"}], "@id": "/labs/leonid-mirny-lab/", "@type": ["Lab", "Item"], "status": "current", "display_title": "Leonid Mirny, MIT", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "crosslinking_time": 10.0, "biosample_quantity": 100000000.0, "crosslinking_method": "1% Formaldehyde", "experiment_relation": [{"experiment": {"@id": "/experiments-hi-c/4DNEXGWOOI8I/", "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "cbabaf13-d076-4ed0-83ed-b8b58e829b17", "display_title": "TCC on hepatocyte with HindIII - 4DNEXGWOOI8I", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "relationship_type": "control for"}, {"experiment": {"@id": "/experiments-hi-c/4DNEXQAO3GNK/", "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "cf441a1c-23ce-4390-ad19-8e20d54c09cc", "display_title": "TCC on hepatocyte with HindIII - 4DNEXQAO3GNK", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "relationship_type": "control for"}], "fragment_size_range": "300-400", "fragmentation_method": "sonication", "ligation_temperature": 16.0, "digestion_temperature": 37.0, "biosample_quantity_units": "cells", "crosslinking_temperature": 22.0, "library_preparation_date": "2014-07-17", "fragment_size_selection_method": "gel", "@id": "/experiments-hi-c/4DNEXN25ESPT/", "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "dfc5e2b1-ccc7-4337-a292-fce5b519099f", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "TCC on hepatocyte with HindIII - 4DNEXN25ESPT", "external_references": [{"ref": "GEO:GSM2453279", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2453279"}], "experiment_sets": [{"experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNESAOU4AAQ/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "status": "released", "accession": "4DNESAOU4AAQ", "uuid": "37adea6e-6a27-41af-bf03-1f2edc8cbf91", "display_title": "4DNESAOU4AAQ", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"title": "Two independent modes of chromatin organization revealed by cohesin removal.", "short_attribution": "Schwarzer W et al. (2017)", "authors": ["Schwarzer W", "Abdennur N", "Goloborodko A", "Pekowska A", "Fudenberg G", "Loe-Mie Y", "Fonseca NA", "Huber W", "H Haering C", "Mirny L", "Spitz F"], "abstract": "Imaging and chromosome conformation capture studies have revealed several layers  of chromosome organization, including segregation into megabase-sized active and  inactive compartments, and partitioning into sub-megabase domains (TADs). It remains unclear, however, how these layers of organization form, interact with one another and influence genome function. Here we show that deletion of the cohesin-loading factor Nipbl in mouse liver leads to a marked reorganization of chromosomal folding. TADs and associated Hi-C peaks vanish globally, even in the  absence of transcriptional changes. By contrast, compartmental segregation is preserved and even reinforced. Strikingly, the disappearance of TADs unmasks a finer compartment structure that accurately reflects the underlying epigenetic landscape. These observations demonstrate that the three-dimensional organization of the genome results from the interplay of two independent mechanisms: cohesin-independent segregation of the genome into fine-scale compartments, defined by chromatin state; and cohesin-dependent formation of TADs, possibly by  loop extrusion, which helps to guide distant enhancers to their target genes.", "@id": "/publications/7343e7a5-1332-4adb-9265-cdd1381348eb/", "status": "current", "date_published": "2017-09-27", "display_title": "Schwarzer W et al. (2017) PMID:29094699", "journal": "Nature", "ID": "PMID:29094699", "@type": ["Publication", "Item"], "uuid": "7343e7a5-1332-4adb-9265-cdd1381348eb", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"date_published": "2017-09-27", "display_title": "Schwarzer W et al. (2017) PMID:29094699", "@id": "/publications/7343e7a5-1332-4adb-9265-cdd1381348eb/", "short_attribution": "Schwarzer W et al. (2017)", "status": "current", "abstract": "Imaging and chromosome conformation capture studies have revealed several layers  of chromosome organization, including segregation into megabase-sized active and  inactive compartments, and partitioning into sub-megabase domains (TADs). It remains unclear, however, how these layers of organization form, interact with one another and influence genome function. Here we show that deletion of the cohesin-loading factor Nipbl in mouse liver leads to a marked reorganization of chromosomal folding. TADs and associated Hi-C peaks vanish globally, even in the  absence of transcriptional changes. By contrast, compartmental segregation is preserved and even reinforced. Strikingly, the disappearance of TADs unmasks a finer compartment structure that accurately reflects the underlying epigenetic landscape. These observations demonstrate that the three-dimensional organization of the genome results from the interplay of two independent mechanisms: cohesin-independent segregation of the genome into fine-scale compartments, defined by chromatin state; and cohesin-dependent formation of TADs, possibly by  loop extrusion, which helps to guide distant enhancers to their target genes.", "uuid": "7343e7a5-1332-4adb-9265-cdd1381348eb", "ID": "PMID:29094699", "authors": ["Schwarzer W", "Abdennur N", "Goloborodko A", "Pekowska A", "Fudenberg G", "Loe-Mie Y", "Fonseca NA", "Huber W", "H Haering C", "Mirny L", "Spitz F"], "title": "Two independent modes of chromatin organization revealed by cohesin removal.", "@type": ["Publication", "Item"], "journal": "Nature", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Enzyme", "value": "HindIII", "combined": "Enzyme: HindIII"}, "experiment_summary": "TCC on hepatocyte with HindIII", "@context": "/terms/", "aggregated-items": {"badges": []}, "validation-errors": []}