{"lab": {"status": "current", "correspondence": [{"contact_email": "ZnNwaXR6QHVjaGljYWdvLmVkdQ==", "@id": "/users/fbcf7895-3eba-4844-950f-855c02be74a2/", "display_title": "Francois Spitz"}], "uuid": "06d4f485-ccf2-4332-b226-d8a05e5497db", "@id": "/labs/francois-spitz-lab/", "display_title": "Francois Spitz, PASTEUR", "@type": ["Lab", "Item"], "title": "Francois Spitz, PASTEUR", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.06d4f485-ccf2-4332-b226-d8a05e5497db"]}}, "award": {"status": "current", "name": "external-award", "@id": "/awards/external-award/", "project": "External", "description": "Funding source is from outside 4DN.", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "@type": ["Award", "Item"], "center": "External", "display_title": "EXTERNAL AWARD", "center_title": "External", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "files": [{"paired_end": "1", "href": "/files-fastq/4DNFIFRK8ERC/@@download/4DNFIFRK8ERC.fastq.gz", "file_size": 656975334, "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_classification": "raw file", "accession": "4DNFIFRK8ERC", "upload_key": "5e648815-6937-4b58-be2a-b96031994dd1/4DNFIFRK8ERC.fastq.gz", "dbxrefs": ["SRA:SRR5168126"], "status": "released", "display_title": "4DNFIFRK8ERC.fastq.gz", "@id": "/files-fastq/4DNFIFRK8ERC/", "file_type_detailed": "reads (fastq)", "uuid": "5e648815-6937-4b58-be2a-b96031994dd1", "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "uuid": "d672fa15-f9b3-4e0e-899e-4eaf676f9012", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "status": "released", "@id": "/files-fastq/4DNFINRE432I/", "display_title": "4DNFINRE432I.fastq.gz", "accession": "4DNFINRE432I", "file_type_detailed": "reads (fastq)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "overall_quality_status": "PASS", "Sequence length": "54", "Total Sequences": 14855150, "uuid": "6435342c-6ac2-4bb8-9364-23f1d5d31eb1", "@id": "/quality-metrics-fastqc/6435342c-6ac2-4bb8-9364-23f1d5d31eb1/", "display_title": "QualityMetricFastqc from 2018-11-26", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIFRK8ERC/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRR5168126", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5168126"}]}, {"paired_end": "2", "href": "/files-fastq/4DNFINRE432I/@@download/4DNFINRE432I.fastq.gz", "file_size": 661952879, "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_classification": "raw file", "accession": "4DNFINRE432I", "upload_key": "d672fa15-f9b3-4e0e-899e-4eaf676f9012/4DNFINRE432I.fastq.gz", "dbxrefs": ["SRA:SRR5168126"], "status": "released", "display_title": "4DNFINRE432I.fastq.gz", "@id": "/files-fastq/4DNFINRE432I/", "file_type_detailed": "reads (fastq)", "uuid": "d672fa15-f9b3-4e0e-899e-4eaf676f9012", "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "uuid": "5e648815-6937-4b58-be2a-b96031994dd1", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "status": "released", "@id": "/files-fastq/4DNFIFRK8ERC/", "display_title": "4DNFIFRK8ERC.fastq.gz", "accession": "4DNFIFRK8ERC", "file_type_detailed": "reads (fastq)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "overall_quality_status": "PASS", "Sequence length": "54", "Total Sequences": 14855150, "uuid": "878bed63-09b3-4cdd-9421-be600c09036f", "@id": "/quality-metrics-fastqc/878bed63-09b3-4cdd-9421-be600c09036f/", "display_title": "QualityMetricFastqc from 2018-11-26", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFINRE432I/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRR5168126", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5168126"}]}, {"paired_end": "1", "href": "/files-fastq/4DNFI6JCETUT/@@download/4DNFI6JCETUT.fastq.gz", "file_size": 612940097, "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_classification": "raw file", "accession": "4DNFI6JCETUT", "upload_key": "8d94315f-2362-42f4-af8a-ae63570e867a/4DNFI6JCETUT.fastq.gz", "dbxrefs": ["SRA:SRR5168127"], "status": "released", "display_title": "4DNFI6JCETUT.fastq.gz", "@id": "/files-fastq/4DNFI6JCETUT/", "file_type_detailed": "reads (fastq)", "uuid": "8d94315f-2362-42f4-af8a-ae63570e867a", "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "uuid": "55475429-a1e5-45e7-90ec-e30e6bd05633", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "status": "released", "@id": "/files-fastq/4DNFI1OF49AP/", "display_title": "4DNFI1OF49AP.fastq.gz", "accession": "4DNFI1OF49AP", "file_type_detailed": "reads (fastq)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "overall_quality_status": "PASS", "Sequence length": "54", "Total Sequences": 14050773, "uuid": "b902df5d-b490-4413-9a87-95f803a4d009", "@id": "/quality-metrics-fastqc/b902df5d-b490-4413-9a87-95f803a4d009/", "display_title": "QualityMetricFastqc from 2018-11-26", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI6JCETUT/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRR5168127", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5168127"}]}, {"paired_end": "2", "href": "/files-fastq/4DNFI1OF49AP/@@download/4DNFI1OF49AP.fastq.gz", "file_size": 618795056, "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_classification": "raw file", "accession": "4DNFI1OF49AP", "upload_key": "55475429-a1e5-45e7-90ec-e30e6bd05633/4DNFI1OF49AP.fastq.gz", "dbxrefs": ["SRA:SRR5168127"], "status": "released", "display_title": "4DNFI1OF49AP.fastq.gz", "@id": "/files-fastq/4DNFI1OF49AP/", "file_type_detailed": "reads (fastq)", "uuid": "55475429-a1e5-45e7-90ec-e30e6bd05633", "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "uuid": "8d94315f-2362-42f4-af8a-ae63570e867a", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "status": "released", "@id": "/files-fastq/4DNFI6JCETUT/", "display_title": "4DNFI6JCETUT.fastq.gz", "accession": "4DNFI6JCETUT", "file_type_detailed": "reads (fastq)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "overall_quality_status": "PASS", "Sequence length": "54", "Total Sequences": 14050773, "uuid": "d42b4fde-cf7f-4e18-8401-134d94b568a4", "@id": "/quality-metrics-fastqc/d42b4fde-cf7f-4e18-8401-134d94b568a4/", "display_title": "QualityMetricFastqc from 2018-11-26", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI1OF49AP/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRR5168127", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5168127"}]}, {"paired_end": "1", "href": "/files-fastq/4DNFIBQDC76O/@@download/4DNFIBQDC76O.fastq.gz", "file_size": 617174118, "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_classification": "raw file", "accession": "4DNFIBQDC76O", "upload_key": "0b7b1af5-aa36-4dd9-af56-113e53d1f673/4DNFIBQDC76O.fastq.gz", "dbxrefs": ["SRA:SRR5168128"], "status": "released", "display_title": "4DNFIBQDC76O.fastq.gz", "@id": "/files-fastq/4DNFIBQDC76O/", "file_type_detailed": "reads (fastq)", "uuid": "0b7b1af5-aa36-4dd9-af56-113e53d1f673", "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "uuid": "f1db6c74-ec45-4485-bfe3-bb13a010ea8e", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "status": "released", "@id": "/files-fastq/4DNFINLEUH65/", "display_title": "4DNFINLEUH65.fastq.gz", "accession": "4DNFINLEUH65", "file_type_detailed": "reads (fastq)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "overall_quality_status": "PASS", "Sequence length": "54", "Total Sequences": 14087139, "uuid": "bbca860a-aa85-4151-9a11-0ee89f9b939a", "@id": "/quality-metrics-fastqc/bbca860a-aa85-4151-9a11-0ee89f9b939a/", "display_title": "QualityMetricFastqc from 2018-11-26", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIBQDC76O/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRR5168128", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5168128"}]}, {"paired_end": "2", "href": "/files-fastq/4DNFINLEUH65/@@download/4DNFINLEUH65.fastq.gz", "file_size": 622432090, "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_classification": "raw file", "accession": "4DNFINLEUH65", "upload_key": "f1db6c74-ec45-4485-bfe3-bb13a010ea8e/4DNFINLEUH65.fastq.gz", "dbxrefs": ["SRA:SRR5168128"], "status": "released", "display_title": "4DNFINLEUH65.fastq.gz", "@id": "/files-fastq/4DNFINLEUH65/", "file_type_detailed": "reads (fastq)", "uuid": "f1db6c74-ec45-4485-bfe3-bb13a010ea8e", "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "uuid": "0b7b1af5-aa36-4dd9-af56-113e53d1f673", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "status": "released", "@id": "/files-fastq/4DNFIBQDC76O/", "display_title": "4DNFIBQDC76O.fastq.gz", "accession": "4DNFIBQDC76O", "file_type_detailed": "reads (fastq)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "overall_quality_status": "PASS", "Sequence length": "54", "Total Sequences": 14087139, "uuid": "71ca2b41-6343-4abf-8288-7c5358afa4f0", "@id": "/quality-metrics-fastqc/71ca2b41-6343-4abf-8288-7c5358afa4f0/", "display_title": "QualityMetricFastqc from 2018-11-26", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFINLEUH65/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRR5168128", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5168128"}]}, {"paired_end": "1", "href": "/files-fastq/4DNFIME6NB5P/@@download/4DNFIME6NB5P.fastq.gz", "file_size": 627350452, "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_classification": "raw file", "accession": "4DNFIME6NB5P", "upload_key": "18f6965f-d69a-4db5-b8fa-61b30b888cd5/4DNFIME6NB5P.fastq.gz", "dbxrefs": ["SRA:SRR5168129"], "status": "released", "display_title": "4DNFIME6NB5P.fastq.gz", "@id": "/files-fastq/4DNFIME6NB5P/", "file_type_detailed": "reads (fastq)", "uuid": "18f6965f-d69a-4db5-b8fa-61b30b888cd5", "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "uuid": "a0606e4f-b72e-4a04-96c8-a079124728d7", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "status": "released", "@id": "/files-fastq/4DNFI6Y9UTQW/", "display_title": "4DNFI6Y9UTQW.fastq.gz", "accession": "4DNFI6Y9UTQW", "file_type_detailed": "reads (fastq)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "overall_quality_status": "PASS", "Sequence length": "54", "Total Sequences": 14269051, "uuid": "ce8ce34d-2934-468a-baba-57b79ea36790", "@id": "/quality-metrics-fastqc/ce8ce34d-2934-468a-baba-57b79ea36790/", "display_title": "QualityMetricFastqc from 2018-11-26", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIME6NB5P/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRR5168129", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5168129"}]}, {"paired_end": "2", "href": "/files-fastq/4DNFI6Y9UTQW/@@download/4DNFI6Y9UTQW.fastq.gz", "file_size": 634336649, "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_classification": "raw file", "accession": "4DNFI6Y9UTQW", "upload_key": "a0606e4f-b72e-4a04-96c8-a079124728d7/4DNFI6Y9UTQW.fastq.gz", "dbxrefs": ["SRA:SRR5168129"], "status": "released", "display_title": "4DNFI6Y9UTQW.fastq.gz", "@id": "/files-fastq/4DNFI6Y9UTQW/", "file_type_detailed": "reads (fastq)", "uuid": "a0606e4f-b72e-4a04-96c8-a079124728d7", "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "uuid": "18f6965f-d69a-4db5-b8fa-61b30b888cd5", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "status": "released", "@id": "/files-fastq/4DNFIME6NB5P/", "display_title": "4DNFIME6NB5P.fastq.gz", "accession": "4DNFIME6NB5P", "file_type_detailed": "reads (fastq)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "overall_quality_status": "PASS", "Sequence length": "54", "Total Sequences": 14269051, "uuid": "c795aa06-62e1-4777-8dfa-cf1ca9f218ad", "@id": "/quality-metrics-fastqc/c795aa06-62e1-4777-8dfa-cf1ca9f218ad/", "display_title": "QualityMetricFastqc from 2018-11-26", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI6Y9UTQW/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRR5168129", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5168129"}]}, {"paired_end": "1", "href": "/files-fastq/4DNFIIWTYL6Z/@@download/4DNFIIWTYL6Z.fastq.gz", "file_size": 625440784, "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_classification": "raw file", "accession": "4DNFIIWTYL6Z", "upload_key": "a4079313-b2a0-4e34-9368-e0f17b77381c/4DNFIIWTYL6Z.fastq.gz", "dbxrefs": ["SRA:SRR5168130"], "status": "released", "display_title": "4DNFIIWTYL6Z.fastq.gz", "@id": "/files-fastq/4DNFIIWTYL6Z/", "file_type_detailed": "reads (fastq)", "uuid": "a4079313-b2a0-4e34-9368-e0f17b77381c", "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "uuid": "3b1dddf4-c030-418a-b5e1-96a40b257715", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "status": "released", "@id": "/files-fastq/4DNFI8DJL4LX/", "display_title": "4DNFI8DJL4LX.fastq.gz", "accession": "4DNFI8DJL4LX", "file_type_detailed": "reads (fastq)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "overall_quality_status": "PASS", "Sequence length": "54", "Total Sequences": 14157140, "uuid": "2fa8f982-56c5-46a0-9c29-3adc152eb75c", "@id": "/quality-metrics-fastqc/2fa8f982-56c5-46a0-9c29-3adc152eb75c/", "display_title": "QualityMetricFastqc from 2018-11-26", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIIWTYL6Z/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRR5168130", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5168130"}]}, {"paired_end": "2", "href": "/files-fastq/4DNFI8DJL4LX/@@download/4DNFI8DJL4LX.fastq.gz", "file_size": 635209184, "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_classification": "raw file", "accession": "4DNFI8DJL4LX", "upload_key": "3b1dddf4-c030-418a-b5e1-96a40b257715/4DNFI8DJL4LX.fastq.gz", "dbxrefs": ["SRA:SRR5168130"], "status": "released", "display_title": "4DNFI8DJL4LX.fastq.gz", "@id": "/files-fastq/4DNFI8DJL4LX/", "file_type_detailed": "reads (fastq)", "uuid": "3b1dddf4-c030-418a-b5e1-96a40b257715", "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "uuid": "a4079313-b2a0-4e34-9368-e0f17b77381c", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "status": "released", "@id": "/files-fastq/4DNFIIWTYL6Z/", "display_title": "4DNFIIWTYL6Z.fastq.gz", "accession": "4DNFIIWTYL6Z", "file_type_detailed": "reads (fastq)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "overall_quality_status": "PASS", "Sequence length": "54", "Total Sequences": 14157140, "uuid": "210a8306-d071-4002-8f75-f84830fb3c06", "@id": "/quality-metrics-fastqc/210a8306-d071-4002-8f75-f84830fb3c06/", "display_title": "QualityMetricFastqc from 2018-11-26", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI8DJL4LX/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRR5168130", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5168130"}]}, {"paired_end": "1", "href": "/files-fastq/4DNFI9M795Y1/@@download/4DNFI9M795Y1.fastq.gz", "file_size": 616622963, "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_classification": "raw file", "accession": "4DNFI9M795Y1", "upload_key": "2d23d728-f0aa-47f2-ac9f-fe1620f516c2/4DNFI9M795Y1.fastq.gz", "dbxrefs": ["SRA:SRR5168131"], "status": "released", "display_title": "4DNFI9M795Y1.fastq.gz", "@id": "/files-fastq/4DNFI9M795Y1/", "file_type_detailed": "reads (fastq)", "uuid": "2d23d728-f0aa-47f2-ac9f-fe1620f516c2", "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "uuid": "f4e831ba-e855-492c-b154-42e80f586dbb", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "status": "released", "@id": "/files-fastq/4DNFIYB4JBLS/", "display_title": "4DNFIYB4JBLS.fastq.gz", "accession": "4DNFIYB4JBLS", "file_type_detailed": "reads (fastq)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "overall_quality_status": "PASS", "Sequence length": "54", "Total Sequences": 14115360, "uuid": "1ba86742-21c6-4ccc-bea5-7fbeea630347", "@id": "/quality-metrics-fastqc/1ba86742-21c6-4ccc-bea5-7fbeea630347/", "display_title": "QualityMetricFastqc from 2018-11-26", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI9M795Y1/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRR5168131", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5168131"}]}, {"paired_end": "2", "href": "/files-fastq/4DNFIYB4JBLS/@@download/4DNFIYB4JBLS.fastq.gz", "file_size": 621161793, "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_classification": "raw file", "accession": "4DNFIYB4JBLS", "upload_key": "f4e831ba-e855-492c-b154-42e80f586dbb/4DNFIYB4JBLS.fastq.gz", "dbxrefs": ["SRA:SRR5168131"], "status": "released", "display_title": "4DNFIYB4JBLS.fastq.gz", "@id": "/files-fastq/4DNFIYB4JBLS/", "file_type_detailed": "reads (fastq)", "uuid": "f4e831ba-e855-492c-b154-42e80f586dbb", "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "uuid": "2d23d728-f0aa-47f2-ac9f-fe1620f516c2", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "status": "released", "@id": "/files-fastq/4DNFI9M795Y1/", "display_title": "4DNFI9M795Y1.fastq.gz", "accession": "4DNFI9M795Y1", "file_type_detailed": "reads (fastq)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "overall_quality_status": "PASS", "Sequence length": "54", "Total Sequences": 14115360, "uuid": "3e13790c-699c-465f-b83d-70c80f259d7d", "@id": "/quality-metrics-fastqc/3e13790c-699c-465f-b83d-70c80f259d7d/", "display_title": "QualityMetricFastqc from 2018-11-26", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIYB4JBLS/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRR5168131", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5168131"}]}, {"paired_end": "1", "href": "/files-fastq/4DNFIWF2PSMP/@@download/4DNFIWF2PSMP.fastq.gz", "file_size": 588933829, "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_classification": "raw file", "accession": "4DNFIWF2PSMP", "upload_key": "d0c1f419-e0c3-4769-bf24-0a9e118137c4/4DNFIWF2PSMP.fastq.gz", "dbxrefs": ["SRA:SRR5168132"], "status": "released", "display_title": "4DNFIWF2PSMP.fastq.gz", "@id": "/files-fastq/4DNFIWF2PSMP/", "file_type_detailed": "reads (fastq)", "uuid": "d0c1f419-e0c3-4769-bf24-0a9e118137c4", "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "uuid": "bfdabc1a-0692-446d-a92f-90abf40ecf7e", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "status": "released", "@id": "/files-fastq/4DNFIPM23CMG/", "display_title": "4DNFIPM23CMG.fastq.gz", "accession": "4DNFIPM23CMG", "file_type_detailed": "reads (fastq)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "overall_quality_status": "PASS", "Sequence length": "51", "Total Sequences": 14501384, "uuid": "83a818c4-23c9-45e1-9042-420eb9f08a69", "@id": "/quality-metrics-fastqc/83a818c4-23c9-45e1-9042-420eb9f08a69/", "display_title": "QualityMetricFastqc from 2018-11-26", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIWF2PSMP/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRR5168132", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5168132"}]}, {"paired_end": "2", "href": "/files-fastq/4DNFIPM23CMG/@@download/4DNFIPM23CMG.fastq.gz", "file_size": 602262284, "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_classification": "raw file", "accession": "4DNFIPM23CMG", "upload_key": "bfdabc1a-0692-446d-a92f-90abf40ecf7e/4DNFIPM23CMG.fastq.gz", "dbxrefs": ["SRA:SRR5168132"], "status": "released", "display_title": "4DNFIPM23CMG.fastq.gz", "@id": "/files-fastq/4DNFIPM23CMG/", "file_type_detailed": "reads (fastq)", "uuid": "bfdabc1a-0692-446d-a92f-90abf40ecf7e", "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "uuid": "d0c1f419-e0c3-4769-bf24-0a9e118137c4", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "status": "released", "@id": "/files-fastq/4DNFIWF2PSMP/", "display_title": "4DNFIWF2PSMP.fastq.gz", "accession": "4DNFIWF2PSMP", "file_type_detailed": "reads (fastq)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "overall_quality_status": "PASS", "Sequence length": "51", "Total Sequences": 14501384, "uuid": "67e64d58-97b8-4ce3-9300-ec5da95ca148", "@id": "/quality-metrics-fastqc/67e64d58-97b8-4ce3-9300-ec5da95ca148/", "display_title": "QualityMetricFastqc from 2018-11-26", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIPM23CMG/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRR5168132", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5168132"}]}, {"paired_end": "1", "href": "/files-fastq/4DNFIJAEADYJ/@@download/4DNFIJAEADYJ.fastq.gz", "file_size": 623873139, "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_classification": "raw file", "accession": "4DNFIJAEADYJ", "upload_key": "5177c08c-a549-4192-965d-e7984d9f8479/4DNFIJAEADYJ.fastq.gz", "dbxrefs": ["SRA:SRR5168133"], "status": "released", "display_title": "4DNFIJAEADYJ.fastq.gz", "@id": "/files-fastq/4DNFIJAEADYJ/", "file_type_detailed": "reads (fastq)", "uuid": "5177c08c-a549-4192-965d-e7984d9f8479", "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "uuid": "5b75ad35-08ea-47cd-97df-22624ea3524c", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "status": "released", "@id": "/files-fastq/4DNFI88RENW4/", "display_title": "4DNFI88RENW4.fastq.gz", "accession": "4DNFI88RENW4", "file_type_detailed": "reads (fastq)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "overall_quality_status": "PASS", "Sequence length": "54", "Total Sequences": 14222182, "uuid": "87a66e03-5a4e-4002-b2b1-6d3a3980562f", "@id": "/quality-metrics-fastqc/87a66e03-5a4e-4002-b2b1-6d3a3980562f/", "display_title": "QualityMetricFastqc from 2018-11-26", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIJAEADYJ/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRR5168133", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5168133"}]}, {"paired_end": "2", "href": "/files-fastq/4DNFI88RENW4/@@download/4DNFI88RENW4.fastq.gz", "file_size": 626013628, "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_classification": "raw file", "accession": "4DNFI88RENW4", "upload_key": "5b75ad35-08ea-47cd-97df-22624ea3524c/4DNFI88RENW4.fastq.gz", "dbxrefs": ["SRA:SRR5168133"], "status": "released", "display_title": "4DNFI88RENW4.fastq.gz", "@id": "/files-fastq/4DNFI88RENW4/", "file_type_detailed": "reads (fastq)", "uuid": "5b75ad35-08ea-47cd-97df-22624ea3524c", "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "uuid": "5177c08c-a549-4192-965d-e7984d9f8479", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "status": "released", "@id": "/files-fastq/4DNFIJAEADYJ/", "display_title": "4DNFIJAEADYJ.fastq.gz", "accession": "4DNFIJAEADYJ", "file_type_detailed": "reads (fastq)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "overall_quality_status": "PASS", "Sequence length": "54", "Total Sequences": 14222182, "uuid": "3bd00356-058c-470b-9c88-580d1925d303", "@id": "/quality-metrics-fastqc/3bd00356-058c-470b-9c88-580d1925d303/", "display_title": "QualityMetricFastqc from 2018-11-26", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI88RENW4/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRR5168133", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5168133"}]}], "status": "released", "aliases": ["leonid-mirny-lab:29094699-TCC-WTrep2"], "dbxrefs": ["GEO:GSM2453280"], "protocol": {"@type": ["Protocol", "Item"], "@id": "/protocols/a5ee0c2d-aa4a-4a39-a84d-c022bc2b0096/", "display_title": "TCC_protocol.pdf", "status": "released", "uuid": "a5ee0c2d-aa4a-4a39-a84d-c022bc2b0096", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNEXQ3PS6HH", "biosample": {"treatments_summary": "mock treatment (5.0d)", "status": "released", "uuid": "12c072ee-71b1-4cb3-8563-c0da586b921a", "biosample_type": "primary cells", "@id": "/biosamples/4DNBSJYQO69H/", "display_title": "4DNBSJYQO69H", "modifications_summary": "None", "@type": ["Biosample", "Item"], "accession": "4DNBSJYQO69H", "biosource_summary": "hepatocyte", "biosource": [{"lab": {"uuid": "06d4f485-ccf2-4332-b226-d8a05e5497db", "@type": ["Lab", "Item"], "display_title": "Francois Spitz, PASTEUR", "@id": "/labs/francois-spitz-lab/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.06d4f485-ccf2-4332-b226-d8a05e5497db"]}}, "award": {"@id": "/awards/external-award/", "display_title": "EXTERNAL AWARD", "status": "current", "@type": ["Award", "Item"], "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"synonyms": ["jecur", "iecur", "Entire liver"], "@type": ["OntologyTerm", "Item"], "term_name": "liver", "@id": "/ontology-terms/UBERON:0002107/", "preferred_name": "liver", "term_id": "UBERON:0002107", "status": "released", "slim_terms": [{"uuid": "111126bc-8535-4448-903e-854af460a233", "status": "released", "display_title": "endocrine system", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0000949/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "111182bc-8535-4448-903e-854af460a233", "status": "released", "display_title": "liver", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0002107/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "111121bc-8535-4448-903e-854af460a233", "status": "released", "display_title": "endoderm", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0000925/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "111129bc-8535-4448-903e-854af460a233", "status": "released", "display_title": "digestive system", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0001007/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "uuid": "111182bc-8535-4448-903e-854af460a233", "display_title": "liver", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["leonid-mirny-lab:Nipbl-flox-cre-hepatocytes"], "accession": "4DNSRMDUDYLW", "cell_line": {"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000182/", "slim_terms": [{"@type": ["OntologyTerm", "Item"], "uuid": "111126bc-8535-4448-903e-854af460a233", "status": "released", "display_title": "endocrine system", "@id": "/ontology-terms/UBERON:0000949/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "uuid": "111129bc-8535-4448-903e-854af460a233", "status": "released", "display_title": "digestive system", "@id": "/ontology-terms/UBERON:0001007/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "uuid": "111182bc-8535-4448-903e-854af460a233", "status": "released", "display_title": "liver", "@id": "/ontology-terms/UBERON:0002107/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "status": "current", "display_title": "cell", "@id": "/ontology-terms/GO:0005623/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "status": "released", "display_title": "cell", "@id": "/ontology-terms/CL:0000000/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "uuid": "111121bc-8535-4448-903e-854af460a233", "status": "released", "display_title": "endoderm", "@id": "/ontology-terms/UBERON:0000925/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "uuid": "a1b0f241-64ca-47a4-b9b8-19c28b5bdedb", "preferred_name": "hepatocyte", "term_id": "CL:0000182", "status": "released", "term_name": "hepatocyte", "display_title": "hepatocyte", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"@type": ["IndividualMouse", "Individual", "Item"], "uuid": "5483ddbf-d764-43a8-9c83-049f6237c64d", "status": "released", "@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": [{"uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "status": "current", "@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": {"name": "mouse", "status": "released", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "@type": ["Organism", "Item"], "@id": "/organisms/10090/", "display_title": "M. musculus", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "modifications": [], "treatments": [{"@id": "/treatments-agent/4c6c9ee6-3176-42ed-bde2-2e514301132e/", "duration_units": "day", "duration": 5.0, "chemical": "mock", "treatment_type": "Chemical", "display_title": "mock treatment (5.0d)", "@type": ["TreatmentAgent", "Treatment", "Item"], "status": "released", "uuid": "4c6c9ee6-3176-42ed-bde2-2e514301132e", "description": "mock injection", "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 2", "sop_mapping": {"has_sop": "No"}, "date_created": "2018-05-10T18:36:48.623563+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-04-24T16:48:56.374797+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": {"uuid": "e95e3626-aadc-464b-9ef0-0cdbea689744", "@id": "/experiment-types/tcc/", "status": "released", "@type": ["ExperimentType", "Item"], "title": "TCC", "display_title": "TCC", "experiment_category": "Sequencing", "assay_subclass_short": "Hi-C", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "ligation_volume": 5.0, "processed_files": [{"file_format": {"file_format": "bam", "display_title": "bam", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "uuid": "f7dbe9b8-35b1-4a71-b8ef-1a6524cfe8ff", "file_classification": "processed file", "accession": "4DNFIYSUPO3T", "upload_key": "f7dbe9b8-35b1-4a71-b8ef-1a6524cfe8ff/4DNFIYSUPO3T.bam", "href": "/files-processed/4DNFIYSUPO3T/@@download/4DNFIYSUPO3T.bam", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/f7dbe9b8-35b1-4a71-b8ef-1a6524cfe8ff/4DNFIYSUPO3T.bam", "file_size": 14243696294, "file_type": "alignments", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIYSUPO3T.bam", "@id": "/files-processed/4DNFIYSUPO3T/", "file_type_detailed": "alignments (bam)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric": {"@id": "/quality-metrics-bamqc/be85350a-78ab-4531-8d2a-3dd23e5a1d84/", "uuid": "be85350a-78ab-4531-8d2a-3dd23e5a1d84", "display_title": "QualityMetricBamqc from 2020-01-17", "overall_quality_status": "PASS", "status": "released", "@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Reads", "value": "114258179", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "21.692", "tooltip": "Percent of total reads (=24.78m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "17.033", "tooltip": "Percent of total reads (=19.46m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "5.372", "tooltip": "Percent of total reads (=6.14m)", "numberType": "percent"}, {"title": "Walks", "value": "0.755", "tooltip": "Percent of total reads (=0.86m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.082", "tooltip": "Percent of total reads (=0.09m)", "numberType": "percent"}]}, "external_references": [], "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 2, Techrep 1", "biosource_name": "hepatocyte", "lab_name": "4DN DCIC, HMS"}}, {"file_format": {"file_format": "pairs", "display_title": "pairs", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "uuid": "33d5d238-eb55-4a05-8b56-4fe8a330c793", "file_classification": "processed file", "accession": "4DNFIGZZ9LOB", "upload_key": "33d5d238-eb55-4a05-8b56-4fe8a330c793/4DNFIGZZ9LOB.pairs.gz", "href": "/files-processed/4DNFIGZZ9LOB/@@download/4DNFIGZZ9LOB.pairs.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/33d5d238-eb55-4a05-8b56-4fe8a330c793/4DNFIGZZ9LOB.pairs.gz", "file_size": 955183863, "file_type": "contact list-replicate", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIGZZ9LOB.pairs.gz", "@id": "/files-processed/4DNFIGZZ9LOB/", "file_type_detailed": "contact list-replicate (pairs)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric": {"@id": "/quality-metrics-pairsqc/bd3ff97e-c50b-423b-8ad9-b15a7d7598cb/", "uuid": "bd3ff97e-c50b-423b-8ad9-b15a7d7598cb", "display_title": "QualityMetricPairsqc from 2018-11-28", "overall_quality_status": "PASS", "Total reads": 63011187, "status": "released", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIGZZ9LOB/pairsqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "63011187", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "46.372", "tooltip": "Percent of filtered reads (=29.22m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "34.12", "tooltip": "Percent of filtered reads (=21.5m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "19.508", "tooltip": "Percent of filtered reads (=12.29m)", "numberType": "percent"}]}, "external_references": [], "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 2, Techrep 1", "biosource_name": "hepatocyte", "lab_name": "4DN DCIC, HMS"}}], "project_release": "2018-07-06", "digestion_enzyme": {"@id": "/enzymes/HindIII/", "name": "HindIII", "display_title": "HindIII", "uuid": "2ace2f00-c913-4bac-a6ef-0b316bc2108e", "@type": ["Enzyme", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"status": "current", "@type": ["Lab", "Item"], "display_title": "Leonid Mirny, MIT", "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/", "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/4DNEX1Y5NYNB/", "status": "released", "display_title": "TCC on hepatocyte with HindIII - 4DNEX1Y5NYNB", "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "8d6fbdeb-875c-4f89-8216-012d2fe3bbc2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "relationship_type": "control for"}, {"experiment": {"@id": "/experiments-hi-c/4DNEXACCWMEN/", "status": "released", "display_title": "TCC on hepatocyte with HindIII - 4DNEXACCWMEN", "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "f8f6f331-45ca-432f-a8b4-427cd29b41f7", "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/4DNEXQ3PS6HH/", "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "b410b0b7-5fad-4ceb-b3f1-80b673a4cb91", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "TCC on hepatocyte with HindIII - 4DNEXQ3PS6HH", "external_references": [{"ref": "GEO:GSM2453280", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2453280"}], "experiment_sets": [{"@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "37adea6e-6a27-41af-bf03-1f2edc8cbf91", "@id": "/experiment-set-replicates/4DNESAOU4AAQ/", "display_title": "4DNESAOU4AAQ", "status": "released", "accession": "4DNESAOU4AAQ", "experimentset_type": "replicate", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"display_title": "Schwarzer W et al. (2017) PMID:29094699", "title": "Two independent modes of chromatin organization revealed by cohesin removal.", "ID": "PMID:29094699", "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.", "journal": "Nature", "date_published": "2017-09-27", "@type": ["Publication", "Item"], "@id": "/publications/7343e7a5-1332-4adb-9265-cdd1381348eb/", "short_attribution": "Schwarzer W et al. (2017)", "uuid": "7343e7a5-1332-4adb-9265-cdd1381348eb", "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"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"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"], "ID": "PMID:29094699", "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.", "status": "current", "@type": ["Publication", "Item"], "uuid": "7343e7a5-1332-4adb-9265-cdd1381348eb", "@id": "/publications/7343e7a5-1332-4adb-9265-cdd1381348eb/", "display_title": "Schwarzer W et al. (2017) PMID:29094699", "title": "Two independent modes of chromatin organization revealed by cohesin removal.", "journal": "Nature", "date_published": "2017-09-27", "short_attribution": "Schwarzer W et al. (2017)", "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": []}