{"lab": {"@id": "/labs/wouter-de-laat-lab/", "@type": ["Lab", "Item"], "title": "Wouter de Laat, HUBRECHT", "uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "correspondence": [{"contact_email": "dy5sYWF0QGh1YnJlY2h0LmV1", "@id": "/users/d6570f35-5a6c-4b14-a818-d1c09491adb0/", "display_title": "Wouter de Laat"}], "status": "current", "display_title": "Wouter de Laat, HUBRECHT", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}, "award": {"description": "Funding source is from outside 4DN.", "center_title": "External", "@id": "/awards/external-award/", "center": "External", "project": "External", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "status": "current", "display_title": "EXTERNAL AWARD", "name": "external-award", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "files": [{"file_classification": "raw file", "status": "restricted", "href": "/files-fastq/4DNFI8LNKTCB/@@download/4DNFI8LNKTCB.fastq.gz", "uuid": "4840a884-6f23-4093-acf6-9678a0c58e83", "file_type_detailed": "reads (fastq)", "upload_key": "4840a884-6f23-4093-acf6-9678a0c58e83/4DNFI8LNKTCB.fastq.gz", "paired_end": "1", "file_type": "reads", "accession": "4DNFI8LNKTCB", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFI8LNKTCB/", "file_size": 16298851212, "display_title": "4DNFI8LNKTCB.fastq.gz", "quality_metric": {"display_title": "QualityMetricFastqc from 2023-04-22", "Total Sequences": 208365012, "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI8LNKTCB/fastqc_report.html", "Sequence length": "100", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/bfa992d9-8197-4f85-9fb4-9df76845544a/", "uuid": "bfa992d9-8197-4f85-9fb4-9df76845544a", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"accession": "4DNFIU8JMRNS", "display_title": "4DNFIU8JMRNS.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "paired_end": "2", "@id": "/files-fastq/4DNFIU8JMRNS/", "uuid": "694342a5-b232-49d7-add3-2709e961ae7d", "@type": ["FileFastq", "File", "Item"], "status": "restricted", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": []}, {"file_classification": "raw file", "status": "restricted", "href": "/files-fastq/4DNFIU8JMRNS/@@download/4DNFIU8JMRNS.fastq.gz", "uuid": "694342a5-b232-49d7-add3-2709e961ae7d", "file_type_detailed": "reads (fastq)", "upload_key": "694342a5-b232-49d7-add3-2709e961ae7d/4DNFIU8JMRNS.fastq.gz", "paired_end": "2", "file_type": "reads", "accession": "4DNFIU8JMRNS", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIU8JMRNS/", "file_size": 16702943898, "display_title": "4DNFIU8JMRNS.fastq.gz", "quality_metric": {"display_title": "QualityMetricFastqc from 2023-04-22", "Total Sequences": 208365012, "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIU8JMRNS/fastqc_report.html", "Sequence length": "100", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/48740d24-8b3b-437c-b258-5728f72f7f3b/", "uuid": "48740d24-8b3b-437c-b258-5728f72f7f3b", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"accession": "4DNFI8LNKTCB", "display_title": "4DNFI8LNKTCB.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "paired_end": "1", "@id": "/files-fastq/4DNFI8LNKTCB/", "uuid": "4840a884-6f23-4093-acf6-9678a0c58e83", "@type": ["FileFastq", "File", "Item"], "status": "restricted", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": []}, {"file_classification": "raw file", "status": "restricted", "href": "/files-fastq/4DNFIHNRAND1/@@download/4DNFIHNRAND1.fastq.gz", "uuid": "262ebd37-78c5-43e6-9eec-627934ffe997", "file_type_detailed": "reads (fastq)", "upload_key": "262ebd37-78c5-43e6-9eec-627934ffe997/4DNFIHNRAND1.fastq.gz", "paired_end": "1", "file_type": "reads", "accession": "4DNFIHNRAND1", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIHNRAND1/", "file_size": 3368256338, "display_title": "4DNFIHNRAND1.fastq.gz", "quality_metric": {"display_title": "QualityMetricFastqc from 2023-04-21", "Total Sequences": 65799299, "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIHNRAND1/fastqc_report.html", "Sequence length": "35-76", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/df68d18e-d397-45bd-be79-0bd9c3b65102/", "uuid": "df68d18e-d397-45bd-be79-0bd9c3b65102", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"accession": "4DNFIPLXGLR8", "display_title": "4DNFIPLXGLR8.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "paired_end": "2", "@id": "/files-fastq/4DNFIPLXGLR8/", "uuid": "a6496d22-ee03-49f1-8d7d-09aa6717a346", "@type": ["FileFastq", "File", "Item"], "status": "restricted", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": []}, {"file_classification": "raw file", "status": "restricted", "href": "/files-fastq/4DNFIPLXGLR8/@@download/4DNFIPLXGLR8.fastq.gz", "uuid": "a6496d22-ee03-49f1-8d7d-09aa6717a346", "file_type_detailed": "reads (fastq)", "upload_key": "a6496d22-ee03-49f1-8d7d-09aa6717a346/4DNFIPLXGLR8.fastq.gz", "paired_end": "2", "file_type": "reads", "accession": "4DNFIPLXGLR8", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIPLXGLR8/", "file_size": 3472590659, "display_title": "4DNFIPLXGLR8.fastq.gz", "quality_metric": {"display_title": "QualityMetricFastqc from 2023-04-21", "Total Sequences": 65799299, "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIPLXGLR8/fastqc_report.html", "Sequence length": "53-76", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/b7b7b18a-cc0b-4f64-b6c9-aaefd666add4/", "uuid": "b7b7b18a-cc0b-4f64-b6c9-aaefd666add4", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"accession": "4DNFIHNRAND1", "display_title": "4DNFIHNRAND1.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "paired_end": "1", "@id": "/files-fastq/4DNFIHNRAND1/", "uuid": "262ebd37-78c5-43e6-9eec-627934ffe997", "@type": ["FileFastq", "File", "Item"], "status": "restricted", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": []}, {"file_classification": "raw file", "status": "restricted", "href": "/files-fastq/4DNFIWK4R79U/@@download/4DNFIWK4R79U.fastq.gz", "uuid": "92a2c8b8-b395-482c-b476-6be4ea5cf601", "file_type_detailed": "reads (fastq)", "upload_key": "92a2c8b8-b395-482c-b476-6be4ea5cf601/4DNFIWK4R79U.fastq.gz", "paired_end": "1", "file_type": "reads", "accession": "4DNFIWK4R79U", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIWK4R79U/", "file_size": 3518335023, "display_title": "4DNFIWK4R79U.fastq.gz", "quality_metric": {"display_title": "QualityMetricFastqc from 2023-04-21", "Total Sequences": 66800033, "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIWK4R79U/fastqc_report.html", "Sequence length": "35-76", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/1ab4cb1b-971a-4a31-b853-2131d7fad264/", "uuid": "1ab4cb1b-971a-4a31-b853-2131d7fad264", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"accession": "4DNFIGD5C2ST", "display_title": "4DNFIGD5C2ST.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "paired_end": "2", "@id": "/files-fastq/4DNFIGD5C2ST/", "uuid": "b6871d86-6bb5-46e6-b06c-6dea65241e0d", "@type": ["FileFastq", "File", "Item"], "status": "restricted", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": []}, {"file_classification": "raw file", "status": "restricted", "href": "/files-fastq/4DNFIGD5C2ST/@@download/4DNFIGD5C2ST.fastq.gz", "uuid": "b6871d86-6bb5-46e6-b06c-6dea65241e0d", "file_type_detailed": "reads (fastq)", "upload_key": "b6871d86-6bb5-46e6-b06c-6dea65241e0d/4DNFIGD5C2ST.fastq.gz", "paired_end": "2", "file_type": "reads", "accession": "4DNFIGD5C2ST", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIGD5C2ST/", "file_size": 3604756474, "display_title": "4DNFIGD5C2ST.fastq.gz", "quality_metric": {"display_title": "QualityMetricFastqc from 2023-04-21", "Total Sequences": 66800033, "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIGD5C2ST/fastqc_report.html", "Sequence length": "54-76", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/80fd2e7c-52ed-4deb-aec8-584ded0514ae/", "uuid": "80fd2e7c-52ed-4deb-aec8-584ded0514ae", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"accession": "4DNFIWK4R79U", "display_title": "4DNFIWK4R79U.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "paired_end": "1", "@id": "/files-fastq/4DNFIWK4R79U/", "uuid": "92a2c8b8-b395-482c-b476-6be4ea5cf601", "@type": ["FileFastq", "File", "Item"], "status": "restricted", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": []}, {"file_classification": "raw file", "status": "restricted", "href": "/files-fastq/4DNFIZ99GAZE/@@download/4DNFIZ99GAZE.fastq.gz", "uuid": "4c007b7d-bd10-4e4a-ad8c-cc73c24c4b62", "file_type_detailed": "reads (fastq)", "upload_key": "4c007b7d-bd10-4e4a-ad8c-cc73c24c4b62/4DNFIZ99GAZE.fastq.gz", "paired_end": "1", "file_type": "reads", "accession": "4DNFIZ99GAZE", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIZ99GAZE/", "file_size": 5781743599, "display_title": "4DNFIZ99GAZE.fastq.gz", "quality_metric": {"display_title": "QualityMetricFastqc from 2023-04-21", "Total Sequences": 221458349, "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIZ99GAZE/fastqc_report.html", "Sequence length": "51", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/91b463b6-2002-4aaf-b743-7d25dba0fae6/", "uuid": "91b463b6-2002-4aaf-b743-7d25dba0fae6", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"accession": "4DNFIX5KS7A4", "display_title": "4DNFIX5KS7A4.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "paired_end": "2", "@id": "/files-fastq/4DNFIX5KS7A4/", "uuid": "b5427c14-4733-4280-a143-05e054b98611", "@type": ["FileFastq", "File", "Item"], "status": "restricted", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": []}, {"file_classification": "raw file", "status": "restricted", "href": "/files-fastq/4DNFIX5KS7A4/@@download/4DNFIX5KS7A4.fastq.gz", "uuid": "b5427c14-4733-4280-a143-05e054b98611", "file_type_detailed": "reads (fastq)", "upload_key": "b5427c14-4733-4280-a143-05e054b98611/4DNFIX5KS7A4.fastq.gz", "paired_end": "2", "file_type": "reads", "accession": "4DNFIX5KS7A4", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIX5KS7A4/", "file_size": 5942249041, "display_title": "4DNFIX5KS7A4.fastq.gz", "quality_metric": {"display_title": "QualityMetricFastqc from 2023-04-21", "Total Sequences": 221458349, "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIX5KS7A4/fastqc_report.html", "Sequence length": "51", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/d9a96796-effb-4754-8130-b8f02a0003f7/", "uuid": "d9a96796-effb-4754-8130-b8f02a0003f7", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"accession": "4DNFIZ99GAZE", "display_title": "4DNFIZ99GAZE.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "paired_end": "1", "@id": "/files-fastq/4DNFIZ99GAZE/", "uuid": "4c007b7d-bd10-4e4a-ad8c-cc73c24c4b62", "@type": ["FileFastq", "File", "Item"], "status": "restricted", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": []}, {"file_classification": "raw file", "status": "restricted", "href": "/files-fastq/4DNFI26CPNUK/@@download/4DNFI26CPNUK.fastq.gz", "uuid": "5338df03-4bd9-4ff5-a8f4-f1409cfc8671", "file_type_detailed": "reads (fastq)", "upload_key": "5338df03-4bd9-4ff5-a8f4-f1409cfc8671/4DNFI26CPNUK.fastq.gz", "paired_end": "1", "file_type": "reads", "accession": "4DNFI26CPNUK", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFI26CPNUK/", "file_size": 9178647, "display_title": "4DNFI26CPNUK.fastq.gz", "quality_metric": {"display_title": "QualityMetricFastqc from 2023-04-21", "Total Sequences": 258904, "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI26CPNUK/fastqc_report.html", "Sequence length": "35-76", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/29260465-1f66-4105-8a48-bb250ac2c812/", "uuid": "29260465-1f66-4105-8a48-bb250ac2c812", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"accession": "4DNFILIJJW2G", "display_title": "4DNFILIJJW2G.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "paired_end": "2", "@id": "/files-fastq/4DNFILIJJW2G/", "uuid": "40155f84-b76b-429c-909b-b9f840cc7515", "@type": ["FileFastq", "File", "Item"], "status": "restricted", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": []}, {"file_classification": "raw file", "status": "restricted", "href": "/files-fastq/4DNFILIJJW2G/@@download/4DNFILIJJW2G.fastq.gz", "uuid": "40155f84-b76b-429c-909b-b9f840cc7515", "file_type_detailed": "reads (fastq)", "upload_key": "40155f84-b76b-429c-909b-b9f840cc7515/4DNFILIJJW2G.fastq.gz", "paired_end": "2", "file_type": "reads", "accession": "4DNFILIJJW2G", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFILIJJW2G/", "file_size": 9288692, "display_title": "4DNFILIJJW2G.fastq.gz", "quality_metric": {"display_title": "QualityMetricFastqc from 2023-04-21", "Total Sequences": 258904, "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFILIJJW2G/fastqc_report.html", "Sequence length": "61-76", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/14b8700f-1f89-458e-9d7e-a6b4d8dfa870/", "uuid": "14b8700f-1f89-458e-9d7e-a6b4d8dfa870", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"accession": "4DNFI26CPNUK", "display_title": "4DNFI26CPNUK.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "paired_end": "1", "@id": "/files-fastq/4DNFI26CPNUK/", "uuid": "5338df03-4bd9-4ff5-a8f4-f1409cfc8671", "@type": ["FileFastq", "File", "Item"], "status": "restricted", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": []}], "status": "released", "aliases": ["wouter-de-laat-lab:experiment_hic_left_ventricle_p01160_B1_T1"], "protocol": {"status": "released", "uuid": "8a32fa33-c401-4f28-81d4-a30c26df87bc", "@id": "/protocols/8a32fa33-c401-4f28-81d4-a30c26df87bc/", "@type": ["Protocol", "Item"], "display_title": "In situ HiC", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNEX5WAFFCH", "biosample": {"modifications_summary": "None", "@id": "/biosamples/4DNBSF7YBH6R/", "accession": "4DNBSF7YBH6R", "treatments_summary": "None", "biosource_summary": "heart left ventricle", "display_title": "4DNBSF7YBH6R", "uuid": "126fd533-1191-408b-ad6c-bb18de1921a1", "@type": ["Biosample", "Item"], "status": "released", "biosample_type": "tissue", "biosource": [{"lab": {"uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "status": "current", "display_title": "Wouter de Laat, HUBRECHT", "@type": ["Lab", "Item"], "@id": "/labs/wouter-de-laat-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}, "award": {"uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "status": "current", "@type": ["Award", "Item"], "@id": "/awards/external-award/", "display_title": "EXTERNAL AWARD", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"status": "released", "term_id": "UBERON:0002084", "uuid": "5c3cfbf3-fc0a-482f-aa54-09163a7af31b", "display_title": "heart left ventricle", "@id": "/ontology-terms/UBERON:0002084/", "@type": ["OntologyTerm", "Item"], "preferred_name": "heart left ventricle", "slim_terms": [{"status": "released", "display_title": "circulatory system", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0001009/", "uuid": "111131bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "mesoderm", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0000926/", "uuid": "111120bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "heart", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0000948/", "uuid": "111187bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "synonyms": ["left cardiac ventricle", "left ventricle", "left ventricle of heart", "cardiac left ventricle"], "term_name": "heart left ventricle", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["wouter-de-laat-lab:LV_tissue_donor_p01160"], "accession": "4DNSR2O131XI", "individual": {"@type": ["IndividualHuman", "Individual", "Item"], "@id": "/individuals-human/4DNINJ46WLU3/", "uuid": "fd5aedde-db43-444a-b9f3-166aa38e6f03", "status": "released", "display_title": "4DNINJ46WLU3", "protected_data": true, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "description": "Primary cardiac tissue from the Left Ventricle of Donor P01160", "date_created": "2023-03-02T17:11:09.221201+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2023-05-05T14:31:39.327937+00:00"}, "biosource_type": "tissue", "cell_line_tier": "Unclassified", "public_release": "2023-05-05", "schema_version": "2", "project_release": "2023-05-05", "biosource_vendor": {"status": "released", "@id": "/vendors/magnet/", "display_title": "MAGNet", "@type": ["Vendor", "Item"], "uuid": "094c56d5-70ba-4855-874b-801af6c8e47b", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@id": "/biosources/4DNSR2O131XI/", "@type": ["Biosource", "Item"], "uuid": "d036e19b-8dd2-4fba-8bf7-7cfbdea8e761", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "heart left ventricle - 4DNSR2O131XI", "external_references": [], "biosource_name": "heart left ventricle", "biosource_category": ["Multicellular Tissue"], "organism": {"uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "@id": "/organisms/9606/", "status": "released", "@type": ["Organism", "Item"], "display_title": "H. sapiens", "name": "human", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pcr_cycles": 10, "sop_mapping": {"has_sop": "No"}, "date_created": "2023-04-20T09:44:58.176347+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-07-19T12:44:14.180412+00:00"}, "ligation_time": 960.0, "biotin_removed": "No", "digestion_time": 1200.0, "public_release": "2023-05-05", "schema_version": "2", "tagging_method": "biotin-14-dATP", "experiment_type": {"display_title": "in situ Hi-C", "experiment_category": "Sequencing", "uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "status": "released", "title": "in situ Hi-C", "@id": "/experiment-types/in-situ-hi-c/", "@type": ["ExperimentType", "Item"], "assay_subclass_short": "Hi-C", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "ligation_volume": 1.2, "processed_files": [{"accession": "4DNFIE6JZ2DS", "file_size": 97617529340, "display_title": "4DNFIE6JZ2DS.bam", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "file_format": "bam", "status": "released", "@id": "/file-formats/bam/", "@type": ["FileFormat", "Item"], "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "href": "/files-processed/4DNFIE6JZ2DS/@@download/4DNFIE6JZ2DS.bam", "status": "restricted", "@id": "/files-processed/4DNFIE6JZ2DS/", "@type": ["FileProcessed", "File", "Item"], "file_type": "alignments", "file_type_detailed": "alignments (bam)", "uuid": "f5236eb7-881a-45ee-870a-99aceff7f382", "file_classification": "processed file", "upload_key": "f5236eb7-881a-45ee-870a-99aceff7f382/4DNFIE6JZ2DS.bam", "quality_metric": {"uuid": "871e607c-50fe-4586-b749-2bbb055247d4", "overall_quality_status": "PASS", "@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "@id": "/quality-metrics-bamqc/871e607c-50fe-4586-b749-2bbb055247d4/", "display_title": "QualityMetricBamqc from 2023-04-23", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Reads", "value": "562681597", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "11.715", "tooltip": "Percent of total reads (=65.92m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "17.74", "tooltip": "Percent of total reads (=99.82m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "6.423", "tooltip": "Percent of total reads (=36.14m)", "numberType": "percent"}, {"title": "Walks", "value": "6.191", "tooltip": "Percent of total reads (=34.84m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.308", "tooltip": "Percent of total reads (=1.73m)", "numberType": "percent"}]}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Wouter de Laat, HUBRECHT", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "DpnII", "dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01160", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "heart left ventricle", "lab_name": "4DN DCIC, HMS"}}, {"accession": "4DNFIV27V1HH", "file_size": 7548707767, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/259e27c0-e0c6-4514-ab91-76e0ea116cdf/4DNFIV27V1HH.pairs.gz", "display_title": "4DNFIV27V1HH.pairs.gz", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "pairs", "status": "released", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "href": "/files-processed/4DNFIV27V1HH/@@download/4DNFIV27V1HH.pairs.gz", "status": "released", "@id": "/files-processed/4DNFIV27V1HH/", "@type": ["FileProcessed", "File", "Item"], "file_type": "contact list-replicate", "file_type_detailed": "contact list-replicate (pairs)", "uuid": "259e27c0-e0c6-4514-ab91-76e0ea116cdf", "file_classification": "processed file", "upload_key": "259e27c0-e0c6-4514-ab91-76e0ea116cdf/4DNFIV27V1HH.pairs.gz", "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIV27V1HH/pairsqc_report.html", "uuid": "aa99376c-72aa-47ba-9754-dd8bd01875da", "overall_quality_status": "PASS", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "@id": "/quality-metrics-pairsqc/aa99376c-72aa-47ba-9754-dd8bd01875da/", "Total reads": 325964824, "display_title": "QualityMetricPairsqc from 2023-04-23", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "325964824", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "39.478", "tooltip": "Percent of filtered reads (=128.68m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "25.527", "tooltip": "Percent of filtered reads (=83.21m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "34.995", "tooltip": "Percent of filtered reads (=114.07m)", "numberType": "percent"}]}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Wouter de Laat, HUBRECHT", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "DpnII", "dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01160", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "heart left ventricle", "lab_name": "4DN DCIC, HMS"}}], "project_release": "2023-05-05", "digestion_enzyme": {"name": "DpnII", "uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "display_title": "DpnII", "status": "released", "@id": "/enzymes/DpnII/", "@type": ["Enzyme", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "library_prep_kit": "TruSeq Nano kit (Illumina)", "crosslinking_time": 10.0, "biosample_quantity": 25.0, "crosslinking_method": "2% Formaldehyde", "fragment_size_range": "200-600", "fragmentation_method": "shearing", "ligation_temperature": 16.0, "average_fragment_size": 389, "digestion_temperature": 37.0, "other_processed_files": [{"type": "preliminary", "files": [{"@id": "/files-processed/4DNFIJUO5NF4/", "genome_assembly": "GRCh38", "file_type": "alignments", "display_title": "4DNFIJUO5NF4.bam", "uuid": "f387abc7-dfc5-406e-b58e-560eeb40468d", "@type": ["FileProcessed", "File", "Item"], "status": "restricted", "file_size": 97210527952, "accession": "4DNFIJUO5NF4", "file_type_detailed": "alignments (bam)", "href": "/files-processed/4DNFIJUO5NF4/@@download/4DNFIJUO5NF4.bam", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "status": "released", "file_format": "bam", "@id": "/file-formats/bam/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Wouter de Laat, HUBRECHT", "experiment_type": "in situ Hi-C", "experiment_bucket": "HiC Processing Pipeline - v0.3.0", "assay_info": "DpnII", "dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01160", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "heart left ventricle", "lab_name": "4DN DCIC, HMS"}, "last_modified": {"date_modified": "2024-10-04T17:26:55.056671+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/files-processed/4DNFIXWZJXP3/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/16f5b6bc-d9a5-4da2-8680-b62d1c5344cb/4DNFIXWZJXP3.pairs.gz", "genome_assembly": "GRCh38", "file_type": "contact list-replicate", "display_title": "4DNFIXWZJXP3.pairs.gz", "uuid": "16f5b6bc-d9a5-4da2-8680-b62d1c5344cb", "@type": ["FileProcessed", "File", "Item"], "status": "released", "file_size": 7169303164, "accession": "4DNFIXWZJXP3", "file_type_detailed": "contact list-replicate (pairs)", "href": "/files-processed/4DNFIXWZJXP3/@@download/4DNFIXWZJXP3.pairs.gz", "quality_metric": {"status": "released", "uuid": "360c8b57-889a-47c4-9595-fa43226c6bef", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIXWZJXP3/pairsqc_report.html", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "display_title": "QualityMetricPairsqc from 2024-07-10", "@id": "/quality-metrics-pairsqc/360c8b57-889a-47c4-9595-fa43226c6bef/", "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "345745689", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "39.464", "tooltip": "Percent of filtered reads (=136.44m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "25.348", "tooltip": "Percent of filtered reads (=87.64m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "35.188", "tooltip": "Percent of filtered reads (=121.66m)", "numberType": "percent"}]}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "pairs", "status": "released", "file_format": "pairs", "@id": "/file-formats/pairs/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Wouter de Laat, HUBRECHT", "experiment_type": "in situ Hi-C", "experiment_bucket": "HiC Processing Pipeline - v0.3.0", "assay_info": "DpnII", "dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01160", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "heart left ventricle", "lab_name": "4DN DCIC, HMS"}, "last_modified": {"date_modified": "2024-08-07T22:28:59.179566+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "title": "HiC Processing Pipeline - v0.3.0", "description": "These are files generated using the updated Hi-C processing pipeline. They should be largely similar to those available in the Processed Files tab, which were generated with the previous version of the standard pipeline.  One potential difference of note is that the version of cooler used to generate the mcool file has a bug fix to prevent a pixel duplication issue which is observed in some files generated by the previous version of the pipeline.  Another notable difference is that a filter is applied to remove reads with MAPQ scores below 30 prior to mcool file generation."}], "biosample_quantity_units": "mg", "crosslinking_temperature": 23.0, "library_preparation_date": "2015-11-02", "fragment_size_selection_method": "SPRI beads", "@id": "/experiments-hi-c/4DNEX5WAFFCH/", "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "3c6d2e39-dae3-414e-91ab-2e7299047207", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "in situ Hi-C on heart left ventricle with DpnII - 4DNEX5WAFFCH", "external_references": [], "experiment_sets": [{"experimentset_type": "replicate", "uuid": "edb53ef8-34e8-4b2a-b548-7e619e4aaf72", "accession": "4DNESW1HL87C", "display_title": "4DNESW1HL87C", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "@id": "/experiment-set-replicates/4DNESW1HL87C/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"display_title": "Bianchi V et al. (2019) doi:10.1101/705715", "uuid": "395b511a-5db1-4080-b5a7-b180769b7328", "status": "current", "authors": ["Bianchi V", "Geeven G", "Tucker N", "Hilvering CRE", "Hall AW", "Roselli C", "Hill MC", "Martin JF", "Margulies KB", "Ellinor PT", "deLaat W"], "@type": ["Publication", "Item"], "abstract": "Most disease-associated variants identified by population based genetic studies are non-coding, which compromises finding causative genes and mechanisms. Presumably they interact through looping with nearby genes to modulate transcription. Hi-C provides the most complete and unbiased method for genome-wide identification of potential regulatory interactions, but finding chromatin loops in Hi-C data remains difficult and tissue specific data are limited. We have generated Hi-C data from primary cardiac tissue and developed a method, peakHiC, for sensitive and quantitative loop calling to uncover the human heart regulatory interactome. We identify complex CTCF-dependent and -independent contact networks, with loops between coding and non-coding gene promoters, shared enhancers and repressive sites. Across the genome, enhancer interaction strength correlates with gene transcriptional output and loop dynamics follows CTCF, cohesin and H3K27Ac occupancy levels. Finally, we demonstrate that intersection of the human heart regulatory interactome with cardiovascular disease variants facilitates prioritizing disease-causative genes.", "@id": "/publications/395b511a-5db1-4080-b5a7-b180769b7328/", "title": "Detailed Regulatory Interaction Map of the Human Heart Facilitates Gene Discovery for Cardiovascular Disease", "short_attribution": "Bianchi V et al. (2019)", "ID": "doi:10.1101/705715", "date_published": "2019-07-17", "journal": "bioRxiv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"status": "current", "@id": "/publications/395b511a-5db1-4080-b5a7-b180769b7328/", "journal": "bioRxiv", "title": "Detailed Regulatory Interaction Map of the Human Heart Facilitates Gene Discovery for Cardiovascular Disease", "date_published": "2019-07-17", "abstract": "Most disease-associated variants identified by population based genetic studies are non-coding, which compromises finding causative genes and mechanisms. Presumably they interact through looping with nearby genes to modulate transcription. Hi-C provides the most complete and unbiased method for genome-wide identification of potential regulatory interactions, but finding chromatin loops in Hi-C data remains difficult and tissue specific data are limited. We have generated Hi-C data from primary cardiac tissue and developed a method, peakHiC, for sensitive and quantitative loop calling to uncover the human heart regulatory interactome. We identify complex CTCF-dependent and -independent contact networks, with loops between coding and non-coding gene promoters, shared enhancers and repressive sites. Across the genome, enhancer interaction strength correlates with gene transcriptional output and loop dynamics follows CTCF, cohesin and H3K27Ac occupancy levels. Finally, we demonstrate that intersection of the human heart regulatory interactome with cardiovascular disease variants facilitates prioritizing disease-causative genes.", "authors": ["Bianchi V", "Geeven G", "Tucker N", "Hilvering CRE", "Hall AW", "Roselli C", "Hill MC", "Martin JF", "Margulies KB", "Ellinor PT", "deLaat W"], "short_attribution": "Bianchi V et al. (2019)", "uuid": "395b511a-5db1-4080-b5a7-b180769b7328", "ID": "doi:10.1101/705715", "@type": ["Publication", "Item"], "display_title": "Bianchi V et al. (2019) doi:10.1101/705715", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Enzyme", "value": "DpnII", "combined": "Enzyme: DpnII"}, "experiment_summary": "in situ Hi-C on heart left ventricle with DpnII", "@context": "/terms/", "aggregated-items": {"badges": []}, "validation-errors": []}