{"lab": {"@type": ["Lab", "Item"], "@id": "/labs/rafael-casellas-lab/", "status": "current", "title": "Rafael Casellas, NIH", "display_title": "Rafael Casellas, NIH", "correspondence": [{"contact_email": "Y2FzZWxsYXJAbWFpbC5uaWguZ292", "@id": "/users/68b09572-0c3e-48c7-90a9-7bad21d6bac1/", "display_title": "Rafael Casellas"}], "uuid": "ce54a7f7-af8a-4505-8327-e430634f494b", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.ce54a7f7-af8a-4505-8327-e430634f494b"]}, "pi": {"error": "no view permissions"}}, "award": {"center": "External", "center_title": "External", "project": "External", "description": "Funding source is from outside 4DN.", "@id": "/awards/external-award/", "status": "current", "display_title": "EXTERNAL AWARD", "name": "external-award", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "99d33c29c6d1aa67779f15c2366d96f9", "status": "released", "aliases": ["4dn-dcic-lab:SRR7143489_2_fq"], "dbxrefs": ["SRA:SRR7143489"], "filename": "SRR7143489_2.fastq.gz", "accession": "4DNFI9ADPATH", "file_size": 111816980, "file_type": "reads", "instrument": "Illumina NextSeq 500", "paired_end": "2", "description": "SRA:SRR7143489 from Vian et. al, GEO:GSE98119", "file_format": {"status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "file_format": "fastq", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "read_length": 80, "date_created": "2018-11-27T18:10:46.100111+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2020-04-07T12:12:27.084924+00:00"}, "related_files": [{"file": {"accession": "4DNFIG3659QL", "uuid": "a35e3835-d858-4f70-a334-a19a04e775bb", "display_title": "4DNFIG3659QL.fastq.gz", "@type": ["FileFastq", "File", "Item"], "status": "released", "@id": "/files-fastq/4DNFIG3659QL/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "relationship_type": "paired with"}], "content_md5sum": "3da5728f524e802dd54476303b48d248", "public_release": "2019-11-25", "quality_metric": {"display_title": "QualityMetricFastqc from 2018-11-28", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "39dd69fd-a18c-4210-bbcb-5fd3443be9d4", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI9ADPATH/fastqc_report.html", "status": "released", "overall_quality_status": "PASS", "Total Sequences": 2366205, "Sequence length": "80", "@id": "/quality-metrics-fastqc/39dd69fd-a18c-4210-bbcb-5fd3443be9d4/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "schema_version": "2", "file_first_line": "@1", "project_release": "2019-11-25", "file_classification": "raw file", "@id": "/files-fastq/4DNFI9ADPATH/", "@type": ["FileFastq", "File", "Item"], "uuid": "fac5a593-1790-4ede-a5ab-24a834ba82ca", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFI9ADPATH.fastq.gz", "external_references": [{"ref": "SRA:SRR7143489", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR7143489"}], "experiments": [{"@id": "/experiments-hi-c/4DNEX4WKN1IH/", "uuid": "97902071-17c5-46ab-9a12-3f2a487afef6", "@type": ["ExperimentHiC", "Experiment", "Item"], "display_title": "in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI - 4DNEX4WKN1IH", "status": "released", "accession": "4DNEX4WKN1IH", "experiment_type": {"@id": "/experiment-types/in-situ-hi-c/", "status": "released", "@type": ["ExperimentType", "Item"], "display_title": "in situ Hi-C", "uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "title": "in situ Hi-C", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "biosample": {"@type": ["Biosample", "Item"], "display_title": "4DNBSP7UWF2E", "status": "released", "uuid": "e28c33b0-2514-4adf-9dcf-30ab84bfd932", "@id": "/biosamples/4DNBSP7UWF2E/", "accession": "4DNBSP7UWF2E", "modifications_summary": "None", "treatments_summary": "oligomycin treatment (0.1 \u03bcM, 30.0m) and 2-Deoxy-D-glucose treatment (5.0 mM, 30.0m)", "biosource_summary": "HCT116 with Crispr generated mClover and AID-tagged RAD21", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "biosource": [{"@type": ["Biosource", "Item"], "status": "released", "biosource_type": "immortalized cell line", "display_title": "HCT116 with Crispr generated mClover and AID-tagged RAD21 - 4DNSRG1Q4WCR", "uuid": "2b46c4e3-780f-40bc-929f-f1c1a2e181f1", "@id": "/biosources/4DNSRG1Q4WCR/", "cell_line_tier": "Unclassified", "modifications": [{"uuid": "1cc89862-1db3-48d0-8d1e-2f954f133e2e", "status": "released", "@type": ["Modification", "Item"], "@id": "/modifications/1cc89862-1db3-48d0-8d1e-2f954f133e2e/", "display_title": "Crispr generated mClover and AID-tagged RAD21", "genomic_change": "insertion", "override_modification_name": "Crispr generated mClover and AID-tagged RAD21", "modification_type": "Crispr", "target_of_mod": [{"display_title": "RAD21 gene", "organism_name": "human", "@id": "/bio-features/c3ce0816-5481-4342-b95b-6c8b93199744/", "status": "released", "@type": ["BioFeature", "Item"], "uuid": "c3ce0816-5481-4342-b95b-6c8b93199744", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "relevant_genes": [{"uuid": "a093769c-d596-4a26-8916-06ae491575ba", "@id": "/genes/5885/", "@type": ["Gene", "Item"], "status": "released", "display_title": "RAD21", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "feature_type": {"@id": "/ontology-terms/SO:0000704/", "@type": ["OntologyTerm", "Item"], "display_title": "gene", "status": "released", "uuid": "0231da78-1adc-4b8a-89b9-4f91908412a3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "organism": {"status": "released", "name": "human", "@id": "/organisms/9606/", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "@type": ["Organism", "Item"], "display_title": "H. sapiens", "scientific_name": "Homo sapiens", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"preferred_name": "HCT116", "@type": ["OntologyTerm", "Item"], "term_name": "HCT116", "display_title": "HCT116", "@id": "/ontology-terms/EFO:0002824/", "uuid": "49d090b2-5326-40ce-9c19-7a214c682272", "term_id": "EFO:0002824", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"@type": ["OntologyTerm", "Item"], "status": "released", "term_name": "colon", "uuid": "3e39f551-bc0b-4bee-b932-29d71956fb94", "term_id": "UBERON:0001155", "preferred_name": "colon", "@id": "/ontology-terms/UBERON:0001155/", "display_title": "colon", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"@id": "/individuals-human/4DNINJ6WV6L1/", "@type": ["IndividualHuman", "Individual", "Item"], "display_title": "4DNINJ6WV6L1", "protected_data": false, "uuid": "1f0f0999-c5b4-430e-8650-8ebb3491d699", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "digestion_enzyme": {"uuid": "d8da42d0-bc20-40e5-bacf-c263b8603e03", "display_title": "MboI", "@type": ["Enzyme", "Item"], "status": "released", "@id": "/enzymes/MboI/", "name": "MboI", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_sets": [{"experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNESJ5Y5ZN8/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "5b6bfdb3-c2c8-4833-a950-ba1b9208a5bc", "accession": "4DNESJ5Y5ZN8", "status": "released", "display_title": "4DNESJ5Y5ZN8", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2024-07-15T19:34:04.323795+00:00"}}], "file_type_detailed": "reads (fastq)", "track_and_facet_info": {"experimental_lab": "Rafael Casellas, NIH", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "MboI", "dataset": "Hi-C on RAD21-AID tagged HCT-116", "condition": "no ATP", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 with Crispr generated mClover and AID-tagged RAD21", "lab_name": "Rafael Casellas, NIH"}, "title": "4DNFI9ADPATH", "href": "/files-fastq/4DNFI9ADPATH/@@download/4DNFI9ADPATH.fastq.gz", "upload_key": "fac5a593-1790-4ede-a5ab-24a834ba82ca/4DNFI9ADPATH.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/fac5a593-1790-4ede-a5ab-24a834ba82ca/4DNFI9ADPATH.fastq.gz", "tsv_notes": "", "workflow_run_inputs": [{"display_title": "bwa-mem 0.2.6 run 2019-04-30 20:38:12.170756", "@id": "/workflow-runs-awsem/0a412723-9ecd-4962-b83d-3333d7495d3e/", "status": "released", "uuid": "0a412723-9ecd-4962-b83d-3333d7495d3e", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "out_bam", "value": {"status": "released", "uuid": "f2c2cac2-eb13-4dbe-893a-7ed33d207250", "display_title": "4DNFIR4GD7W5.bam", "@id": "/files-processed/4DNFIR4GD7W5/", "accession": "4DNFIR4GD7W5", "@type": ["FileProcessed", "File", "Item"], "file_format": {"status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "file_format": "bam", "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "input_files": [{"workflow_argument_name": "bwa_index", "value": {"accession": "4DNFIZQZ39L9", "filename": "hg38.bwaIndex.tgz", "display_title": "4DNFIZQZ39L9.bwaIndex.tgz", "@id": "/files-reference/4DNFIZQZ39L9/", "@type": ["FileReference", "File", "Item"], "status": "released", "uuid": "1f53df95-4cf3-41cc-971d-81bb16c486dd", "file_format": {"display_title": "bwaIndex", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "bwaIndex", "uuid": "d13d06cf-218e-4f61-55f0-91f226248b2c", "@id": "/file-formats/bwaIndex/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "fastq1", "value": {"accession": "4DNFIG3659QL", "filename": "SRR7143489_1.fastq.gz", "display_title": "4DNFIG3659QL.fastq.gz", "@id": "/files-fastq/4DNFIG3659QL/", "@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "a35e3835-d858-4f70-a334-a19a04e775bb", "file_format": {"display_title": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "fastq2", "value": {"accession": "4DNFI9ADPATH", "filename": "SRR7143489_2.fastq.gz", "display_title": "4DNFI9ADPATH.fastq.gz", "@id": "/files-fastq/4DNFI9ADPATH/", "@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "fac5a593-1790-4ede-a5ab-24a834ba82ca", "file_format": {"display_title": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"title": "Alignment for Hi-C using bwa-mem 0.2.6", "display_title": "Alignment for Hi-C using bwa-mem 0.2.6 - 4DNWF84NFOQP", "@id": "/workflows/4DNWF84NFOQP/", "uuid": "3feedadc-50f9-4bb4-919b-09a8b731d0cc", "@type": ["Workflow", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "md5 0.2.6 run 2018-11-27 23:07:44.969470", "@id": "/workflow-runs-awsem/b7987a4e-2e96-4e78-b477-8c6b51388b1d/", "status": "released", "uuid": "b7987a4e-2e96-4e78-b477-8c6b51388b1d", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "report"}], "input_files": [{"workflow_argument_name": "input_file", "value": {"accession": "4DNFI9ADPATH", "filename": "SRR7143489_2.fastq.gz", "display_title": "4DNFI9ADPATH.fastq.gz", "@id": "/files-fastq/4DNFI9ADPATH/", "@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "fac5a593-1790-4ede-a5ab-24a834ba82ca", "file_format": {"display_title": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"title": "md5 0.2.6", "display_title": "md5 0.2.6 - 4DNWF2HFF82B", "@id": "/workflows/4DNWF2HFF82B/", "uuid": "c77a117b-9a58-477e-aaa5-291a109a99f6", "@type": ["Workflow", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "fastqc v1 run 2018-11-28 00:52:18.057877", "@id": "/workflow-runs-awsem/c2baa16b-e18e-40c3-a8cf-4a73e824b8cb/", "status": "released", "uuid": "c2baa16b-e18e-40c3-a8cf-4a73e824b8cb", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "report_zip", "value_qc": {"display_title": "QualityMetricFastqc from 2018-11-28", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI9ADPATH/fastqc_report.html", "status": "released", "uuid": "39dd69fd-a18c-4210-bbcb-5fd3443be9d4", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/39dd69fd-a18c-4210-bbcb-5fd3443be9d4/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "input_files": [{"workflow_argument_name": "input_fastq", "value": {"accession": "4DNFI9ADPATH", "filename": "SRR7143489_2.fastq.gz", "display_title": "4DNFI9ADPATH.fastq.gz", "@id": "/files-fastq/4DNFI9ADPATH/", "@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "fac5a593-1790-4ede-a5ab-24a834ba82ca", "file_format": {"display_title": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"title": "FastQC v1", "display_title": "FastQC v1 - 4DNWFAW5VTA5", "@id": "/workflows/4DNWFAW5VTA5/", "uuid": "2324ad76-ff37-4157-8bcc-3ce72b7dace9", "@type": ["Workflow", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "fastq-first-line v2 run 2020-04-07 12:07:15.164741", "@id": "/workflow-runs-awsem/adf7ea4d-acf2-43aa-8d42-f1695b8588b4/", "status": "released", "uuid": "adf7ea4d-acf2-43aa-8d42-f1695b8588b4", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "first_line"}], "input_files": [{"workflow_argument_name": "fastq", "value": {"accession": "4DNFI9ADPATH", "filename": "SRR7143489_2.fastq.gz", "display_title": "4DNFI9ADPATH.fastq.gz", "@id": "/files-fastq/4DNFI9ADPATH/", "@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "fac5a593-1790-4ede-a5ab-24a834ba82ca", "file_format": {"display_title": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"title": "Getting first line of fastq file", "display_title": "Getting first line of fastq file - 4DNWFASTQFO1", "@id": "/workflows/4DNWFASTQFO1/", "uuid": "93a1a931-d55d-4623-adfb-0fa735daf6ae", "@type": ["Workflow", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "workflow_run_outputs": [], "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}