{"lab": {"title": "Keji Zhao, NHLBI", "display_title": "Keji Zhao, NHLBI", "@id": "/labs/keji-zhao-lab/", "correspondence": [{"contact_email": "emhhb2tAbmhsYmkubmloLmdvdg==", "@id": "/users/44d2c6b9-15a0-4991-b84e-601e432df30f/", "display_title": "Keji Zhao"}], "status": "current", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "@type": ["Lab", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "tags": ["2018_01_internal"], "award": {"status": "current", "@id": "/awards/TCPA-2017-08/", "uuid": "0116e3c0-fb5a-491c-a9c2-8e17df70bfc1", "display_title": "DEVELOPMENT OF TRAC-LOOP, A NOVEL TECHNIQUE TO DETECT GENOME-WIDE CHROMATIN INTERACTIONS", "@type": ["Award", "Item"], "center_title": "TCPA - Zhao", "description": "TCPA: Most current techniques for genome-wide analysis of chromatin interactions are based on the \nchromosome conformation capture (3C) technique. Because the traditional Hi-C technique uses a 6-bp restriction enzyme to cut chromatin, which usually finds one cleavage site every 5000bp in the genome, it does not have sufficient resolution for identification of enhancer-promoter interactions. Significant improvement has been achieved by the in situ Hi-C protocol, which uses a 4-bp cutter enzyme and reaches a resolution of about 1kb, thus enabling identification of specific enhancer-promoter interactions at high-resolution. However, this method requires a costly sequencing depth of 5 to 10 billions of paired-end tags (PETs) per library, which prohibits its application to a large number of samples. Other 3C-based techniques have been developed to focus on interactions at selected regions by capture Hi-C or tethered through specific proteins by ChIA-PET have helped to increase resolution by focusing on potential regulatory regions of the genome. However, a recent study compared \nchromatin interactions detected by fluorescence in situ hybridization (FISH) and 3C-based assays and found a high degree of discrepancy between the two techniques, suggesting that cross-validation of interaction data using different strategies is critical. \nWe propose to develop a novel technique, TrAC-loop, for Transposition-mediated Analysis of \nChromatin loops in the genome. The method does not require SDS-mediated partial decondensation of chromatin, restriction enzyme digestion, or proximity-based ligation of chromatin fragments. TrAC-loop directly captures interacting chromatin regions by Tn5-mediated transposition of a bivalent ME (mosaic end) linker without disrupting the nuclear structure. Thus, this novel strategy avoids potential artifacts derived from SDS-mediated partial decondensation of chromatin, restriction enzyme digestion and proximity-based re-ligation of chromatin fragments that are used in the 3C assays. Our strategy represents a shift in paradigm. All other genome-wide methods of mapping chromatin interactions use 3C-based techniques, whereas ours use transposition. Although transposition has been used to tag \nchromatin, this is the first time it is used to join chromatin segments.", "name": "TCPA-2017-08", "project": "4DN", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "a1a609782aee769de6a717c5d2381de5", "status": "released", "aliases": ["zhaolab:SequencingFile_gm12878_b3_S5_L005_R1_001"], "filename": "KZ1515_GB4775_S5_L005_R1_001.fastq.gz", "accession": "4DNFIASBU8FG", "file_size": 992947766, "file_type": "reads", "instrument": "Hiseq3000", "paired_end": "1", "extra_files": [], "file_format": {"@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "display_title": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "read_length": 50, "date_created": "2018-02-09T16:05:32.639623+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-02-20T00:56:11.148063+00:00"}, "related_files": [{"file": {"@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIT2BW6NR.fastq.gz", "@id": "/files-fastq/4DNFIT2BW6NR/", "uuid": "e19617dc-1672-42a4-b607-fda54819e401", "status": "released", "accession": "4DNFIT2BW6NR", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "relationship_type": "paired with"}], "content_md5sum": "a1042ba19e4f2c3f5f7e51cfaddf7e2b", "public_release": "2025-01-28", "quality_metric": {"Sequence length": "50", "@id": "/quality-metrics-fastqc/5570f966-e67e-4bf5-8565-bb4710e45495/", "uuid": "5570f966-e67e-4bf5-8565-bb4710e45495", "overall_quality_status": "PASS", "status": "released", "display_title": "QualityMetricFastqc from 2018-02-11", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIASBU8FG/fastqc_report.html", "Total Sequences": 31765355, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "schema_version": "2", "file_first_line": "@J00139:265:HNGGHBBXX:5:1101:4411:1437 1:N:0:NCTACGCT+NATGCAGT", "project_release": "2018-02-15", "flowcell_details": [], "file_classification": "raw file", "@id": "/files-fastq/4DNFIASBU8FG/", "@type": ["FileFastq", "File", "Item"], "uuid": "983eb20a-db6b-44ed-87f1-be16f702b927", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFIASBU8FG.fastq.gz", "external_references": [], "experiments": [{"@id": "/experiments-seq/4DNEX15HMJS9/", "status": "released", "display_title": "TrAC-loop on GM12878 (Tier 1) - 4DNEX15HMJS9", "uuid": "41eb4f1b-ca6e-4dea-b2cd-5940276060cb", "accession": "4DNEX15HMJS9", "@type": ["ExperimentSeq", "Experiment", "Item"], "biosample": {"biosource_summary": "GM12878 (Tier 1)", "modifications_summary": "None", "treatments_summary": "None", "@type": ["Biosample", "Item"], "status": "released", "@id": "/biosamples/4DNBS4Z97V85/", "uuid": "10777498-f5ba-49d0-98b9-3c690c156c43", "display_title": "4DNBS4Z97V85", "accession": "4DNBS4Z97V85", "biosource": [{"cell_line_tier": "Tier 1", "biosource_type": "immortalized cell line", "display_title": "GM12878 (Tier 1) - 4DNSRH17RFKR", "@type": ["Biosource", "Item"], "status": "released", "@id": "/biosources/4DNSRH17RFKR/", "uuid": "c9affe27-c09e-46be-ac1c-a614df02587a", "organism": {"name": "human", "status": "released", "display_title": "H. sapiens", "@id": "/organisms/9606/", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000945/", "status": "released", "term_name": "lymphocyte of B lineage", "display_title": "B-lymphocyte", "term_id": "CL:0000945", "uuid": "0c98ef0b-9a03-43f3-b409-fb091e62e2f8", "preferred_name": "B-lymphocyte", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "modifications": [], "individual": {"status": "released", "protected_data": false, "@id": "/individuals-human/4DNINGWYEI15/", "display_title": "4DNINGWYEI15", "uuid": "3ec2ff42-6f8c-42e9-a1f0-0fa69f482b85", "@type": ["IndividualHuman", "Individual", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "cell_line": {"status": "released", "preferred_name": "GM12878", "uuid": "b9668b9a-be39-47de-8eab-5bf1b0854417", "term_name": "GM12878", "@id": "/ontology-terms/EFO:0002784/", "term_id": "EFO:0002784", "@type": ["OntologyTerm", "Item"], "display_title": "GM12878", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "cell_culture_details": [{"display_title": "BiosampleCellCulture from 2018-02-09", "in_vitro_differentiated": "No", "@type": ["BiosampleCellCulture", "Item"], "@id": "/biosample-cell-cultures/1db12513-e595-4e60-a3d5-74060436bc9a/", "uuid": "1db12513-e595-4e60-a3d5-74060436bc9a", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"status": "released", "uuid": "13fc76db-939a-4b92-b076-2caa7525b5c9", "@type": ["ExperimentType", "Item"], "title": "TrAC-loop", "@id": "/experiment-types/trac-loop/", "display_title": "TrAC-loop", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_sets": [{"@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "@id": "/experiment-set-replicates/4DNES5BDII8F/", "status": "released", "uuid": "c5db8085-92bd-4d06-a22c-7958e4a78e19", "experimentset_type": "replicate", "display_title": "4DNES5BDII8F", "accession": "4DNES5BDII8F", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "last_modified": {"date_modified": "2025-01-28T20:59:20.185377+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "file_type_detailed": "reads (fastq)", "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "raw file", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "Keji Zhao, NHLBI"}, "title": "4DNFIASBU8FG", "href": "/files-fastq/4DNFIASBU8FG/@@download/4DNFIASBU8FG.fastq.gz", "upload_key": "983eb20a-db6b-44ed-87f1-be16f702b927/4DNFIASBU8FG.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/983eb20a-db6b-44ed-87f1-be16f702b927/4DNFIASBU8FG.fastq.gz", "tsv_notes": "", "workflow_run_inputs": [{"display_title": "md5 0.0.4 run 2018-02-09 16:13:30.669357", "uuid": "f1c34e41-65e0-43bb-a872-5199caf8bf51", "@id": "/workflow-runs-awsem/f1c34e41-65e0-43bb-a872-5199caf8bf51/", "status": "released", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "report"}], "input_files": [{"workflow_argument_name": "input_file", "value": {"filename": "KZ1515_GB4775_S5_L005_R1_001.fastq.gz", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIASBU8FG", "display_title": "4DNFIASBU8FG.fastq.gz", "uuid": "983eb20a-db6b-44ed-87f1-be16f702b927", "@id": "/files-fastq/4DNFIASBU8FG/", "status": "released", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "display_title": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"status": "released", "@type": ["Workflow", "Item"], "display_title": "md5 0.0.4 - 4DNWFG6JOL4D", "title": "md5 0.0.4", "uuid": "d3f25cd3-e726-4b3c-a022-48f844474b41", "@id": "/workflows/4DNWFG6JOL4D/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "fastqc v1 run 2018-02-11 22:39:58.115302", "uuid": "83458224-a0fd-4ddd-9c5e-a608294a2a88", "@id": "/workflow-runs-awsem/83458224-a0fd-4ddd-9c5e-a608294a2a88/", "status": "released", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "report_zip", "value_qc": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "5570f966-e67e-4bf5-8565-bb4710e45495", "display_title": "QualityMetricFastqc from 2018-02-11", "@id": "/quality-metrics-fastqc/5570f966-e67e-4bf5-8565-bb4710e45495/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIASBU8FG/fastqc_report.html", "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "input_files": [{"workflow_argument_name": "input_fastq", "value": {"filename": "KZ1515_GB4775_S5_L005_R1_001.fastq.gz", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIASBU8FG", "display_title": "4DNFIASBU8FG.fastq.gz", "uuid": "983eb20a-db6b-44ed-87f1-be16f702b927", "@id": "/files-fastq/4DNFIASBU8FG/", "status": "released", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "display_title": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"status": "released", "@type": ["Workflow", "Item"], "display_title": "FastQC v1 - 4DNWFAW5VTA5", "title": "FastQC v1", "uuid": "2324ad76-ff37-4157-8bcc-3ce72b7dace9", "@id": "/workflows/4DNWFAW5VTA5/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "bwa-mem 0.2.6 run 2018-02-28 08:07:29.628972", "uuid": "05870812-128d-41c1-aca3-56d9e5f783f8", "@id": "/workflow-runs-awsem/05870812-128d-41c1-aca3-56d9e5f783f8/", "status": "released", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "out_bam", "value": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIJ4B8ZTV", "uuid": "276fbc9c-74c5-400a-9fc8-03b884e78b55", "@id": "/files-processed/4DNFIJ4B8ZTV/", "display_title": "4DNFIJ4B8ZTV.bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "input_files": [{"workflow_argument_name": "fastq1", "value": {"filename": "KZ1515_GB4775_S5_L005_R1_001.fastq.gz", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIASBU8FG", "display_title": "4DNFIASBU8FG.fastq.gz", "uuid": "983eb20a-db6b-44ed-87f1-be16f702b927", "@id": "/files-fastq/4DNFIASBU8FG/", "status": "released", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "display_title": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "fastq2", "value": {"filename": "KZ1515_GB4775_S5_L005_R2_001.fastq.gz", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIT2BW6NR", "display_title": "4DNFIT2BW6NR.fastq.gz", "uuid": "e19617dc-1672-42a4-b607-fda54819e401", "@id": "/files-fastq/4DNFIT2BW6NR/", "status": "released", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "display_title": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "bwa_index", "value": {"filename": "hg38.bwaIndex.tgz", "@type": ["FileReference", "File", "Item"], "accession": "4DNFIZQZ39L9", "display_title": "4DNFIZQZ39L9.bwaIndex.tgz", "uuid": "1f53df95-4cf3-41cc-971d-81bb16c486dd", "@id": "/files-reference/4DNFIZQZ39L9/", "status": "released", "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-91f226248b2c", "@id": "/file-formats/bwaIndex/", "display_title": "bwaIndex", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "bwaIndex", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"status": "released", "@type": ["Workflow", "Item"], "display_title": "Alignment for Hi-C using bwa-mem 0.2.6 - 4DNWF84NFOQP", "title": "Alignment for Hi-C using bwa-mem 0.2.6", "uuid": "3feedadc-50f9-4bb4-919b-09a8b731d0cc", "@id": "/workflows/4DNWF84NFOQP/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "fastq-first-line v2 run 2020-04-09 06:55:49.087910", "uuid": "ec5a1a6b-18a4-4742-a52c-59146be2e459", "@id": "/workflow-runs-awsem/ec5a1a6b-18a4-4742-a52c-59146be2e459/", "status": "released", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "first_line"}], "input_files": [{"workflow_argument_name": "fastq", "value": {"filename": "KZ1515_GB4775_S5_L005_R1_001.fastq.gz", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIASBU8FG", "display_title": "4DNFIASBU8FG.fastq.gz", "uuid": "983eb20a-db6b-44ed-87f1-be16f702b927", "@id": "/files-fastq/4DNFIASBU8FG/", "status": "released", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "display_title": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"status": "released", "@type": ["Workflow", "Item"], "display_title": "Getting first line of fastq file - 4DNWFASTQFO1", "title": "Getting first line of fastq file", "uuid": "93a1a931-d55d-4623-adfb-0fa735daf6ae", "@id": "/workflows/4DNWFASTQFO1/", "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": []}