{"lab": {"@type": ["Lab", "Item"], "@id": "/labs/keji-zhao-lab/", "status": "current", "title": "Keji Zhao, NHLBI", "display_title": "Keji Zhao, NHLBI", "correspondence": [{"contact_email": "emhhb2tAbmhsYmkubmloLmdvdg==", "@id": "/users/44d2c6b9-15a0-4991-b84e-601e432df30f/", "display_title": "Keji Zhao"}], "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}, "pi": {"error": "no view permissions"}}, "tags": ["2018_01_internal", "2018_01_internal_JA"], "award": {"center_title": "TCPA - Zhao", "project": "4DN", "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.", "@id": "/awards/TCPA-2017-08/", "status": "current", "display_title": "DEVELOPMENT OF TRAC-LOOP, A NOVEL TECHNIQUE TO DETECT GENOME-WIDE CHROMATIN INTERACTIONS", "name": "TCPA-2017-08", "uuid": "0116e3c0-fb5a-491c-a9c2-8e17df70bfc1", "@type": ["Award", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "a4fd228f36f764c1438debdd4598b245", "status": "released", "aliases": ["zhaolab:SequencingFile_h1wa01_b2_S4_L008_R2_001"], "filename": "KZ1512_GB4974_S4_L008_R2_001.fastq.gz", "accession": "4DNFIVEYCSDC", "file_size": 1943308280, "file_type": "reads", "instrument": "Hiseq3000", "paired_end": "2", "extra_files": [], "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": 50, "date_created": "2018-02-09T16:05:40.226891+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-02-20T00:44:32.738806+00:00"}, "related_files": [{"file": {"accession": "4DNFI2LUHMUT", "uuid": "c455b0eb-29f1-4eed-802f-eed1bbd6db31", "display_title": "4DNFI2LUHMUT.fastq.gz", "@type": ["FileFastq", "File", "Item"], "status": "released", "@id": "/files-fastq/4DNFI2LUHMUT/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "relationship_type": "paired with"}], "content_md5sum": "6b207020e4be3b2549b065ab9fa8a579", "public_release": "2025-01-28", "quality_metric": {"display_title": "QualityMetricFastqc from 2018-02-11", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "fb17ae9d-3d4d-476b-8ebd-363c7c311651", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIVEYCSDC/fastqc_report.html", "status": "released", "overall_quality_status": "PASS", "Total Sequences": 55790885, "Sequence length": "50", "@id": "/quality-metrics-fastqc/fb17ae9d-3d4d-476b-8ebd-363c7c311651/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "schema_version": "2", "file_first_line": "@J00139:261:HLJ2VBBXX:8:1101:2818:1455 2:N:0:NCCTGAGC+NCTACTCT", "project_release": "2018-02-15", "flowcell_details": [], "file_classification": "raw file", "@id": "/files-fastq/4DNFIVEYCSDC/", "@type": ["FileFastq", "File", "Item"], "uuid": "79a85c69-be92-453a-8f5f-216c5417287d", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFIVEYCSDC.fastq.gz", "external_references": [], "experiments": [{"@id": "/experiments-seq/4DNEX9Q3KJG8/", "uuid": "5c444c9f-12f3-4050-ba0c-6823550a43c5", "@type": ["ExperimentSeq", "Experiment", "Item"], "display_title": "TrAC-loop on H1-hESC (Tier 1) - 4DNEX9Q3KJG8", "status": "released", "accession": "4DNEX9Q3KJG8", "experiment_type": {"@id": "/experiment-types/trac-loop/", "status": "released", "@type": ["ExperimentType", "Item"], "display_title": "TrAC-loop", "uuid": "13fc76db-939a-4b92-b076-2caa7525b5c9", "title": "TrAC-loop", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "biosample": {"@type": ["Biosample", "Item"], "display_title": "4DNBSJ5QL7QY", "status": "released", "uuid": "c779d5e6-6efa-412e-b5e9-d7ad0413c59a", "@id": "/biosamples/4DNBSJ5QL7QY/", "accession": "4DNBSJ5QL7QY", "modifications_summary": "None", "treatments_summary": "None", "biosource_summary": "H1-hESC (Tier 1)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "biosource": [{"@type": ["Biosource", "Item"], "status": "released", "biosource_type": "stem cell derived cell line", "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "@id": "/biosources/4DNSRV3SKQ8M/", "cell_line_tier": "Tier 1", "modifications": [], "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": "H1-hESC", "@type": ["OntologyTerm", "Item"], "term_name": "H1-hESC", "display_title": "H1-hESC", "@id": "/ontology-terms/EFO:0003042/", "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "term_id": "EFO:0003042", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"@type": ["OntologyTerm", "Item"], "status": "released", "term_name": "stem cell", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "term_id": "CL:0000034", "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "display_title": "stem cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"@id": "/individuals-human/4DNIN3RG3ZKE/", "@type": ["IndividualHuman", "Individual", "Item"], "display_title": "4DNIN3RG3ZKE", "protected_data": false, "uuid": "c97775b7-3d00-4132-9598-863797b8ef14", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "cell_culture_details": [{"status": "released", "in_vitro_differentiated": "No", "@type": ["BiosampleCellCulture", "Item"], "uuid": "7f901da7-5d3a-478c-bb4d-4d0c992ea96c", "@id": "/biosample-cell-cultures/7f901da7-5d3a-478c-bb4d-4d0c992ea96c/", "display_title": "BiosampleCellCulture from 2018-02-09", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "experiment_sets": [{"experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNESQBZ6L8Z/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "9b1063f5-c891-44a8-b44a-3b4879257366", "accession": "4DNESQBZ6L8Z", "status": "released", "display_title": "4DNESQBZ6L8Z", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2025-01-28T20:59:19.860726+00:00"}}], "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 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "Keji Zhao, NHLBI"}, "title": "4DNFIVEYCSDC", "href": "/files-fastq/4DNFIVEYCSDC/@@download/4DNFIVEYCSDC.fastq.gz", "upload_key": "79a85c69-be92-453a-8f5f-216c5417287d/4DNFIVEYCSDC.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/79a85c69-be92-453a-8f5f-216c5417287d/4DNFIVEYCSDC.fastq.gz", "tsv_notes": "", "workflow_run_inputs": [{"display_title": "md5 0.0.4 run 2018-02-09 16:22:06.088300", "@id": "/workflow-runs-awsem/77780aa8-0922-4cb0-bd76-b5175ab95a38/", "status": "released", "uuid": "77780aa8-0922-4cb0-bd76-b5175ab95a38", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "report"}], "input_files": [{"workflow_argument_name": "input_file", "value": {"accession": "4DNFIVEYCSDC", "filename": "KZ1512_GB4974_S4_L008_R2_001.fastq.gz", "display_title": "4DNFIVEYCSDC.fastq.gz", "@id": "/files-fastq/4DNFIVEYCSDC/", "@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "79a85c69-be92-453a-8f5f-216c5417287d", "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 0.0.4", "display_title": "md5 0.0.4 - 4DNWFG6JOL4D", "@id": "/workflows/4DNWFG6JOL4D/", "uuid": "d3f25cd3-e726-4b3c-a022-48f844474b41", "@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 2018-02-11 22:37:24.901624", "@id": "/workflow-runs-awsem/72eb2b0f-87fe-48e9-928a-0b4026850df4/", "status": "released", "uuid": "72eb2b0f-87fe-48e9-928a-0b4026850df4", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "report_zip", "value_qc": {"display_title": "QualityMetricFastqc from 2018-02-11", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIVEYCSDC/fastqc_report.html", "status": "released", "uuid": "fb17ae9d-3d4d-476b-8ebd-363c7c311651", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/fb17ae9d-3d4d-476b-8ebd-363c7c311651/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "input_files": [{"workflow_argument_name": "input_fastq", "value": {"accession": "4DNFIVEYCSDC", "filename": "KZ1512_GB4974_S4_L008_R2_001.fastq.gz", "display_title": "4DNFIVEYCSDC.fastq.gz", "@id": "/files-fastq/4DNFIVEYCSDC/", "@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "79a85c69-be92-453a-8f5f-216c5417287d", "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": "bwa-mem 0.2.6 run 2018-02-28 08:02:30.323461", "@id": "/workflow-runs-awsem/5766345a-a406-41ee-93b3-515b5f8915e5/", "status": "released", "uuid": "5766345a-a406-41ee-93b3-515b5f8915e5", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "out_bam", "value": {"status": "released", "uuid": "ca663a63-dd91-43be-a85a-fb2b2ae96d08", "display_title": "4DNFIY29ZHML.bam", "@id": "/files-processed/4DNFIY29ZHML/", "accession": "4DNFIY29ZHML", "@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": "fastq1", "value": {"accession": "4DNFI2LUHMUT", "filename": "KZ1512_GB4974_S4_L008_R1_001.fastq.gz", "display_title": "4DNFI2LUHMUT.fastq.gz", "@id": "/files-fastq/4DNFI2LUHMUT/", "@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "c455b0eb-29f1-4eed-802f-eed1bbd6db31", "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": "4DNFIVEYCSDC", "filename": "KZ1512_GB4974_S4_L008_R2_001.fastq.gz", "display_title": "4DNFIVEYCSDC.fastq.gz", "@id": "/files-fastq/4DNFIVEYCSDC/", "@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "79a85c69-be92-453a-8f5f-216c5417287d", "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": "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": {"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": "fastq-first-line v2 run 2020-04-09 06:50:53.432436", "@id": "/workflow-runs-awsem/b0cd66f4-7fbe-4409-b9a5-efddc256b69d/", "status": "released", "uuid": "b0cd66f4-7fbe-4409-b9a5-efddc256b69d", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "first_line"}], "input_files": [{"workflow_argument_name": "fastq", "value": {"accession": "4DNFIVEYCSDC", "filename": "KZ1512_GB4974_S4_L008_R2_001.fastq.gz", "display_title": "4DNFIVEYCSDC.fastq.gz", "@id": "/files-fastq/4DNFIVEYCSDC/", "@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "79a85c69-be92-453a-8f5f-216c5417287d", "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": []}