{"lab": {"correspondence": [{"contact_email": "c3RldmVoQGZoY3JjLm9yZw==", "@id": "/users/bed386a9-7ee0-4ac0-ab50-741018edf928/", "display_title": "Steve Henikoff"}], "uuid": "3a41e042-a9f3-4205-a28a-4c20ba2edda2", "status": "current", "display_title": "Steve Henikoff, FREDHUTCH", "@type": ["Lab", "Item"], "title": "Steve Henikoff, FREDHUTCH", "@id": "/labs/steve-henikoff-lab/", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3a41e042-a9f3-4205-a28a-4c20ba2edda2"]}}, "tags": ["4DN Joint Analysis 2018"], "award": {"display_title": "TETHERED NUCLEASE STRATEGIES FOR IN SITU MAPPING OF 3D NUCLEAR ORGANIZATION", "status": "current", "name": "TCPA-2017-04", "project": "4DN", "description": "TCPA: The 4D Nucleome project focuses on describing the 3D organization within the nucleus, with \nthe ultimate goal of understanding this organization in mechanistic terms. Our project uses novel methods for epigenomic profiling that detect 3D contact sites without cross-linking and with much higher resolution than current technologies. We recently introduced a novel strategy for chromatin profiling called CUT&RUN (Cleavage Under Targets & Release Using Nuclease), in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the supernatant for paired-end DNA sequencing. The method yields precise transcription factor (TF) profiles, yet is simple to perform and is inherently robust, with extremely low backgrounds requiring ~1/10 th the sequencing depth of chromatin immunoprecipitation (ChIP). CUT&RUN binding and cleavage occurs in situ, allowing for both quantitative high-resolution chromatin mapping and probing of the 3D chromatin environment. Together with our new native ChIP-seq protocol, we distinguish direct \u201canchor\u201d sites of a \nchromatin-bound protein from contacting sites without fixation, a kind of inference has not been possible with current methods of interrogating 3D chromatin architecture. We have two Aims: First, we will annotate the genome at high density for CTCF and cohesin sites, distinguishing between anchor and contact sites in 4D Nucleome cell lines. Second, we will continue development of a new replacement technology for 3D contact mapping, using CUT&RUN as a \u201cfront-end\u201d for proximity ligation (CUT&PASTE \u2013 Cleave Under Targets & Polish And Splice Touching Ends), building on our novel sci-HiC protocol for high-resolution TF-specific 3D interaction mapping. By annotating more contact sites in genomes and assigning the directionality of contacts, we move towards a mechanistic model of how topology within the nucleus is organized. Participation in the 4DN program would provide the opportunity to compare and integrate our CUT&RUN/PASTE datasets with 4DN datasets on common cell lines and differentiating tissues, ideally positioning consortium investigators to adopt our alternative strategy for their own 4DN efforts.", "@type": ["Award", "Item"], "uuid": "4ddcac2d-72b6-40a7-ac68-67efba21a0d0", "@id": "/awards/TCPA-2017-04/", "center_title": "TCPA - Henikoff", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "pi": {"error": "no view permissions"}}, "files": [{"accession": "4DNFIPEG1M36", "file_size": 109928058, "upload_key": "cd8c9581-cccd-491e-a2d4-63962e3f03b3/4DNFIPEG1M36.fastq.gz", "display_title": "4DNFIPEG1M36.fastq.gz", "status": "released", "href": "/files-fastq/4DNFIPEG1M36/@@download/4DNFIPEG1M36.fastq.gz", "file_classification": "raw file", "file_type": "reads", "file_type_detailed": "reads (fastq)", "@id": "/files-fastq/4DNFIPEG1M36/", "uuid": "cd8c9581-cccd-491e-a2d4-63962e3f03b3", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "uuid": "1b83f489-b98a-4a48-b975-653b8ea450cd", "@id": "/files-fastq/4DNFIOGGQHBL/", "status": "released", "display_title": "4DNFIOGGQHBL.fastq.gz", "accession": "4DNFIOGGQHBL", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"display_title": "QualityMetricFastqc from 2018-02-27", "overall_quality_status": "PASS", "uuid": "d0f7d26a-466a-4690-8fa4-10e0d310b79a", "Total Sequences": 4000000, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "25", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIPEG1M36/fastqc_report.html", "@id": "/quality-metrics-fastqc/d0f7d26a-466a-4690-8fa4-10e0d310b79a/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFIOGGQHBL", "file_size": 112096895, "upload_key": "1b83f489-b98a-4a48-b975-653b8ea450cd/4DNFIOGGQHBL.fastq.gz", "display_title": "4DNFIOGGQHBL.fastq.gz", "status": "released", "href": "/files-fastq/4DNFIOGGQHBL/@@download/4DNFIOGGQHBL.fastq.gz", "file_classification": "raw file", "file_type": "reads", "file_type_detailed": "reads (fastq)", "@id": "/files-fastq/4DNFIOGGQHBL/", "uuid": "1b83f489-b98a-4a48-b975-653b8ea450cd", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "uuid": "cd8c9581-cccd-491e-a2d4-63962e3f03b3", "@id": "/files-fastq/4DNFIPEG1M36/", "status": "released", "display_title": "4DNFIPEG1M36.fastq.gz", "accession": "4DNFIPEG1M36", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"display_title": "QualityMetricFastqc from 2018-02-27", "overall_quality_status": "PASS", "uuid": "0b1c5a16-2151-463d-bb89-975e1bfe68b6", "Total Sequences": 4000000, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "25", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIOGGQHBL/fastqc_report.html", "@id": "/quality-metrics-fastqc/0b1c5a16-2151-463d-bb89-975e1bfe68b6/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFIBO59EVI", "file_size": 110118388, "upload_key": "e2c60212-0f81-4a2e-b54e-331b0ef6baab/4DNFIBO59EVI.fastq.gz", "display_title": "4DNFIBO59EVI.fastq.gz", "status": "released", "href": "/files-fastq/4DNFIBO59EVI/@@download/4DNFIBO59EVI.fastq.gz", "file_classification": "raw file", "file_type": "reads", "file_type_detailed": "reads (fastq)", "@id": "/files-fastq/4DNFIBO59EVI/", "uuid": "e2c60212-0f81-4a2e-b54e-331b0ef6baab", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "uuid": "9cf461f0-39e8-4aea-8ca8-86ea16ca4caf", "@id": "/files-fastq/4DNFISY5ED3Q/", "status": "released", "display_title": "4DNFISY5ED3Q.fastq.gz", "accession": "4DNFISY5ED3Q", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"display_title": "QualityMetricFastqc from 2018-02-27", "overall_quality_status": "PASS", "uuid": "62c4fbb3-3520-409a-8e82-b2e263880026", "Total Sequences": 4000000, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "25", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIBO59EVI/fastqc_report.html", "@id": "/quality-metrics-fastqc/62c4fbb3-3520-409a-8e82-b2e263880026/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFISY5ED3Q", "file_size": 112024974, "upload_key": "9cf461f0-39e8-4aea-8ca8-86ea16ca4caf/4DNFISY5ED3Q.fastq.gz", "display_title": "4DNFISY5ED3Q.fastq.gz", "status": "released", "href": "/files-fastq/4DNFISY5ED3Q/@@download/4DNFISY5ED3Q.fastq.gz", "file_classification": "raw file", "file_type": "reads", "file_type_detailed": "reads (fastq)", "@id": "/files-fastq/4DNFISY5ED3Q/", "uuid": "9cf461f0-39e8-4aea-8ca8-86ea16ca4caf", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "uuid": "e2c60212-0f81-4a2e-b54e-331b0ef6baab", "@id": "/files-fastq/4DNFIBO59EVI/", "status": "released", "display_title": "4DNFIBO59EVI.fastq.gz", "accession": "4DNFIBO59EVI", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"display_title": "QualityMetricFastqc from 2018-03-06", "overall_quality_status": "PASS", "uuid": "d909b43a-7b30-44fd-8702-4323cce72d43", "Total Sequences": 4000000, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "25", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFISY5ED3Q/fastqc_report.html", "@id": "/quality-metrics-fastqc/d909b43a-7b30-44fd-8702-4323cce72d43/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFI3DIN9EH", "file_size": 85006641, "upload_key": "39778b01-9cfc-4bce-ab2f-40ae5f398dee/4DNFI3DIN9EH.fastq.gz", "display_title": "4DNFI3DIN9EH.fastq.gz", "status": "released", "href": "/files-fastq/4DNFI3DIN9EH/@@download/4DNFI3DIN9EH.fastq.gz", "file_classification": "raw file", "file_type": "reads", "file_type_detailed": "reads (fastq)", "@id": "/files-fastq/4DNFI3DIN9EH/", "uuid": "39778b01-9cfc-4bce-ab2f-40ae5f398dee", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "uuid": "5d2b2d85-bd6e-4351-a73b-08348c564b24", "@id": "/files-fastq/4DNFI8VFV8IK/", "status": "released", "display_title": "4DNFI8VFV8IK.fastq.gz", "accession": "4DNFI8VFV8IK", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"display_title": "QualityMetricFastqc from 2018-02-27", "overall_quality_status": "PASS", "uuid": "25298123-bb9c-4f48-b95e-153f600f4623", "Total Sequences": 3097280, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "25", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI3DIN9EH/fastqc_report.html", "@id": "/quality-metrics-fastqc/25298123-bb9c-4f48-b95e-153f600f4623/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFI8VFV8IK", "file_size": 86460088, "upload_key": "5d2b2d85-bd6e-4351-a73b-08348c564b24/4DNFI8VFV8IK.fastq.gz", "display_title": "4DNFI8VFV8IK.fastq.gz", "status": "released", "href": "/files-fastq/4DNFI8VFV8IK/@@download/4DNFI8VFV8IK.fastq.gz", "file_classification": "raw file", "file_type": "reads", "file_type_detailed": "reads (fastq)", "@id": "/files-fastq/4DNFI8VFV8IK/", "uuid": "5d2b2d85-bd6e-4351-a73b-08348c564b24", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "uuid": "39778b01-9cfc-4bce-ab2f-40ae5f398dee", "@id": "/files-fastq/4DNFI3DIN9EH/", "status": "released", "display_title": "4DNFI3DIN9EH.fastq.gz", "accession": "4DNFI3DIN9EH", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"display_title": "QualityMetricFastqc from 2018-02-27", "overall_quality_status": "PASS", "uuid": "10a467d0-dd18-48ed-a3e7-fc5377c00582", "Total Sequences": 3097280, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "25", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI8VFV8IK/fastqc_report.html", "@id": "/quality-metrics-fastqc/10a467d0-dd18-48ed-a3e7-fc5377c00582/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "notes": "Old Target: 1c9fcffc-0a2e-4c68-a5fc-1a50d6672a1a", "status": "released", "aliases": ["henikoff_lab:cutnrun_H1_K27a_20sec_rep1"], "antibody": {"antibody_name": "anti-H3K27ac", "@id": "/antibodys/anti-H3K27ac-ab4729/", "uuid": "e7dd27f6-6f91-463f-865b-fb673f168924", "antibody_product_no": "ab4729", "display_title": "anti-H3K27ac (Abcam, ab4729)", "@type": ["Antibody", "Item"], "status": "released", "antibody_vendor": {"@type": ["Vendor", "Item"], "title": "Abcam", "display_title": "Abcam", "uuid": "13540f71-312d-441e-a2dc-ea0dfa7e0841", "@id": "/vendors/abcam/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "protocol": {"display_title": "Protocol_Direct-Ligation_CUTnRUN_2.6.18.pdf", "@id": "/protocols/aba6ee1b-e138-4751-8da1-7b31821d254a/", "status": "released", "uuid": "aba6ee1b-e138-4751-8da1-7b31821d254a", "@type": ["Protocol", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNEXNGY75VF", "biosample": {"status": "released", "biosample_type": "stem cells", "modifications_summary": "None", "@type": ["Biosample", "Item"], "display_title": "4DNBS2VVWK2V", "accession": "4DNBS2VVWK2V", "biosource_summary": "H1-hESC (Tier 1)", "uuid": "70812637-9d80-4cd4-bf44-89127f0c7c9d", "treatments_summary": "None", "@id": "/biosamples/4DNBS2VVWK2V/", "biosource": [{"lab": {"@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "url": "https://www.wicell.org/home/stem-cell-lines/catalog-of-stem-cell-lines/wa01.cmsx", "award": {"@type": ["Award", "Item"], "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "@id": "/awards/1U01CA200059-01/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "term_name": "stem cell", "term_id": "CL:0000034", "display_title": "stem cell", "synonyms": ["animal stem cell"], "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "status": "released", "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/ontology-terms/CL:0000034/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["dcic:h1wa01T1", "4dn-dcic-lab:h1wa01T1"], "accession": "4DNSRV3SKQ8M", "cell_line": {"@type": ["OntologyTerm", "Item"], "status": "released", "preferred_name": "H1-hESC", "term_name": "H1-hESC", "term_id": "EFO:0003042", "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "synonyms": ["H1"], "@id": "/ontology-terms/EFO:0003042/", "display_title": "H1-hESC", "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"status": "released", "display_title": "4DNIN3RG3ZKE", "@type": ["IndividualHuman", "Individual", "Item"], "@id": "/individuals-human/4DNIN3RG3ZKE/", "uuid": "c97775b7-3d00-4132-9598-863797b8ef14", "protected_data": false, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "references": [], "description": "Homo sapiens male H1 embryonic stem cell (WA01)", "date_created": "2017-04-10T01:14:03.094143+00:00", "submitted_by": {"error": "no view permissions"}, "SOP_cell_line": {"status": "released", "@id": "/protocols/c0319394-33f9-4f4e-8e20-b3d413c4eed6/", "@type": ["Protocol", "Item"], "uuid": "c0319394-33f9-4f4e-8e20-b3d413c4eed6", "display_title": "4DN_H1_SOP-220126_2.pdf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-08-29T13:33:38.896302+00:00"}, "modifications": [], "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "public_release": "2017-07-26", "schema_version": "2", "project_release": "2017-07-26", "biosource_vendor": {"uuid": "41784f69-697d-42c2-82b1-b52bc5ea3519", "@id": "/vendors/wicellorg/", "@type": ["Vendor", "Item"], "status": "released", "display_title": "WiCell.org", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "alternate_accessions": [], "@id": "/biosources/4DNSRV3SKQ8M/", "@type": ["Biosource", "Item"], "uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "external_references": [], "biosource_name": "H1-hESC (Tier 1)", "biosource_category": ["H1-hESC", "Human stem cell"], "organism": {"status": "released", "name": "human", "@id": "/organisms/9606/", "@type": ["Organism", "Item"], "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "display_title": "H. sapiens", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "modifications": [], "badges": [{"messages": ["Biosample missing doubling_number"], "badge": {"badge_classification": "Warning", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "title": "Biosample Metadata Incomplete", "display_title": "Biosample Metadata Incomplete", "badge_icon": "/static/img/badges/biosample-icon.svg", "@id": "/badges/biosample-metadata-incomplete/", "status": "released", "warning": "Biosample Metadata Incomplete", "@type": ["Badge", "Item"], "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "treatments": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "description": "CUT&RUN on H1 cells using H3K27ac (ab4729) with a digestion time of 20sec replicate 1", "follows_sop": "Yes", "sop_mapping": {"has_sop": "No"}, "date_created": "2018-02-23T08:43:22.159394+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-11-22T17:27:14.985046+00:00"}, "reaction_time": 20.0, "public_release": "2019-06-27", "schema_version": "5", "antibody_lot_id": "GR144577-1", "experiment_type": {"uuid": "64166b28-444f-46d6-bf98-f419eb72ccac", "status": "released", "assay_subclass_short": "DNA binding", "@id": "/experiment-types/cut-n-run/", "display_title": "CUT&RUN", "title": "CUT&RUN", "experiment_category": "Sequencing", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"href": "/files-processed/4DNFILVB7TTJ/@@download/4DNFILVB7TTJ.bam", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/1a2150db-b594-452e-80e0-71f57d94dc9f/4DNFILVB7TTJ.bam", "file_classification": "processed file", "display_title": "4DNFILVB7TTJ.bam", "file_format": {"@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "upload_key": "1a2150db-b594-452e-80e0-71f57d94dc9f/4DNFILVB7TTJ.bam", "file_size": 4352447193, "status": "released", "file_type_detailed": "read positions (bam)", "accession": "4DNFILVB7TTJ", "@type": ["FileProcessed", "File", "Item"], "file_type": "read positions", "uuid": "1a2150db-b594-452e-80e0-71f57d94dc9f", "@id": "/files-processed/4DNFILVB7TTJ/", "external_references": [], "track_and_facet_info": {"experimental_lab": "Steve Henikoff, FREDHUTCH", "experiment_type": "CUT&RUN", "experiment_bucket": "processed file", "assay_info": "H3K27ac", "dataset": "H3K27ac - H1-ESC", "condition": "ab4729", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"error": "no view permissions"}], "project_release": "2018-03-02", "targeted_factor": [{"uuid": "1d471e44-7f9a-4a9b-b6a9-f66878243b23", "@type": ["BioFeature", "Item"], "display_title": "H3K27ac", "status": "released", "@id": "/bio-features/1d471e44-7f9a-4a9b-b6a9-f66878243b23/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "antibody_dilution": "1: 200", "biosample_quantity": 1000000.0, "3p_adenylation_time": 60.0, "experiment_relation": [{"experiment": {"uuid": "21d8d814-59ec-490d-8bdb-41268d57e21d", "display_title": "CUT&RUN against IgG protein on H1-hESC (Tier 1) - 4DNEXT4MG8XY", "@type": ["ExperimentSeq", "Experiment", "Item"], "@id": "/experiments-seq/4DNEXT4MG8XY/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "relationship_type": "controlled by"}], "biosample_quantity_units": "cells", "library_preparation_date": "2017-11-28", "3p_adenylation_temperature": 58.0, "@id": "/experiments-seq/4DNEXNGY75VF/", "@type": ["ExperimentSeq", "Experiment", "Item"], "uuid": "6f50b6c1-2595-4915-ba26-1dcf2a5ad172", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "CUT&RUN against H3K27ac on H1-hESC (Tier 1) - 4DNEXNGY75VF", "external_references": [], "experiment_sets": [{"display_title": "4DNES33LF165", "experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNES33LF165/", "accession": "4DNES33LF165", "status": "released", "uuid": "1ccbaf1f-36d5-4274-bb0f-1e649d92d758", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "publications_of_exp": [], "experiment_categorizer": {"field": "Target", "value": "H3K27ac", "combined": "Target: H3K27ac"}, "experiment_summary": "CUT&RUN against H3K27ac on H1-hESC (Tier 1)", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBS2VVWK2V/", "embedded_path": "biosample.badges", "item": {"messages": ["Biosample missing doubling_number"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}]}, "validation-errors": []}