{"lab": {"title": "Carl Wu, JHU", "@type": ["Lab", "Item"], "status": "current", "correspondence": [{"contact_email": "d3VjQGpodS5lZHU=", "@id": "/users/3b01cb1e-6923-4271-8c65-653d83678502/", "display_title": "Carl Wu"}], "display_title": "Carl Wu, JHU", "@id": "/labs/carl-wu-lab/", "uuid": "cab8fd2f-201b-4a09-bfd5-e72e902acfdf", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.cab8fd2f-201b-4a09-bfd5-e72e902acfdf"]}}, "tags": ["many_replicates"], "award": {"center_title": "Ha", "display_title": "CHROMATIN FUNCTION DURING TRANSCRIPTION AND DNA REPAIR AT SINGLE MOLECULE RESOLUTION IN LIVING CELLS", "description": "RT-CDF: Eukaryotic genomes are packaged in chromatin, linear arrays of nucleosomes in association with nonhistone proteins performing structural, enzymatic, and regulatory functions. This proposal aims to elucidate the interplay between chromatin organization, remodeling and modification and two key nuclear functions: gene transcription and DNA repair, using single molecule imaging in living cells to obtain comprehensive datasets on the real-time dynamics of transcription and DNA repair proteins and chromatin motions, and their integration with theory and modeling with predictive power.  We will apply single molecule tracking (SMT) to image at high spatiotemporal resolution the organization, dynamics, regulation and function of a prototypical pioneer transcription factor, GAGA factor (GAF) in Drosophila. We will image the global and local nuclear organization and dynamics of wild-type and mutant GAF binding to cognate DNA elements genome-wide, and at Hsp70 promoters in live hemocytes. We will image the global and local dynamics of eight prominent chromatin and transcription protein effectors linked to GAF functions. SMT datasets from the factors imaged above are used to construct theoretical models for GAF interactions with chromatin targets and test models by experimental manipulation. Studies will be extended to human NF-Y, a distinct pioneer factor that makes accessible chromatin at the Hsp70 promoter in human cells.  We will examine the interplay between chromatin organization and dynamics and DNA repair, using very fast (vf) CRISPR that can generate a double strand break (DSB) anywhere in the genome with high spatiotemporal resolution. We will determine DSB repair kinetics and chromatin reorganization through time- resolved chromatin analysis and real-time imaging of repair factors after generating DSB. We will determine the impact of topologically associated domains and loop extrusion on chromatin modifications and relaxations that accompany DNA repair, and integrate chromatin and DNA repair kinetics datasets to construct theoretical models for 4D chromatin reorganization during DSB repair. We will employ a series of chromatin remodeler and DNA damage response mutants to document causal relationships, and expand the reach of vfCRISPR to other DNA repair processes including base excision repair and mismatch repair.  We will merge the above approaches to explore how DNA repair-mediated chromatin alterations affect transcription in human cells, and reciprocally, how transcription and associated chromatin changes influence DNA repair dynamics. We will image dynamics of pioneer and non-pioneer factors and key DNA repair enzymes at the active Hsp70 gene in living human cells, varying the timing of DSB and heat shock to evaluate the influence of DSB on different stages of transcription. Simultaneous imaging of labeled locus and nascent Hsp70 mRNA will reveal how transcription affects dynamics of the damaged locus.", "uuid": "b9ff5f2d-68aa-4a4b-9c3d-54707e1798ec", "status": "current", "name": "1U01DK127432-01", "@id": "/awards/1U01DK127432-01/", "project": "4DN", "@type": ["Award", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["carl-wu-lab:Halo-GAF_deltaQ_slow"], "accession": "4DNES32KCISG", "condition": "Halo-GAF deltaQ, slow tracking", "description": "SPT (slow tracking) on Halo-GAF mutant (deletion of C-terminal Q-rich domains)", "date_created": "2021-11-02T18:49:23.276320+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "SPT for GAGA transcription factor", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-11-12T08:51:01.739080+00:00"}, "public_release": "2021-11-12", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-mic/4DNEXW29OTJU/", "@type": ["ExperimentMic", "Experiment", "Item"], "display_title": "SPT on embryonic/larval hemocyte (Drosophila) - 4DNEXW29OTJU", "uuid": "1713155f-1bb9-4ddf-b5dd-16d307bbcd77", "status": "released", "accession": "4DNEXW29OTJU", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_headers": [{"lab": {"display_title": "4DN DCIC, HMS", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "**SPT**\n\nSingle particle tracking (SPT) is a method to track the position\n of a single molecule over time in live cells. Advances in \nmicroscopy and molecular biology techniques have enabled a \nbroad range of applications.\n\nThe protocol involves preparing the target molecule to be \nidentifiable under the microscope, tracking its position over \ntime and analyzing its trajectory. Generally, the preparation \nof the molecule of interest is performed by genetically \nmodifying it with tags followed by the binding of reporter \nmolecules such as fluorescent dyes. However, depending on the \nmolecule of interest, the goal of the experiment and the type \nof microscope used, different techniques are also implemented.\n Following the preparation of the molecule, a high-resolution \nmicroscope is used to take snapshots of the position of the \nmolecule at different intervals of time. Tracking a single \nmolecule in a live cell is a demanding task, requiring both \nsensitivity and accuracy. Tailored to the application, this \ncan be achieved by specialized microscopy techniques like TIRF\n or PALM. Analysis of the resulting images results in a file \nthat describes the trajectory of the molecule.\n\n4DN processed files are in a format that includes the ID of a \ntrajectory, the time interval, and the coordinates of the \nposition. Further analysis of the trajectory of the molecule \nis necessary to gain biological insight. \n", "name": "item-page-headers.ExperimentType.spt", "award": {"@id": "/awards/1U01CA200059-01/", "@type": ["Award", "Item"], "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Assay Description", "status": "released", "aliases": ["4dn-dcic-lab:experiment_infobox_spt"], "options": {"filetype": "md", "collapsible": false, "default_open": false}, "date_created": "2018-09-07T15:49:58.130720+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-08-04T22:53:31.013900+00:00"}, "schema_version": "2", "@id": "/static-sections/6a313162-e70c-4fbe-93c5-bc78f5faf0c7/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "6a313162-e70c-4fbe-93c5-bc78f5faf0c7", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.56c9c683-bb11-471b-b590-c656f7dc03c1"]}, "display_title": "Assay Description", "external_references": [], "content": "**SPT**\n\nSingle particle tracking (SPT) is a method to track the position\n of a single molecule over time in live cells. Advances in \nmicroscopy and molecular biology techniques have enabled a \nbroad range of applications.\n\nThe protocol involves preparing the target molecule to be \nidentifiable under the microscope, tracking its position over \ntime and analyzing its trajectory. Generally, the preparation \nof the molecule of interest is performed by genetically \nmodifying it with tags followed by the binding of reporter \nmolecules such as fluorescent dyes. However, depending on the \nmolecule of interest, the goal of the experiment and the type \nof microscope used, different techniques are also implemented.\n Following the preparation of the molecule, a high-resolution \nmicroscope is used to take snapshots of the position of the \nmolecule at different intervals of time. Tracking a single \nmolecule in a live cell is a demanding task, requiring both \nsensitivity and accuracy. Tailored to the application, this \ncan be achieved by specialized microscopy techniques like TIRF\n or PALM. Analysis of the resulting images results in a file \nthat describes the trajectory of the molecule.\n\n4DN processed files are in a format that includes the ID of a \ntrajectory, the time interval, and the coordinates of the \nposition. Further analysis of the trajectory of the molecule \nis necessary to gain biological insight. \n", "filetype": "md", "content_as_html": "<div class=\"markdown-container\"><p><strong>SPT</strong></p>\n<p>Single particle tracking (SPT) is a method to track the position\n of a single molecule over time in live cells. Advances in \nmicroscopy and molecular biology techniques have enabled a \nbroad range of applications.</p>\n<p>The protocol involves preparing the target molecule to be \nidentifiable under the microscope, tracking its position over \ntime and analyzing its trajectory. Generally, the preparation \nof the molecule of interest is performed by genetically \nmodifying it with tags followed by the binding of reporter \nmolecules such as fluorescent dyes. However, depending on the \nmolecule of interest, the goal of the experiment and the type \nof microscope used, different techniques are also implemented.\n Following the preparation of the molecule, a high-resolution \nmicroscope is used to take snapshots of the position of the \nmolecule at different intervals of time. Tracking a single \nmolecule in a live cell is a demanding task, requiring both \nsensitivity and accuracy. Tailored to the application, this \ncan be achieved by specialized microscopy techniques like TIRF\n or PALM. Analysis of the resulting images results in a file \nthat describes the trajectory of the molecule.</p>\n<p>4DN processed files are in a format that includes the ID of a \ntrajectory, the time interval, and the coordinates of the \nposition. Further analysis of the trajectory of the molecule \nis necessary to gain biological insight. </p></div>"}, {"lab": {"display_title": "4DN DCIC, HMS", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "Data from multiple experimental replicates were pooled and are presented as a single Processed File associated with this Replicate Set.", "name": "item-page-headers.note.pf-from-pooled-reps", "award": {"@id": "/awards/2U01CA200059-06/", "@type": ["Award", "Item"], "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Note on replicates", "status": "released", "aliases": ["4dn-dcic-lab:note_pf_from_pooled_reps"], "options": {"filetype": "md", "collapsible": false, "default_open": true}, "date_created": "2021-11-05T18:57:07.971025+00:00", "section_type": "Page Section", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-08-08T19:28:01.609664+00:00"}, "schema_version": "2", "@id": "/static-sections/a279f639-f198-409f-8630-19abdb37b9d0/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "a279f639-f198-409f-8630-19abdb37b9d0", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.e4a22298-1da4-4e59-8a65-9e661f47fb48"]}, "display_title": "Note on replicates", "external_references": [], "content": "Data from multiple experimental replicates were pooled and are presented as a single Processed File associated with this Replicate Set.", "filetype": "md", "content_as_html": "<div class=\"markdown-container\"><p>Data from multiple experimental replicates were pooled and are presented as a single Processed File associated with this Replicate Set.</p></div>"}], "processed_files": [{"file_type_detailed": "spt results (spt)", "@id": "/files-processed/4DNFIU7HGDG9/", "file_size": 969892, "display_title": "4DNFIU7HGDG9.spt", "accession": "4DNFIU7HGDG9", "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f446118b2c", "display_title": "spt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/spt/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "06390b6363282f9c6c48d3c6c087f187", "status": "released", "upload_key": "2497dee0-3813-452f-9180-2380fed9441c/4DNFIU7HGDG9.spt", "href": "/files-processed/4DNFIU7HGDG9/@@download/4DNFIU7HGDG9.spt", "file_type": "spt results", "@type": ["FileProcessed", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/2497dee0-3813-452f-9180-2380fed9441c/4DNFIU7HGDG9.spt", "file_classification": "processed file", "uuid": "2497dee0-3813-452f-9180-2380fed9441c", "lab": {"display_title": "Carl Wu, JHU", "@type": ["Lab", "Item"], "name": "carl-wu-lab", "status": "current", "@id": "/labs/carl-wu-lab/", "uuid": "cab8fd2f-201b-4a09-bfd5-e72e902acfdf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.cab8fd2f-201b-4a09-bfd5-e72e902acfdf"]}}, "last_modified": {"date_modified": "2022-03-09T22:04:21.956984+00:00"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "SPT for GAGA transcription factor", "condition": "Halo-GAF deltaQ, slow tracking", "experimental_lab": "Carl Wu, JHU", "replicate_info": "unreplicated", "experiment_bucket": "processed file", "experiment_type": "SPT", "assay_info": "GAF-\u0394Q protein with N-terminus HaloTag knock-in (fruit fly)", "biosource_name": "embryonic/larval hemocyte (Drosophila)", "lab_name": "Carl Wu, JHU"}}], "project_release": "2021-11-12", "experiments_in_set": [{"@type": ["ExperimentMic", "Experiment", "Item"], "status": "released", "accession": "4DNEXW29OTJU", "uuid": "1713155f-1bb9-4ddf-b5dd-16d307bbcd77", "@id": "/experiments-mic/4DNEXW29OTJU/", "display_title": "SPT on embryonic/larval hemocyte (Drosophila) - 4DNEXW29OTJU", "biosample": {"accession": "4DNBSLIHYQCZ", "status": "released", "@id": "/biosamples/4DNBSLIHYQCZ/", "biosample_type": "tissue", "display_title": "4DNBSLIHYQCZ", "treatments_summary": "None", "biosample_category": ["Multicellular Tissue"], "@type": ["Biosample", "Item"], "uuid": "cae0f1ba-506a-40d8-a98f-1702f0528ec5", "modifications_summary": "None", "biosource_summary": "embryonic/larval hemocyte (Drosophila)", "biosource": [{"biosource_type": "tissue", "@id": "/biosources/4DNSR2PRO8WJ/", "status": "released", "accession": "4DNSR2PRO8WJ", "uuid": "41067090-4dd1-4c59-8010-69b2dd75f2c5", "cell_line_tier": "Unclassified", "display_title": "embryonic/larval hemocyte (Drosophila) - 4DNSR2PRO8WJ", "@type": ["Biosource", "Item"], "tissue": {"status": "released", "display_title": "embryonic/larval hemocyte (Drosophila)", "preferred_name": "embryonic/larval hemocyte (Drosophila)", "synonyms": ["embryonic/larval blood cell", "embryonic/larval haemocyte", "larval hemocyte"], "@type": ["OntologyTerm", "Item"], "uuid": "81acbf4b-22d7-49c4-b177-b0c623c67385", "term_name": "embryonic/larval hemocyte (Drosophila)", "@id": "/ontology-terms/FBbt:00001684/", "term_id": "FBbt:00001684", "slim_terms": [{"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "111131bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0001009/", "status": "released", "display_title": "circulatory system", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "111120bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0000926/", "status": "released", "display_title": "mesoderm", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"uuid": "b3911449-1b28-44cf-af23-084ae4eff147", "display_title": "D. melanogaster", "@type": ["Organism", "Item"], "status": "released", "@id": "/organisms/7227/", "name": "fruit fly", "scientific_name": "Drosophila melanogaster", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "tissue_organ_info": {"tissue_source": "embryonic/larval hemocyte (Drosophila)", "organ_system": ["circulatory system", "mesoderm"]}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"@id": "/experiment-types/spt/", "title": "SPT", "experiment_category": "Microscopy", "status": "released", "assay_subclass_short": "SPT", "assay_subclassification": "Single Particle Tracking", "@type": ["ExperimentType", "Item"], "assay_classification": "Fluorescence Localization", "display_title": "SPT", "uuid": "d654c884-fc4f-4d53-818c-fc06fc33dfb3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2021-11-12T08:53:17.016147+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "experiment_categorizer": {"field": "Target", "value": "GAF-\u0394Q protein with N-terminus HaloTag knock-in (fruit fly)", "combined": "Target: GAF-\u0394Q protein with N-terminus HaloTag knock-in (fruit fly)"}}], "experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNES32KCISG/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "37a155b0-7d98-44db-b828-e5df3631397c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNES32KCISG", "external_references": [], "produced_in_pub": {"display_title": "Tang X et al. (2022) PMID:35835866", "@id": "/publications/6b80b5ba-d364-4f87-8f9e-11ebaba46816/", "status": "current", "uuid": "6b80b5ba-d364-4f87-8f9e-11ebaba46816", "journal": "Nature structural & molecular biology", "abstract": "How pioneer factors interface with chromatin to promote accessibility for transcription control is poorly understood in vivo. Here, we directly visualize chromatin association by the prototypical GAGA pioneer factor (GAF) in live Drosophila hemocytes. Single-particle tracking reveals that most GAF is chromatin bound, with a stable-binding fraction showing nucleosome-like confinement residing on chromatin for more than 2 min, far longer than the dynamic range of most transcription factors. These kinetic properties require the full complement  of GAF's DNA-binding, multimerization and intrinsically disordered domains, and are autonomous from recruited chromatin remodelers NURF and PBAP, whose activities primarily benefit GAF's neighbors such as Heat Shock Factor. Evaluation of GAF kinetics together with its endogenous abundance indicates that, despite on-off dynamics, GAF constitutively and fully occupies major chromatin targets, thereby providing a temporal mechanism that sustains open chromatin for  transcriptional responses to homeostatic, environmental and developmental signals.", "url": "https://www.ncbi.nlm.nih.gov/pubmed/35835866", "short_attribution": "Tang X et al. (2022)", "ID": "PMID:35835866", "date_published": "2022-07", "authors": ["Tang X", "Li T", "Liu S", "Wisniewski J", "Zheng Q", "Rong Y", "Lavis LD", "Wu C"], "title": "Kinetic principles underlying pioneer function of GAGA transcription factor in live cells.", "@type": ["Publication", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"authors": ["Tang X", "Li T", "Liu S", "Wisniewski J", "Zheng Q", "Rong Y", "Lavis LD", "Wu C"], "@type": ["Publication", "Item"], "abstract": "How pioneer factors interface with chromatin to promote accessibility for transcription control is poorly understood in vivo. Here, we directly visualize chromatin association by the prototypical GAGA pioneer factor (GAF) in live Drosophila hemocytes. Single-particle tracking reveals that most GAF is chromatin bound, with a stable-binding fraction showing nucleosome-like confinement residing on chromatin for more than 2 min, far longer than the dynamic range of most transcription factors. These kinetic properties require the full complement  of GAF's DNA-binding, multimerization and intrinsically disordered domains, and are autonomous from recruited chromatin remodelers NURF and PBAP, whose activities primarily benefit GAF's neighbors such as Heat Shock Factor. Evaluation of GAF kinetics together with its endogenous abundance indicates that, despite on-off dynamics, GAF constitutively and fully occupies major chromatin targets, thereby providing a temporal mechanism that sustains open chromatin for  transcriptional responses to homeostatic, environmental and developmental signals.", "title": "Kinetic principles underlying pioneer function of GAGA transcription factor in live cells.", "date_published": "2022-07", "uuid": "6b80b5ba-d364-4f87-8f9e-11ebaba46816", "status": "current", "display_title": "Tang X et al. (2022) PMID:35835866", "ID": "PMID:35835866", "@id": "/publications/6b80b5ba-d364-4f87-8f9e-11ebaba46816/", "journal": "Nature structural & molecular biology", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 1, "imaging_paths": [{"path": {"@id": "/imaging-paths/ac00cbf3-11bb-4c8b-948d-71064d2fe5f1/", "display_title": "GAF-\u0394Q protein with N-terminus HaloTag knock-in (fruit fly) targeted by JF552", "status": "released", "@type": ["ImagingPath", "Item"], "uuid": "ac00cbf3-11bb-4c8b-948d-71064d2fe5f1", "target": [{"preferred_label": "GAF-\u0394Q protein with N-terminus HaloTag knock-in", "status": "released", "@id": "/bio-features/ad1e952e-00e4-4fd3-b171-ec1f100cd70b/", "uuid": "ad1e952e-00e4-4fd3-b171-ec1f100cd70b", "feature_mods": [{"mod_type": "HaloTag", "mod_position": "N-terminus"}], "@type": ["BioFeature", "Item"], "display_title": "GAF-\u0394Q protein with N-terminus HaloTag knock-in (fruit fly)", "organism_name": "fruit fly", "relevant_genes": [{"status": "released", "@type": ["Gene", "Item"], "preferred_symbol": "Trl", "geneid": "2768981", "uuid": "755af870-8f35-41fb-bbc1-36b2453fd6b6", "display_title": "Trl", "@id": "/genes/2768981/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "feature_type": {"term_id": "SO:0000104", "term_name": "polypeptide", "uuid": "91f427e6-5246-4992-8123-b4f8fa9eef01", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "protein", "preferred_name": "protein", "@id": "/ontology-terms/SO:0000104/", "term_url": "http://purl.obolibrary.org/obo/SO_0000104", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "channel": "ch00"}], "@context": "/terms/", "aggregated-items": {"badges": []}, "validation-errors": []}