{"lab": {"title": "Alistair Boettiger, STANFORD", "uuid": "312cb909-76a6-405d-a96c-c3292abf08a1", "display_title": "Alistair Boettiger, STANFORD", "status": "current", "@type": ["Lab", "Item"], "correspondence": [{"contact_email": "YWJvZXR0aWdAc3RhbmZvcmQuZWR1", "@id": "/users/b8835c78-05e3-4173-a6c5-1ab93b4d12cc/", "display_title": "Alistair Boettiger"}], "@id": "/labs/alistair-boettiger-lab/", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.312cb909-76a6-405d-a96c-c3292abf08a1"]}}, "award": {"name": "1U01DK127419-01", "description": "RT-CDF: Chromatin structure and transcription regulation are essential for cellular function, and their dynamics are highly correlated both in development and in disease. However, despite decades of amazing work identifying the molecular players involved in these processes, and mapping their interactions genome-wide, we are currently unable to describe the function connecting 3D chromatin structure and transcription dynamics. This limitation stems from the fact that chromatin structure and gene expression emerge from intrinsically stochastic transitions at the single-cell level, and we are missing the critical temporal parameters associated with these transitions. Therefore, new tools to measure both chromatin structure and transcription over time in single cells are critical for understanding how the human genome is read and for predictively controlling the epigenome.  Here, we propose to develop a new set of live single-cell imaging technologies to simultaneously measure changes in 3D chromatin structures and their associated dynamics of gene expression across a large range of timescales: from dynamics of individual topologically associated domains and enhancer-promoter interactions, to changes associated with stable epigenetic memory across cell cycles. For the shorter timescales (under a cell cycle), our new imaging approach combines live super-resolution microscopy of fluorescently labeled loci with end-point demultiplexing of loci identity using Optical Reconstruction of Chromatin Architecture (ORCA), in order to track and trace 3-12 points within a functional chromatin unit. This new technique, which we call live-ORCA, will allow us to measure for the first time the temporal dynamics of an entire topologically associated domain in single cells. We will use live-ORCA in conjunction with time-lapse imaging of transcriptional bursting to study the dynamics of promoter-enhancer activity throughout cell differentiation and under perturbations of the chromatin network. For the longer timescale (across multiple cell cycles), our approach will combine time-lapse microscopy of gene expression, monitoring the distance between two tagged genomic loci as a live reporter of chromatin structure, and end-point chromatin tracing of the entire gene neighborhood using ORCA. We will perform these measurements in two systems: at a highly controlled synthetic reporter where we can induce either short-term silencing or long-term epigenetic memory, and at time points in differentiation when genes commit epigenetically to a new transcriptional state. Moreover, in order to further investigate the mechanism of epigenetic inheritance, we will develop a novel microfluidic device that allows us to track changes in chromatin 3D structures across individual cell lineages. Finally, to test our quantitative understanding, we will go back and forth between these single-cell data and theoretical modelling of chromatin dynamics. This research plan will greatly advance our understanding of chromatin dynamics and its functional role in transcription regulation, while at the same time contributing a whole new set of novel imaging technologies and engineered cell lines that will serve as a jumping board for the 4D Nucleome and broader scientific community.", "@id": "/awards/1U01DK127419-01/", "uuid": "b7c5d0c8-053e-4da3-b446-b68787a5a738", "project": "4DN", "status": "current", "center_title": "Bintu", "display_title": "LIVE-CELL MULTIPLEX SUPER-RESOLUTION IMAGING OF CHROMATIN STATE TRANSITIONS", "@type": ["Award", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["alistair-boettiger-lab:experiment_FubHomo_B1"], "protocol": {"status": "released", "uuid": "d92eb063-1d98-4f78-bdc5-438ffd795b42", "display_title": "ORCA protocol", "@type": ["Protocol", "Item"], "@id": "/protocols/d92eb063-1d98-4f78-bdc5-438ffd795b42/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNEXLGO7DVE", "biosample": {"biosource_summary": "embryo", "biosample_type": "tissue", "display_title": "4DNBS8K5D532", "@id": "/biosamples/4DNBS8K5D532/", "uuid": "97ca3956-51a4-42a6-83d4-31376f6921c5", "modifications_summary": "None", "status": "released", "treatments_summary": "None", "accession": "4DNBS8K5D532", "@type": ["Biosample", "Item"], "biosource": [{"lab": {"@id": "/labs/alistair-boettiger-lab/", "@type": ["Lab", "Item"], "status": "current", "display_title": "Alistair Boettiger, STANFORD", "uuid": "312cb909-76a6-405d-a96c-c3292abf08a1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.312cb909-76a6-405d-a96c-c3292abf08a1"]}}, "award": {"@type": ["Award", "Item"], "status": "current", "uuid": "b7c5d0c8-053e-4da3-b446-b68787a5a738", "display_title": "LIVE-CELL MULTIPLEX SUPER-RESOLUTION IMAGING OF CHROMATIN STATE TRANSITIONS", "@id": "/awards/1U01DK127419-01/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"term_id": "UBERON:0000922", "synonyms": ["embryonic organism"], "@id": "/ontology-terms/UBERON:0000922/", "uuid": "94a7d7e3-b38e-462a-91e6-55df4a2c120f", "preferred_name": "embryo", "status": "released", "display_title": "embryo", "term_name": "embryo", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["alistair-boettiger-lab:biosource_fubHomo"], "accession": "4DNSRULDLAD7", "individual": {"uuid": "708ad66a-17df-43bc-8dee-5d712a300910", "status": "released", "@type": ["IndividualFly", "Individual", "Item"], "display_title": "4DNINMUWAV3B", "@id": "/individuals-fly/4DNINMUWAV3B/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "description": "Front-Ultraabdominal (Fub) homozygous fly embryos, carrying a 4-kb deletion spanning the TAD border between genetic domains 2 and 3, 10-12 hours post-fertilization", "date_created": "2023-03-14T17:35:41.839956+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2023-03-15T15:22:52.123376+00:00"}, "biosource_type": "tissue", "cell_line_tier": "Unclassified", "public_release": "2023-03-15", "schema_version": "2", "project_release": "2023-03-15", "@id": "/biosources/4DNSRULDLAD7/", "@type": ["Biosource", "Item"], "uuid": "e0412de1-a5a8-4920-be12-97cd88d49f56", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "embryo - 4DNSRULDLAD7", "external_references": [], "biosource_name": "embryo", "biosource_category": ["Multicellular Tissue"], "organism": {"uuid": "b3911449-1b28-44cf-af23-084ae4eff147", "@type": ["Organism", "Item"], "@id": "/organisms/7227/", "display_title": "D. melanogaster", "name": "fruit fly", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "sop_mapping": {"has_sop": "No"}, "date_created": "2023-03-14T17:37:25.908381+00:00", "submitted_by": {"error": "no view permissions"}, "imaging_paths": [{"path": {"other_probes": ["oligo probe library"], "@type": ["ImagingPath", "Item"], "labeled_probe": "fiducial oligo probes", "display_title": "70 consecutive 10-kb loci in the BX-C region (fruit fly) targeted by oligo probe library (with Cy3-labeled fiducial oligo probes)", "@id": "/imaging-paths/889c2e0d-2648-450b-9687-05a8a3ffa1ce/", "uuid": "889c2e0d-2648-450b-9687-05a8a3ffa1ce", "status": "released", "experiment_type": {"display_title": "DNA FISH", "@type": ["ExperimentType", "Item"], "title": "DNA FISH", "@id": "/experiment-types/dna-fish/", "uuid": "5761d0ec-35b0-4aa8-8b81-aac94def59b8", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "target": [{"display_title": "70 consecutive 10-kb loci in the BX-C region (fruit fly)", "status": "released", "@type": ["BioFeature", "Item"], "organism_name": "fruit fly", "uuid": "3b1b4c35-1476-4bfe-a3e9-0fbf179fd727", "@id": "/bio-features/3b1b4c35-1476-4bfe-a3e9-0fbf179fd727/", "preferred_label": "70 consecutive 10-kb loci in the BX-C region", "feature_type": {"uuid": "41b7a2c5-f2d9-46b4-a49d-51502fe61bb3", "display_title": "region", "preferred_name": "region", "@id": "/ontology-terms/SO:0000001/", "term_name": "region", "@type": ["OntologyTerm", "Item"], "status": "released", "term_id": "SO:0000001", "term_url": "http://purl.obolibrary.org/obo/SO_0000001", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "genome_location": [{"chromosome": "3R", "display_title": "dm6:3R:16645834-16960889", "genome_assembly": "dm6", "start_coordinate": 16645834, "location_description": "a 700-kb region including the bithorax complex (BX-C) and flanking domains on chromosome 3R", "uuid": "23cf5bc1-a3e0-4740-89cc-318ed14dd6d2", "end_coordinate": 16960889, "@id": "/genomic-regions/23cf5bc1-a3e0-4740-89cc-318ed14dd6d2/", "status": "released", "@type": ["GenomicRegion", "Item"], "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"}, {"path": {"other_probes": ["oligo probe library", "readout oligo library"], "@type": ["ImagingPath", "Item"], "labeled_probe": "imaging oligos", "display_title": "70 consecutive 10-kb loci in the BX-C region (fruit fly) targeted by oligo probe library, readout oligo library (with Cy5-labeled imaging oligos)", "@id": "/imaging-paths/f1a86ce0-0ce6-4946-965a-6c248b43a115/", "uuid": "f1a86ce0-0ce6-4946-965a-6c248b43a115", "status": "released", "experiment_type": {"display_title": "DNA FISH", "@type": ["ExperimentType", "Item"], "title": "DNA FISH", "@id": "/experiment-types/dna-fish/", "uuid": "5761d0ec-35b0-4aa8-8b81-aac94def59b8", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "target": [{"display_title": "70 consecutive 10-kb loci in the BX-C region (fruit fly)", "status": "released", "@type": ["BioFeature", "Item"], "organism_name": "fruit fly", "uuid": "3b1b4c35-1476-4bfe-a3e9-0fbf179fd727", "@id": "/bio-features/3b1b4c35-1476-4bfe-a3e9-0fbf179fd727/", "preferred_label": "70 consecutive 10-kb loci in the BX-C region", "feature_type": {"uuid": "41b7a2c5-f2d9-46b4-a49d-51502fe61bb3", "display_title": "region", "preferred_name": "region", "@id": "/ontology-terms/SO:0000001/", "term_name": "region", "@type": ["OntologyTerm", "Item"], "status": "released", "term_id": "SO:0000001", "term_url": "http://purl.obolibrary.org/obo/SO_0000001", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "genome_location": [{"chromosome": "3R", "display_title": "dm6:3R:16645834-16960889", "genome_assembly": "dm6", "start_coordinate": 16645834, "location_description": "a 700-kb region including the bithorax complex (BX-C) and flanking domains on chromosome 3R", "uuid": "23cf5bc1-a3e0-4740-89cc-318ed14dd6d2", "end_coordinate": 16960889, "@id": "/genomic-regions/23cf5bc1-a3e0-4740-89cc-318ed14dd6d2/", "status": "released", "@type": ["GenomicRegion", "Item"], "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": "ch01"}, {"path": {"other_probes": ["oligo probe library", "readout oligo library"], "@type": ["ImagingPath", "Item"], "labeled_probe": "imaging oligos", "display_title": "29 mRNAs and nascent RNAs (fruit fly) targeted by oligo probe library, readout oligo library (with Cy5-labeled imaging oligos)", "@id": "/imaging-paths/83be5875-9b00-4f3d-b4cd-68ea5935a801/", "uuid": "83be5875-9b00-4f3d-b4cd-68ea5935a801", "status": "released", "experiment_type": {"display_title": "RNA FISH", "@type": ["ExperimentType", "Item"], "title": "RNA FISH", "@id": "/experiment-types/rna-fish/", "uuid": "b819cdfd-d865-4e4b-8399-4dd9c628c3a4", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "target": [{"display_title": "29 mRNAs and nascent RNAs (fruit fly)", "status": "released", "@type": ["BioFeature", "Item"], "organism_name": "fruit fly", "uuid": "11ced4a0-fb72-4f4c-86a5-3593de76ac92", "@id": "/bio-features/11ced4a0-fb72-4f4c-86a5-3593de76ac92/", "preferred_label": "29 mRNAs and nascent RNAs", "feature_type": {"uuid": "e8f56a24-20ce-4e7c-9e8d-a4f409398574", "display_title": "transcript", "preferred_name": "transcript", "@id": "/ontology-terms/SO:0000673/", "term_name": "transcript", "@type": ["OntologyTerm", "Item"], "status": "released", "term_id": "SO:0000673", "term_url": "http://purl.obolibrary.org/obo/SO_0000673", "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": "ch01"}], "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2023-03-15T15:22:25.180201+00:00"}, "fiducial_label": "fiducial oligos binding the entire probe library", "public_release": "2023-03-15", "schema_version": "3", "experiment_type": {"@id": "/experiment-types/multiplexed-fish/", "assay_subclass_short": "FISH", "experiment_category": "Microscopy", "uuid": "bcdda46a-489d-4d22-be80-c9c21552c915", "display_title": "multiplexed FISH", "@type": ["ExperimentType", "Item"], "status": "released", "title": "multiplexed FISH", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/csv/", "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "file_format": "csv", "display_title": "csv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNFI6XJHC9B", "file_size": 30700070, "@id": "/files-processed/4DNFI6XJHC9B/", "file_type_detailed": "FOF-CT - DNA-spot/trace core (csv)", "file_classification": "processed file", "uuid": "a121b69d-ce0e-4862-b707-24b7e76fedb0", "status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFI6XJHC9B.csv", "href": "/files-processed/4DNFI6XJHC9B/@@download/4DNFI6XJHC9B.csv", "upload_key": "a121b69d-ce0e-4862-b707-24b7e76fedb0/4DNFI6XJHC9B.csv", "file_type": "FOF-CT - DNA-spot/trace core", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/a121b69d-ce0e-4862-b707-24b7e76fedb0/4DNFI6XJHC9B.csv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Alistair Boettiger, STANFORD", "experiment_type": "multiplexed FISH", "experiment_bucket": "processed file", "assay_info": "29 mRNAs and nascent RNAs (fruit fly), 70 consecutive 10-kb loci in the BX-C region (fruit fly)", "dataset": "Chromatin tracing of BX-C in Drosophila", "condition": "Fub Homozygous mutant, 10-kb resolution", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "embryo", "lab_name": "Alistair Boettiger, STANFORD"}}, {"file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/csv/", "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "file_format": "csv", "display_title": "csv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNFIBZXBX2A", "file_size": 4408284, "@id": "/files-processed/4DNFIBZXBX2A/", "file_type_detailed": "FOF-CT - spot quality (csv)", "file_classification": "processed file", "uuid": "bcefd0c4-ea65-42da-b82e-9deacd348d2c", "status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIBZXBX2A.csv", "href": "/files-processed/4DNFIBZXBX2A/@@download/4DNFIBZXBX2A.csv", "upload_key": "bcefd0c4-ea65-42da-b82e-9deacd348d2c/4DNFIBZXBX2A.csv", "file_type": "FOF-CT - spot quality", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/bcefd0c4-ea65-42da-b82e-9deacd348d2c/4DNFIBZXBX2A.csv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Alistair Boettiger, STANFORD", "experiment_type": "multiplexed FISH", "experiment_bucket": "processed file", "assay_info": "29 mRNAs and nascent RNAs (fruit fly), 70 consecutive 10-kb loci in the BX-C region (fruit fly)", "dataset": "Chromatin tracing of BX-C in Drosophila", "condition": "Fub Homozygous mutant, 10-kb resolution", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "embryo", "lab_name": "Alistair Boettiger, STANFORD"}}, {"file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/csv/", "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "file_format": "csv", "display_title": "csv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNFID1M4J7H", "file_size": 1635458, "@id": "/files-processed/4DNFID1M4J7H/", "file_type_detailed": "FOF-CT - cell data (csv)", "file_classification": "processed file", "uuid": "4976f11f-5399-4c2e-8ef0-bc26d4de5179", "status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFID1M4J7H.csv", "href": "/files-processed/4DNFID1M4J7H/@@download/4DNFID1M4J7H.csv", "upload_key": "4976f11f-5399-4c2e-8ef0-bc26d4de5179/4DNFID1M4J7H.csv", "file_type": "FOF-CT - cell data", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/4976f11f-5399-4c2e-8ef0-bc26d4de5179/4DNFID1M4J7H.csv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Alistair Boettiger, STANFORD", "experiment_type": "multiplexed FISH", "experiment_bucket": "processed file", "assay_info": "29 mRNAs and nascent RNAs (fruit fly), 70 consecutive 10-kb loci in the BX-C region (fruit fly)", "dataset": "Chromatin tracing of BX-C in Drosophila", "condition": "Fub Homozygous mutant, 10-kb resolution", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "embryo", "lab_name": "Alistair Boettiger, STANFORD"}}], "project_release": "2023-03-15", "reference_files": [{"file_type_detailed": "target regions (bed)", "uuid": "65b5735c-4ba9-48bb-99e6-0579cb9308fe", "accession": "4DNFIGVGQA8V", "@type": ["FileReference", "File", "Item"], "status": "released", "display_title": "4DNFIGVGQA8V.bed.gz", "file_type": "target regions", "file_size": 941, "file_classification": "ancillary file", "@id": "/files-reference/4DNFIGVGQA8V/", "file_format": {"status": "released", "file_format": "bed", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "display_title": "bed", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bed/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"uuid": "94842fe1-3c32-4136-9ae3-09940cbd0139", "@id": "/higlass-view-configs/94842fe1-3c32-4136-9ae3-09940cbd0139/", "@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFIGVGQA8V", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "oligo sequences (zip)", "uuid": "956eca8a-e546-4462-a75b-2a9e47ae3e0d", "accession": "4DNFIK62FTWO", "@type": ["FileReference", "File", "Item"], "status": "released", "display_title": "4DNFIK62FTWO.zip", "file_type": "oligo sequences", "file_size": 1853410, "file_classification": "ancillary file", "@id": "/files-reference/4DNFIK62FTWO/", "file_format": {"status": "released", "file_format": "zip", "uuid": "d13d06cf-218e-4f61-44f0-91f226248b2c", "display_title": "zip", "@type": ["FileFormat", "Item"], "@id": "/file-formats/zip/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "extinguishing_method": "strand displacement", "microscopy_technique": "Highly Inclined Laminated Optical Sheet", "microscope_configuration_master": {"status": "released", "title": "Stanford-Boettiger_lab_ORCA_Nikon_Eclipse_Ti-U_Scope1", "@type": ["MicroscopeConfiguration", "UserContent", "Item"], "display_title": "Stanford-Boettiger_lab_ORCA_Nikon_Eclipse_Ti-U_Scope1", "@id": "/microscope-configurations/84d52890-7e46-4cf8-810c-071ed0673ce8/", "uuid": "84d52890-7e46-4cf8-810c-071ed0673ce8", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "microscope": {"Name": "Stanford-Boettiger_lab_ORCA_Nikon_Eclipse_Ti-U_Scope1"}}, "@id": "/experiments-mic/4DNEXLGO7DVE/", "@type": ["ExperimentMic", "Experiment", "Item"], "uuid": "346f76cd-cdcb-4a39-9edd-ded9f19dcdd3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "multiplexed FISH on embryo - 4DNEXLGO7DVE", "external_references": [], "experiment_sets": [{"experimentset_type": "replicate", "display_title": "4DNESPSDU14J", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "accession": "4DNESPSDU14J", "uuid": "525908ee-3ea8-46c0-9d12-16883315e2b3", "@id": "/experiment-set-replicates/4DNESPSDU14J/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"@type": ["Publication", "Item"], "ID": "PMID:30886393", "date_published": "2019-04", "abstract": "The establishment of cell types during development requires precise interactions  between genes and distal regulatory sequences. We have a limited understanding of  how these interactions look in three dimensions, vary across cell types in  complex tissue, and relate to transcription. Here we describe optical  reconstruction of chromatin architecture (ORCA), a method that can trace the DNA  path in single cells with nanoscale accuracy and genomic resolution reaching two  kilobases. We used ORCA to study a Hox gene cluster in cryosectioned Drosophila  embryos and labelled around 30 RNA species in parallel. We identified  cell-type-specific physical borders between active and Polycomb-repressed DNA,  and unexpected Polycomb-independent borders. Deletion of Polycomb-independent  borders led to ectopic enhancer-promoter contacts, aberrant gene expression, and  developmental defects. Together, these results illustrate an approach for  high-resolution, single-cell DNA domain analysis in vivo, identify domain  structures that change with cell identity, and show that border elements  contribute to the formation of physical domains in Drosophila.", "title": "Visualizing DNA folding and RNA in embryos at single-cell resolution.", "short_attribution": "Mateo LJ et al. (2019)", "status": "current", "authors": ["Mateo LJ", "Murphy SE", "Hafner A", "Cinquini IS", "Walker CA", "Boettiger AN"], "uuid": "6c007db6-3eba-41d8-9d50-cb7e7c05841f", "display_title": "Mateo LJ et al. (2019) PMID:30886393", "journal": "Nature", "@id": "/publications/6c007db6-3eba-41d8-9d50-cb7e7c05841f/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"date_published": "2019-04", "authors": ["Mateo LJ", "Murphy SE", "Hafner A", "Cinquini IS", "Walker CA", "Boettiger AN"], "title": "Visualizing DNA folding and RNA in embryos at single-cell resolution.", "@id": "/publications/6c007db6-3eba-41d8-9d50-cb7e7c05841f/", "short_attribution": "Mateo LJ et al. (2019)", "display_title": "Mateo LJ et al. (2019) PMID:30886393", "abstract": "The establishment of cell types during development requires precise interactions  between genes and distal regulatory sequences. We have a limited understanding of  how these interactions look in three dimensions, vary across cell types in  complex tissue, and relate to transcription. Here we describe optical  reconstruction of chromatin architecture (ORCA), a method that can trace the DNA  path in single cells with nanoscale accuracy and genomic resolution reaching two  kilobases. We used ORCA to study a Hox gene cluster in cryosectioned Drosophila  embryos and labelled around 30 RNA species in parallel. We identified  cell-type-specific physical borders between active and Polycomb-repressed DNA,  and unexpected Polycomb-independent borders. Deletion of Polycomb-independent  borders led to ectopic enhancer-promoter contacts, aberrant gene expression, and  developmental defects. Together, these results illustrate an approach for  high-resolution, single-cell DNA domain analysis in vivo, identify domain  structures that change with cell identity, and show that border elements  contribute to the formation of physical domains in Drosophila.", "journal": "Nature", "uuid": "6c007db6-3eba-41d8-9d50-cb7e7c05841f", "@type": ["Publication", "Item"], "ID": "PMID:30886393", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Target", "value": "29 mRNAs and nascent RNAs (fruit fly), 70 consecutive 10-kb loci in the BX-C region (fruit fly)", "combined": "Target: 29 mRNAs and nascent RNAs (fruit fly), 70 consecutive 10-kb loci in the BX-C region (fruit fly)"}, "experiment_summary": "multiplexed FISH on embryo", "@context": "/terms/", "aggregated-items": {"badges": []}, "validation-errors": []}