{"lab": {"title": "Mitchell Guttman, CALTECH", "status": "current", "@type": ["Lab", "Item"], "uuid": "c17e88b5-912a-496a-acc7-28dd71215a7d", "display_title": "Mitchell Guttman, CALTECH", "@id": "/labs/mitchell-guttman-lab/", "correspondence": [{"contact_email": "bWd1dHRtYW5AY2FsdGVjaC5lZHU=", "@id": "/users/ac3920c8-caa6-444b-be8a-48b52a1dcb3e/", "display_title": "Mitchell Guttman"}], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c17e88b5-912a-496a-acc7-28dd71215a7d"]}}, "award": {"uuid": "4de1cf81-1ea0-4a19-bc7a-dd3343b34438", "project": "4DN", "description": "NBC: The nucleus of each cell is a complex arrangement of DNA, RNA, and protein that is dynamically organized into various nuclear bodies and compartments that are often arranged around shared functional and regulatory roles. Yet, while many of these nuclear compartments were first identified several decades ago a major challenge with characterizing these compartments is that there are currently no biochemical methods for isolating individual nuclear compartments. Importantly, many nuclear bodies are marked and maintained by nuclear retained long non-coding RNAs (lncRNAs). Here we aim to develop several novel technologies to purify the molecular constituents of nuclear domains and their necessity and sufficiency in forming these compartments. Together these technologies will allow us to systematically address the following questions: Aim 1: What are the optimal biochemical conditions in which to specifically and accurately purify specific nuclear bodies and compartments in order to identify their DNA, RNA and protein components? A critical aspect of biochemical purifications is the fine balance between cross-linking conditions that identify direct molecular interactions while not over-crosslinking that could result in indirect interactions. Usin known nuclear compartments such as the nucleolus, nuclear speckles, and paraspeckles we will optimize RAP for isolating DNA-RNA, RNA-RNA, RNA-protein interactions. We aim to identify universally applicable purification conditions to identify molecular interactions within nuclear and other subcellular structures. Aim 2: What are the DNA, RNA and protein factors involved in nuclear compartments? Although most known nuclear bodies are characterized by lncRNAs the other RNA, DNA and protein factors remain less well defined. Here we will develop technologies to catalog the molecular factors that comprise various nuclear bodies. We will further validate these components through colocalization of these components within a nuclear domain using visualization approaches (e.g. RNA-DNA Co-FISH). Overall we aim to apply new technologies to systematic and comprehensive catalog of RNA, DNA and Proteins in nuclear bodies. Aim 3: Are lncRNAs and proteins necessary and/or sufficient for nuclear compartmentalization? Here we will develop a novel technology platform, termed CRISPR-Display, which allows long RNA cargos to be appended and delivered by CRISPR-Cas9 systems to a desired site in the genome. We will develop this technology to test if lncRNA molecules are sufficient to drive nuclear organization. We will also use CRISPR-Display to multiplex several RNA aptamers that can be used to recruit proteins (with reciprocal protein epitopes that bind RNA aptamers) and test if they are sufficient to form nuclear compartments. In parallel we will perform loss-of- function approaches to identify protein and or RNA components are required for establishing nuclear domains. Collectively our proposal aims to develop powerful and multifaceted technologies to catalog the molecular components of subnuclear structures, validate these interactions and test their biological importance.", "status": "current", "@type": ["Award", "Item"], "center_title": "NBC - Guttman", "name": "1U01DA040612-01", "@id": "/awards/1U01DA040612-01/", "display_title": "DECIPHERING THE FUNCTION AND MECHANISMS OF LNCRNA-MEDIATED ORGANIZATION OF NUCLEAR COMPARTMENTS", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "badges": [{"badge": {"display_title": "Replicate Numbers", "title": "Replicate Numbers", "@id": "/badges/replicate-numbers/", "description": "Issues with replicate numbers", "warning": "Replicate Numbers", "badge_classification": "Warning", "badge_icon": "/static/img/badges/replicates-orange-circle.svg", "@type": ["Badge", "Item"], "status": "released", "uuid": "24a64a84-3c33-4d76-aaf2-e5ef45eff347", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "messages": ["Replicate set contains only a single biological replicate"]}], "status": "released", "aliases": ["mitchell-guttman-lab:Chr18I_SC35_set"], "accession": "4DNESCXK9T73", "condition": "Chr18 inactive region + nuclear speckle", "description": "FISH/IF of Chromosome 18-NOR and Nuclear Speckle", "date_created": "2018-05-05T04:05:11.135133+00:00", "sample_image": {"caption": "Sample Image", "status": "released", "uuid": "12ed420e-29db-4baa-aed4-0585a6446f95", "display_title": "Thumbnail for 4DNFIJUHK5ID", "@type": ["Image", "Item"], "@id": "/images/12ed420e-29db-4baa-aed4-0585a6446f95/", "microscopy_file": {"@id": "/files-microscopy/4DNFIJUHK5ID/", "@type": ["FileMicroscopy", "File", "Item"], "omerolink": "https://omero.hms.harvard.edu/pathviewer/viewer/untiled/1040341/", "display_title": "4DNFIJUHK5ID.r3d", "status": "released", "uuid": "a5d3cc4a-162d-4926-b6b7-f75bae2af215", "accession": "4DNFIJUHK5ID", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "attachment": {"md5sum": "010575950498a82068ce5df9f97c26f4", "href": "@@download/attachment/4DNFIJUHK5ID.jpeg", "download": "4DNFIJUHK5ID.jpeg", "height": 200, "type": "image/jpeg", "width": 200}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "submitted_by": {"error": "no view permissions"}, "dataset_label": "FISH for DNA SPRITE", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-11-08T19:39:25.266187+00:00"}, "public_release": "2018-06-01", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"uuid": "be48e05d-6fcf-4fe3-86d1-2f8601b1833a", "@type": ["ExperimentMic", "Experiment", "Item"], "status": "released", "@id": "/experiments-mic/4DNEXNDIAZIG/", "accession": "4DNEXNDIAZIG", "display_title": "DNA FISH on F1 2-1 mESC line - 4DNEXNDIAZIG", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_headers": [{"body": "**DNA FISH**\n\nDNA FISH is a method to detect the position of specific DNA regions in the cell through fluorescent labeling. It can be used to measure the 3D distances between multiple genomic loci. Additionally, it is often used to corroborate the findings of chromosome capture techniques (3C).\n\nThe protocol involves fixing and permeabilizing the cells. Then, the DNA is slightly denatured to allow the binding of fluorescently labeled probes to the region of interest (hybridization). After the hybridization is performed, unbound and partially unbound probes are removed. The target loci are then visualized using fluorescent microscopy. Analysis of the resulting images provides the physical localization of the target genomic regions in the cell.", "name": "item-page-headers.ExperimentType.fish", "award": {"@type": ["Award", "Item"], "@id": "/awards/1U01CA200059-01/", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Assay Description", "status": "released", "aliases": ["4dn-dcic-lab:experiment_infobox_fish"], "options": {"filetype": "md", "collapsible": false, "default_open": false}, "date_created": "2018-09-07T18:16:30.519497+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-11-15T18:24:04.176123+00:00"}, "schema_version": "2", "@id": "/static-sections/911424f9-21c7-49fc-b1df-865dd64ae91e/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "911424f9-21c7-49fc-b1df-865dd64ae91e", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.56c9c683-bb11-471b-b590-c656f7dc03c1"]}, "display_title": "Assay Description", "external_references": [], "content": "**DNA FISH**\n\nDNA FISH is a method to detect the position of specific DNA regions in the cell through fluorescent labeling. It can be used to measure the 3D distances between multiple genomic loci. Additionally, it is often used to corroborate the findings of chromosome capture techniques (3C).\n\nThe protocol involves fixing and permeabilizing the cells. Then, the DNA is slightly denatured to allow the binding of fluorescently labeled probes to the region of interest (hybridization). After the hybridization is performed, unbound and partially unbound probes are removed. The target loci are then visualized using fluorescent microscopy. Analysis of the resulting images provides the physical localization of the target genomic regions in the cell.", "filetype": "md", "content_as_html": "<div class=\"markdown-container\"><p><strong>DNA FISH</strong></p>\n<p>DNA FISH is a method to detect the position of specific DNA regions in the cell through fluorescent labeling. It can be used to measure the 3D distances between multiple genomic loci. Additionally, it is often used to corroborate the findings of chromosome capture techniques (3C).</p>\n<p>The protocol involves fixing and permeabilizing the cells. Then, the DNA is slightly denatured to allow the binding of fluorescently labeled probes to the region of interest (hybridization). After the hybridization is performed, unbound and partially unbound probes are removed. The target loci are then visualized using fluorescent microscopy. Analysis of the resulting images provides the physical localization of the target genomic regions in the cell.</p></div>"}], "project_release": "2018-06-01", "experiments_in_set": [{"uuid": "be48e05d-6fcf-4fe3-86d1-2f8601b1833a", "accession": "4DNEXNDIAZIG", "status": "released", "display_title": "DNA FISH on F1 2-1 mESC line - 4DNEXNDIAZIG", "files": [{"file_size": 1056975712, "@type": ["FileMicroscopy", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/a5d3cc4a-162d-4926-b6b7-f75bae2af215/4DNFIJUHK5ID.r3d", "@id": "/files-microscopy/4DNFIJUHK5ID/", "file_type_detailed": "z-stack (r3d)", "display_title": "4DNFIJUHK5ID.r3d", "accession": "4DNFIJUHK5ID", "uuid": "a5d3cc4a-162d-4926-b6b7-f75bae2af215", "file_classification": "raw file", "file_type": "z-stack", "md5sum": "d2c1095cd8268ab8a97cafe1b533096c", "upload_key": "a5d3cc4a-162d-4926-b6b7-f75bae2af215/4DNFIJUHK5ID.r3d", "href": "/files-microscopy/4DNFIJUHK5ID/@@download/4DNFIJUHK5ID.r3d", "status": "released", "lab": {"uuid": "c17e88b5-912a-496a-acc7-28dd71215a7d", "display_title": "Mitchell Guttman, CALTECH", "name": "mitchell-guttman-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/mitchell-guttman-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c17e88b5-912a-496a-acc7-28dd71215a7d"]}}, "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f886118b2c", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "r3d", "file_format": "r3d", "@id": "/file-formats/r3d/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Mitchell Guttman, CALTECH", "experiment_type": "DNA FISH", "experiment_bucket": "raw file", "assay_info": "Chromosomes, GRCm38:18:3004000-5000150 mouse region, Srsf2 mouse protein", "dataset": "FISH for DNA SPRITE", "condition": "Chr18 inactive region + nuclear speckle", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Mitchell Guttman, CALTECH"}}, {"file_size": 1056975712, "@type": ["FileMicroscopy", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/d9904d60-a25e-4665-b187-c011f0c5b815/4DNFIV3IWIOU.r3d", "@id": "/files-microscopy/4DNFIV3IWIOU/", "file_type_detailed": "z-stack (r3d)", "display_title": "4DNFIV3IWIOU.r3d", "accession": "4DNFIV3IWIOU", "uuid": "d9904d60-a25e-4665-b187-c011f0c5b815", "file_classification": "raw file", "file_type": "z-stack", "md5sum": "c4cfe541e605889e709008f04b12cbbd", "upload_key": "d9904d60-a25e-4665-b187-c011f0c5b815/4DNFIV3IWIOU.r3d", "href": "/files-microscopy/4DNFIV3IWIOU/@@download/4DNFIV3IWIOU.r3d", "status": "released", "lab": {"uuid": "c17e88b5-912a-496a-acc7-28dd71215a7d", "display_title": "Mitchell Guttman, CALTECH", "name": "mitchell-guttman-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/mitchell-guttman-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c17e88b5-912a-496a-acc7-28dd71215a7d"]}}, "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f886118b2c", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "r3d", "file_format": "r3d", "@id": "/file-formats/r3d/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Mitchell Guttman, CALTECH", "experiment_type": "DNA FISH", "experiment_bucket": "raw file", "assay_info": "Chromosomes, GRCm38:18:3004000-5000150 mouse region, Srsf2 mouse protein", "dataset": "FISH for DNA SPRITE", "condition": "Chr18 inactive region + nuclear speckle", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Mitchell Guttman, CALTECH"}}, {"file_size": 1056975712, "@type": ["FileMicroscopy", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/59fce2d5-5ceb-46ff-9439-6299eee317a3/4DNFIT1JRWXN.r3d", "@id": "/files-microscopy/4DNFIT1JRWXN/", "file_type_detailed": "z-stack (r3d)", "display_title": "4DNFIT1JRWXN.r3d", "accession": "4DNFIT1JRWXN", "uuid": "59fce2d5-5ceb-46ff-9439-6299eee317a3", "file_classification": "raw file", "file_type": "z-stack", "md5sum": "eed109c442e0c679bb5376aec9645616", "upload_key": "59fce2d5-5ceb-46ff-9439-6299eee317a3/4DNFIT1JRWXN.r3d", "href": "/files-microscopy/4DNFIT1JRWXN/@@download/4DNFIT1JRWXN.r3d", "status": "released", "lab": {"uuid": "c17e88b5-912a-496a-acc7-28dd71215a7d", "display_title": "Mitchell Guttman, CALTECH", "name": "mitchell-guttman-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/mitchell-guttman-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c17e88b5-912a-496a-acc7-28dd71215a7d"]}}, "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f886118b2c", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "r3d", "file_format": "r3d", "@id": "/file-formats/r3d/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Mitchell Guttman, CALTECH", "experiment_type": "DNA FISH", "experiment_bucket": "raw file", "assay_info": "Chromosomes, GRCm38:18:3004000-5000150 mouse region, Srsf2 mouse protein", "dataset": "FISH for DNA SPRITE", "condition": "Chr18 inactive region + nuclear speckle", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Mitchell Guttman, CALTECH"}}, {"file_size": 1056975712, "@type": ["FileMicroscopy", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/79711238-da6d-40b3-92f2-0109b9d8c08e/4DNFIHZEHI3R.r3d", "@id": "/files-microscopy/4DNFIHZEHI3R/", "file_type_detailed": "z-stack (r3d)", "display_title": "4DNFIHZEHI3R.r3d", "accession": "4DNFIHZEHI3R", "uuid": "79711238-da6d-40b3-92f2-0109b9d8c08e", "file_classification": "raw file", "file_type": "z-stack", "md5sum": "bbdfb1f1d6315c9783dffe49f43ef9e4", "upload_key": "79711238-da6d-40b3-92f2-0109b9d8c08e/4DNFIHZEHI3R.r3d", "href": "/files-microscopy/4DNFIHZEHI3R/@@download/4DNFIHZEHI3R.r3d", "status": "released", "lab": {"uuid": "c17e88b5-912a-496a-acc7-28dd71215a7d", "display_title": "Mitchell Guttman, CALTECH", "name": "mitchell-guttman-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/mitchell-guttman-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c17e88b5-912a-496a-acc7-28dd71215a7d"]}}, "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f886118b2c", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "r3d", "file_format": "r3d", "@id": "/file-formats/r3d/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Mitchell Guttman, CALTECH", "experiment_type": "DNA FISH", "experiment_bucket": "raw file", "assay_info": "Chromosomes, GRCm38:18:3004000-5000150 mouse region, Srsf2 mouse protein", "dataset": "FISH for DNA SPRITE", "condition": "Chr18 inactive region + nuclear speckle", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Mitchell Guttman, CALTECH"}}, {"file_size": 1056975712, "@type": ["FileMicroscopy", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/6a393078-847a-49e0-837d-f567073a651c/4DNFIEZESSC6.r3d", "@id": "/files-microscopy/4DNFIEZESSC6/", "file_type_detailed": "z-stack (r3d)", "display_title": "4DNFIEZESSC6.r3d", "accession": "4DNFIEZESSC6", "uuid": "6a393078-847a-49e0-837d-f567073a651c", "file_classification": "raw file", "file_type": "z-stack", "md5sum": "7aedcac785647e508816b76ddca8210d", "upload_key": "6a393078-847a-49e0-837d-f567073a651c/4DNFIEZESSC6.r3d", "href": "/files-microscopy/4DNFIEZESSC6/@@download/4DNFIEZESSC6.r3d", "status": "released", "lab": {"uuid": "c17e88b5-912a-496a-acc7-28dd71215a7d", "display_title": "Mitchell Guttman, CALTECH", "name": "mitchell-guttman-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/mitchell-guttman-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c17e88b5-912a-496a-acc7-28dd71215a7d"]}}, "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f886118b2c", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "r3d", "file_format": "r3d", "@id": "/file-formats/r3d/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Mitchell Guttman, CALTECH", "experiment_type": "DNA FISH", "experiment_bucket": "raw file", "assay_info": "Chromosomes, GRCm38:18:3004000-5000150 mouse region, Srsf2 mouse protein", "dataset": "FISH for DNA SPRITE", "condition": "Chr18 inactive region + nuclear speckle", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Mitchell Guttman, CALTECH"}}, {"file_size": 1056975712, "@type": ["FileMicroscopy", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/a9523653-fc64-4f6f-95a5-09502e9e77e0/4DNFI7ATHAPZ.r3d", "@id": "/files-microscopy/4DNFI7ATHAPZ/", "file_type_detailed": "z-stack (r3d)", "display_title": "4DNFI7ATHAPZ.r3d", "accession": "4DNFI7ATHAPZ", "uuid": "a9523653-fc64-4f6f-95a5-09502e9e77e0", "file_classification": "raw file", "file_type": "z-stack", "md5sum": "a6807ec29b502cfd924e38f1a3c2960c", "upload_key": "a9523653-fc64-4f6f-95a5-09502e9e77e0/4DNFI7ATHAPZ.r3d", "href": "/files-microscopy/4DNFI7ATHAPZ/@@download/4DNFI7ATHAPZ.r3d", "status": "released", "lab": {"uuid": "c17e88b5-912a-496a-acc7-28dd71215a7d", "display_title": "Mitchell Guttman, CALTECH", "name": "mitchell-guttman-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/mitchell-guttman-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c17e88b5-912a-496a-acc7-28dd71215a7d"]}}, "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f886118b2c", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "r3d", "file_format": "r3d", "@id": "/file-formats/r3d/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Mitchell Guttman, CALTECH", "experiment_type": "DNA FISH", "experiment_bucket": "raw file", "assay_info": "Chromosomes, GRCm38:18:3004000-5000150 mouse region, Srsf2 mouse protein", "dataset": "FISH for DNA SPRITE", "condition": "Chr18 inactive region + nuclear speckle", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Mitchell Guttman, CALTECH"}}, {"file_size": 1056975712, "@type": ["FileMicroscopy", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/37f2a946-3bc1-4aaa-b55b-feae093f16a6/4DNFIZSLKZFE.r3d", "@id": "/files-microscopy/4DNFIZSLKZFE/", "file_type_detailed": "z-stack (r3d)", "display_title": "4DNFIZSLKZFE.r3d", "accession": "4DNFIZSLKZFE", "uuid": "37f2a946-3bc1-4aaa-b55b-feae093f16a6", "file_classification": "raw file", "file_type": "z-stack", "md5sum": "cac2519e6115ea43927878f4343d741f", "upload_key": "37f2a946-3bc1-4aaa-b55b-feae093f16a6/4DNFIZSLKZFE.r3d", "href": "/files-microscopy/4DNFIZSLKZFE/@@download/4DNFIZSLKZFE.r3d", "status": "released", "lab": {"uuid": "c17e88b5-912a-496a-acc7-28dd71215a7d", "display_title": "Mitchell Guttman, CALTECH", "name": "mitchell-guttman-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/mitchell-guttman-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c17e88b5-912a-496a-acc7-28dd71215a7d"]}}, "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f886118b2c", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "r3d", "file_format": "r3d", "@id": "/file-formats/r3d/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Mitchell Guttman, CALTECH", "experiment_type": "DNA FISH", "experiment_bucket": "raw file", "assay_info": "Chromosomes, GRCm38:18:3004000-5000150 mouse region, Srsf2 mouse protein", "dataset": "FISH for DNA SPRITE", "condition": "Chr18 inactive region + nuclear speckle", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Mitchell Guttman, CALTECH"}}, {"file_size": 1056975712, "@type": ["FileMicroscopy", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/242a5c27-541b-4791-897c-057e7d226d91/4DNFILRGZ797.r3d", "@id": "/files-microscopy/4DNFILRGZ797/", "file_type_detailed": "z-stack (r3d)", "display_title": "4DNFILRGZ797.r3d", "accession": "4DNFILRGZ797", "uuid": "242a5c27-541b-4791-897c-057e7d226d91", "file_classification": "raw file", "file_type": "z-stack", "md5sum": "c3880d0246f070ab93e3c4891f467e77", "upload_key": "242a5c27-541b-4791-897c-057e7d226d91/4DNFILRGZ797.r3d", "href": "/files-microscopy/4DNFILRGZ797/@@download/4DNFILRGZ797.r3d", "status": "released", "lab": {"uuid": "c17e88b5-912a-496a-acc7-28dd71215a7d", "display_title": "Mitchell Guttman, CALTECH", "name": "mitchell-guttman-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/mitchell-guttman-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c17e88b5-912a-496a-acc7-28dd71215a7d"]}}, "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f886118b2c", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "r3d", "file_format": "r3d", "@id": "/file-formats/r3d/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Mitchell Guttman, CALTECH", "experiment_type": "DNA FISH", "experiment_bucket": "raw file", "assay_info": "Chromosomes, GRCm38:18:3004000-5000150 mouse region, Srsf2 mouse protein", "dataset": "FISH for DNA SPRITE", "condition": "Chr18 inactive region + nuclear speckle", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Mitchell Guttman, CALTECH"}}, {"file_size": 1056975712, "@type": ["FileMicroscopy", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/06fde7c2-3ee0-47cc-8513-4ffc7e20ca0a/4DNFI89W7TCJ.r3d", "@id": "/files-microscopy/4DNFI89W7TCJ/", "file_type_detailed": "z-stack (r3d)", "display_title": "4DNFI89W7TCJ.r3d", "accession": "4DNFI89W7TCJ", "uuid": "06fde7c2-3ee0-47cc-8513-4ffc7e20ca0a", "file_classification": "raw file", "file_type": "z-stack", "md5sum": "00bac981def22cab4369cf272642808f", "upload_key": "06fde7c2-3ee0-47cc-8513-4ffc7e20ca0a/4DNFI89W7TCJ.r3d", "href": "/files-microscopy/4DNFI89W7TCJ/@@download/4DNFI89W7TCJ.r3d", "status": "released", "lab": {"uuid": "c17e88b5-912a-496a-acc7-28dd71215a7d", "display_title": "Mitchell Guttman, CALTECH", "name": "mitchell-guttman-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/mitchell-guttman-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c17e88b5-912a-496a-acc7-28dd71215a7d"]}}, "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f886118b2c", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "r3d", "file_format": "r3d", "@id": "/file-formats/r3d/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Mitchell Guttman, CALTECH", "experiment_type": "DNA FISH", "experiment_bucket": "raw file", "assay_info": "Chromosomes, GRCm38:18:3004000-5000150 mouse region, Srsf2 mouse protein", "dataset": "FISH for DNA SPRITE", "condition": "Chr18 inactive region + nuclear speckle", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Mitchell Guttman, CALTECH"}}, {"file_size": 1056975712, "@type": ["FileMicroscopy", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/79adc08d-4c39-4608-9c55-970685d936b8/4DNFI4LAY13U.r3d", "@id": "/files-microscopy/4DNFI4LAY13U/", "file_type_detailed": "z-stack (r3d)", "display_title": "4DNFI4LAY13U.r3d", "accession": "4DNFI4LAY13U", "uuid": "79adc08d-4c39-4608-9c55-970685d936b8", "file_classification": "raw file", "file_type": "z-stack", "md5sum": "121ef7683f923782eb0a2b432f4ba538", "upload_key": "79adc08d-4c39-4608-9c55-970685d936b8/4DNFI4LAY13U.r3d", "href": "/files-microscopy/4DNFI4LAY13U/@@download/4DNFI4LAY13U.r3d", "status": "released", "lab": {"uuid": "c17e88b5-912a-496a-acc7-28dd71215a7d", "display_title": "Mitchell Guttman, CALTECH", "name": "mitchell-guttman-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/mitchell-guttman-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c17e88b5-912a-496a-acc7-28dd71215a7d"]}}, "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f886118b2c", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "r3d", "file_format": "r3d", "@id": "/file-formats/r3d/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Mitchell Guttman, CALTECH", "experiment_type": "DNA FISH", "experiment_bucket": "raw file", "assay_info": "Chromosomes, GRCm38:18:3004000-5000150 mouse region, Srsf2 mouse protein", "dataset": "FISH for DNA SPRITE", "condition": "Chr18 inactive region + nuclear speckle", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Mitchell Guttman, CALTECH"}}, {"file_size": 1056975712, "@type": ["FileMicroscopy", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/5d2c62a1-fb37-4730-9cbf-a1e282222486/4DNFI2YS39KK.r3d", "@id": "/files-microscopy/4DNFI2YS39KK/", "file_type_detailed": "z-stack (r3d)", "display_title": "4DNFI2YS39KK.r3d", "accession": "4DNFI2YS39KK", "uuid": "5d2c62a1-fb37-4730-9cbf-a1e282222486", "file_classification": "raw file", "file_type": "z-stack", "md5sum": "e8805b27abb500673d423ab0b94092e1", "upload_key": "5d2c62a1-fb37-4730-9cbf-a1e282222486/4DNFI2YS39KK.r3d", "href": "/files-microscopy/4DNFI2YS39KK/@@download/4DNFI2YS39KK.r3d", "status": "released", "lab": {"uuid": "c17e88b5-912a-496a-acc7-28dd71215a7d", "display_title": "Mitchell Guttman, CALTECH", "name": "mitchell-guttman-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/mitchell-guttman-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c17e88b5-912a-496a-acc7-28dd71215a7d"]}}, "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f886118b2c", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "r3d", "file_format": "r3d", "@id": "/file-formats/r3d/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Mitchell Guttman, CALTECH", "experiment_type": "DNA FISH", "experiment_bucket": "raw file", "assay_info": "Chromosomes, GRCm38:18:3004000-5000150 mouse region, Srsf2 mouse protein", "dataset": "FISH for DNA SPRITE", "condition": "Chr18 inactive region + nuclear speckle", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Mitchell Guttman, CALTECH"}}, {"file_size": 1056975712, "@type": ["FileMicroscopy", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/3e8711c7-975d-44d4-83bb-bf19f74da843/4DNFIB8SL8LS.r3d", "@id": "/files-microscopy/4DNFIB8SL8LS/", "file_type_detailed": "z-stack (r3d)", "display_title": "4DNFIB8SL8LS.r3d", "accession": "4DNFIB8SL8LS", "uuid": "3e8711c7-975d-44d4-83bb-bf19f74da843", "file_classification": "raw file", "file_type": "z-stack", "md5sum": "4946a668bea2e3902322045cfcb30848", "upload_key": "3e8711c7-975d-44d4-83bb-bf19f74da843/4DNFIB8SL8LS.r3d", "href": "/files-microscopy/4DNFIB8SL8LS/@@download/4DNFIB8SL8LS.r3d", "status": "released", "lab": {"uuid": "c17e88b5-912a-496a-acc7-28dd71215a7d", "display_title": "Mitchell Guttman, CALTECH", "name": "mitchell-guttman-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/mitchell-guttman-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c17e88b5-912a-496a-acc7-28dd71215a7d"]}}, "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f886118b2c", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "r3d", "file_format": "r3d", "@id": "/file-formats/r3d/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Mitchell Guttman, CALTECH", "experiment_type": "DNA FISH", "experiment_bucket": "raw file", "assay_info": "Chromosomes, GRCm38:18:3004000-5000150 mouse region, Srsf2 mouse protein", "dataset": "FISH for DNA SPRITE", "condition": "Chr18 inactive region + nuclear speckle", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Mitchell Guttman, CALTECH"}}, {"file_size": 1056975712, "@type": ["FileMicroscopy", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/aa90756d-c523-474c-a269-5376d78a9647/4DNFI3USK59K.r3d", "@id": "/files-microscopy/4DNFI3USK59K/", "file_type_detailed": "z-stack (r3d)", "display_title": "4DNFI3USK59K.r3d", "accession": "4DNFI3USK59K", "uuid": "aa90756d-c523-474c-a269-5376d78a9647", "file_classification": "raw file", "file_type": "z-stack", "md5sum": "dc0593be7894991e064cf0654c2224d8", "upload_key": "aa90756d-c523-474c-a269-5376d78a9647/4DNFI3USK59K.r3d", "href": "/files-microscopy/4DNFI3USK59K/@@download/4DNFI3USK59K.r3d", "status": "released", "lab": {"uuid": "c17e88b5-912a-496a-acc7-28dd71215a7d", "display_title": "Mitchell Guttman, CALTECH", "name": "mitchell-guttman-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/mitchell-guttman-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c17e88b5-912a-496a-acc7-28dd71215a7d"]}}, "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f886118b2c", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "r3d", "file_format": "r3d", "@id": "/file-formats/r3d/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Mitchell Guttman, CALTECH", "experiment_type": "DNA FISH", "experiment_bucket": "raw file", "assay_info": "Chromosomes, GRCm38:18:3004000-5000150 mouse region, Srsf2 mouse protein", "dataset": "FISH for DNA SPRITE", "condition": "Chr18 inactive region + nuclear speckle", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Mitchell Guttman, CALTECH"}}, {"file_size": 1056975712, "@type": ["FileMicroscopy", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/d20bc4d1-a0c8-4337-a660-a618c021faa2/4DNFIPEMN4ZN.r3d", "@id": "/files-microscopy/4DNFIPEMN4ZN/", "file_type_detailed": "z-stack (r3d)", "display_title": "4DNFIPEMN4ZN.r3d", "accession": "4DNFIPEMN4ZN", "uuid": "d20bc4d1-a0c8-4337-a660-a618c021faa2", "file_classification": "raw file", "file_type": "z-stack", "md5sum": "be7e0d2435e2bfcdba6e134ef63bcceb", "upload_key": "d20bc4d1-a0c8-4337-a660-a618c021faa2/4DNFIPEMN4ZN.r3d", "href": "/files-microscopy/4DNFIPEMN4ZN/@@download/4DNFIPEMN4ZN.r3d", "status": "released", "lab": {"uuid": "c17e88b5-912a-496a-acc7-28dd71215a7d", "display_title": "Mitchell Guttman, CALTECH", "name": "mitchell-guttman-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/mitchell-guttman-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c17e88b5-912a-496a-acc7-28dd71215a7d"]}}, "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f886118b2c", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "r3d", "file_format": "r3d", "@id": "/file-formats/r3d/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Mitchell Guttman, CALTECH", "experiment_type": "DNA FISH", "experiment_bucket": "raw file", "assay_info": "Chromosomes, GRCm38:18:3004000-5000150 mouse region, Srsf2 mouse protein", "dataset": "FISH for DNA SPRITE", "condition": "Chr18 inactive region + nuclear speckle", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Mitchell Guttman, CALTECH"}}, {"file_size": 1056975712, "@type": ["FileMicroscopy", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/7201636f-d3a4-41b4-b93e-e0fc8a8dad81/4DNFIOGZ19I5.r3d", "@id": "/files-microscopy/4DNFIOGZ19I5/", "file_type_detailed": "z-stack (r3d)", "display_title": "4DNFIOGZ19I5.r3d", "accession": "4DNFIOGZ19I5", "uuid": "7201636f-d3a4-41b4-b93e-e0fc8a8dad81", "file_classification": "raw file", "file_type": "z-stack", "md5sum": "57088773cb84dc26745891b12c54a456", "upload_key": "7201636f-d3a4-41b4-b93e-e0fc8a8dad81/4DNFIOGZ19I5.r3d", "href": "/files-microscopy/4DNFIOGZ19I5/@@download/4DNFIOGZ19I5.r3d", "status": "released", "lab": {"uuid": "c17e88b5-912a-496a-acc7-28dd71215a7d", "display_title": "Mitchell Guttman, CALTECH", "name": "mitchell-guttman-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/mitchell-guttman-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c17e88b5-912a-496a-acc7-28dd71215a7d"]}}, "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f886118b2c", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "r3d", "file_format": "r3d", "@id": "/file-formats/r3d/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Mitchell Guttman, CALTECH", "experiment_type": "DNA FISH", "experiment_bucket": "raw file", "assay_info": "Chromosomes, GRCm38:18:3004000-5000150 mouse region, Srsf2 mouse protein", "dataset": "FISH for DNA SPRITE", "condition": "Chr18 inactive region + nuclear speckle", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Mitchell Guttman, CALTECH"}}, {"file_size": 1056975712, "@type": ["FileMicroscopy", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/5570b95d-6560-48b0-92ab-041547757f7a/4DNFI7V41LA2.r3d", "@id": "/files-microscopy/4DNFI7V41LA2/", "file_type_detailed": "z-stack (r3d)", "display_title": "4DNFI7V41LA2.r3d", "accession": "4DNFI7V41LA2", "uuid": "5570b95d-6560-48b0-92ab-041547757f7a", "file_classification": "raw file", "file_type": "z-stack", "md5sum": "e58d60e2c6d76c66b2989d331c7d1612", "upload_key": "5570b95d-6560-48b0-92ab-041547757f7a/4DNFI7V41LA2.r3d", "href": "/files-microscopy/4DNFI7V41LA2/@@download/4DNFI7V41LA2.r3d", "status": "released", "lab": {"uuid": "c17e88b5-912a-496a-acc7-28dd71215a7d", "display_title": "Mitchell Guttman, CALTECH", "name": "mitchell-guttman-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/mitchell-guttman-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c17e88b5-912a-496a-acc7-28dd71215a7d"]}}, "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f886118b2c", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "r3d", "file_format": "r3d", "@id": "/file-formats/r3d/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Mitchell Guttman, CALTECH", "experiment_type": "DNA FISH", "experiment_bucket": "raw file", "assay_info": "Chromosomes, GRCm38:18:3004000-5000150 mouse region, Srsf2 mouse protein", "dataset": "FISH for DNA SPRITE", "condition": "Chr18 inactive region + nuclear speckle", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Mitchell Guttman, CALTECH"}}, {"file_size": 1056975712, "@type": ["FileMicroscopy", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/d2f317cf-43fa-484f-97ca-446e3f81bcae/4DNFILKNO88L.r3d", "@id": "/files-microscopy/4DNFILKNO88L/", "file_type_detailed": "z-stack (r3d)", "display_title": "4DNFILKNO88L.r3d", "accession": "4DNFILKNO88L", "uuid": "d2f317cf-43fa-484f-97ca-446e3f81bcae", "file_classification": "raw file", "file_type": "z-stack", "md5sum": "e5fbfe17c542f03c0992691b00ee85fe", "upload_key": "d2f317cf-43fa-484f-97ca-446e3f81bcae/4DNFILKNO88L.r3d", "href": "/files-microscopy/4DNFILKNO88L/@@download/4DNFILKNO88L.r3d", "status": "released", "lab": {"uuid": "c17e88b5-912a-496a-acc7-28dd71215a7d", "display_title": "Mitchell Guttman, CALTECH", "name": "mitchell-guttman-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/mitchell-guttman-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c17e88b5-912a-496a-acc7-28dd71215a7d"]}}, "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f886118b2c", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "r3d", "file_format": "r3d", "@id": "/file-formats/r3d/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Mitchell Guttman, CALTECH", "experiment_type": "DNA FISH", "experiment_bucket": "raw file", "assay_info": "Chromosomes, GRCm38:18:3004000-5000150 mouse region, Srsf2 mouse protein", "dataset": "FISH for DNA SPRITE", "condition": "Chr18 inactive region + nuclear speckle", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Mitchell Guttman, CALTECH"}}, {"file_size": 1056975712, "@type": ["FileMicroscopy", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/2ee0cd6a-6ffc-47e4-9e42-0b1b3710c871/4DNFIH1KOG63.r3d", "@id": "/files-microscopy/4DNFIH1KOG63/", "file_type_detailed": "z-stack (r3d)", "display_title": "4DNFIH1KOG63.r3d", "accession": "4DNFIH1KOG63", "uuid": "2ee0cd6a-6ffc-47e4-9e42-0b1b3710c871", "file_classification": "raw file", "file_type": "z-stack", "md5sum": "80231864057726b9b00d4d70c2af9bb9", "upload_key": "2ee0cd6a-6ffc-47e4-9e42-0b1b3710c871/4DNFIH1KOG63.r3d", "href": "/files-microscopy/4DNFIH1KOG63/@@download/4DNFIH1KOG63.r3d", "status": "released", "lab": {"uuid": "c17e88b5-912a-496a-acc7-28dd71215a7d", "display_title": "Mitchell Guttman, CALTECH", "name": "mitchell-guttman-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/mitchell-guttman-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c17e88b5-912a-496a-acc7-28dd71215a7d"]}}, "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f886118b2c", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "r3d", "file_format": "r3d", "@id": "/file-formats/r3d/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Mitchell Guttman, CALTECH", "experiment_type": "DNA FISH", "experiment_bucket": "raw file", "assay_info": "Chromosomes, GRCm38:18:3004000-5000150 mouse region, Srsf2 mouse protein", "dataset": "FISH for DNA SPRITE", "condition": "Chr18 inactive region + nuclear speckle", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Mitchell Guttman, CALTECH"}}, {"file_size": 1056975712, "@type": ["FileMicroscopy", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/20b7809d-3115-415c-bd74-63da220241c4/4DNFIP23MJVI.r3d", "@id": "/files-microscopy/4DNFIP23MJVI/", "file_type_detailed": "z-stack (r3d)", "display_title": "4DNFIP23MJVI.r3d", "accession": "4DNFIP23MJVI", "uuid": "20b7809d-3115-415c-bd74-63da220241c4", "file_classification": "raw file", "file_type": "z-stack", "md5sum": "60d3192cf0aa2bc2ee6f26d073e78839", "upload_key": "20b7809d-3115-415c-bd74-63da220241c4/4DNFIP23MJVI.r3d", "href": "/files-microscopy/4DNFIP23MJVI/@@download/4DNFIP23MJVI.r3d", "status": "released", "lab": {"uuid": "c17e88b5-912a-496a-acc7-28dd71215a7d", "display_title": "Mitchell Guttman, CALTECH", "name": "mitchell-guttman-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/mitchell-guttman-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c17e88b5-912a-496a-acc7-28dd71215a7d"]}}, "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f886118b2c", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "r3d", "file_format": "r3d", "@id": "/file-formats/r3d/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Mitchell Guttman, CALTECH", "experiment_type": "DNA FISH", "experiment_bucket": "raw file", "assay_info": "Chromosomes, GRCm38:18:3004000-5000150 mouse region, Srsf2 mouse protein", "dataset": "FISH for DNA SPRITE", "condition": "Chr18 inactive region + nuclear speckle", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Mitchell Guttman, CALTECH"}}, {"file_size": 1056975712, "@type": ["FileMicroscopy", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/0147d45b-a83c-4953-8c0c-cea3a6580c24/4DNFIJ9AKHTE.r3d", "@id": "/files-microscopy/4DNFIJ9AKHTE/", "file_type_detailed": "z-stack (r3d)", "display_title": "4DNFIJ9AKHTE.r3d", "accession": "4DNFIJ9AKHTE", "uuid": "0147d45b-a83c-4953-8c0c-cea3a6580c24", "file_classification": "raw file", "file_type": "z-stack", "md5sum": "6d47d4a0574fc23fe88563c74d5f40ef", "upload_key": "0147d45b-a83c-4953-8c0c-cea3a6580c24/4DNFIJ9AKHTE.r3d", "href": "/files-microscopy/4DNFIJ9AKHTE/@@download/4DNFIJ9AKHTE.r3d", "status": "released", "lab": {"uuid": "c17e88b5-912a-496a-acc7-28dd71215a7d", "display_title": "Mitchell Guttman, CALTECH", "name": "mitchell-guttman-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/mitchell-guttman-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c17e88b5-912a-496a-acc7-28dd71215a7d"]}}, "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f886118b2c", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "r3d", "file_format": "r3d", "@id": "/file-formats/r3d/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Mitchell Guttman, CALTECH", "experiment_type": "DNA FISH", "experiment_bucket": "raw file", "assay_info": "Chromosomes, GRCm38:18:3004000-5000150 mouse region, Srsf2 mouse protein", "dataset": "FISH for DNA SPRITE", "condition": "Chr18 inactive region + nuclear speckle", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Mitchell Guttman, CALTECH"}}, {"file_size": 1056975712, "@type": ["FileMicroscopy", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/3e949498-e10d-454c-85c5-6c8ec70cfe40/4DNFIJ4OJC5C.r3d", "@id": "/files-microscopy/4DNFIJ4OJC5C/", "file_type_detailed": "z-stack (r3d)", "display_title": "4DNFIJ4OJC5C.r3d", "accession": "4DNFIJ4OJC5C", "uuid": "3e949498-e10d-454c-85c5-6c8ec70cfe40", "file_classification": "raw file", "file_type": "z-stack", "md5sum": "e066b6031f16490451f46d2b58e852d0", "upload_key": "3e949498-e10d-454c-85c5-6c8ec70cfe40/4DNFIJ4OJC5C.r3d", "href": "/files-microscopy/4DNFIJ4OJC5C/@@download/4DNFIJ4OJC5C.r3d", "status": "released", "lab": {"uuid": "c17e88b5-912a-496a-acc7-28dd71215a7d", "display_title": "Mitchell Guttman, CALTECH", "name": "mitchell-guttman-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/mitchell-guttman-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c17e88b5-912a-496a-acc7-28dd71215a7d"]}}, "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f886118b2c", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "r3d", "file_format": "r3d", "@id": "/file-formats/r3d/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Mitchell Guttman, CALTECH", "experiment_type": "DNA FISH", "experiment_bucket": "raw file", "assay_info": "Chromosomes, GRCm38:18:3004000-5000150 mouse region, Srsf2 mouse protein", "dataset": "FISH for DNA SPRITE", "condition": "Chr18 inactive region + nuclear speckle", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Mitchell Guttman, CALTECH"}}, {"file_size": 1056975712, "@type": ["FileMicroscopy", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/4547c68f-1361-4f38-9419-ee32dd21fcb9/4DNFIJP8HQX1.r3d", "@id": "/files-microscopy/4DNFIJP8HQX1/", "file_type_detailed": "z-stack (r3d)", "display_title": "4DNFIJP8HQX1.r3d", "accession": "4DNFIJP8HQX1", "uuid": "4547c68f-1361-4f38-9419-ee32dd21fcb9", "file_classification": "raw file", "file_type": "z-stack", "md5sum": "ee26bb37576e3c0c5bf0e0ad2ebe6b8e", "upload_key": "4547c68f-1361-4f38-9419-ee32dd21fcb9/4DNFIJP8HQX1.r3d", "href": "/files-microscopy/4DNFIJP8HQX1/@@download/4DNFIJP8HQX1.r3d", "status": "released", "lab": {"uuid": "c17e88b5-912a-496a-acc7-28dd71215a7d", "display_title": "Mitchell Guttman, CALTECH", "name": "mitchell-guttman-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/mitchell-guttman-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c17e88b5-912a-496a-acc7-28dd71215a7d"]}}, "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f886118b2c", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "r3d", "file_format": "r3d", "@id": "/file-formats/r3d/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Mitchell Guttman, CALTECH", "experiment_type": "DNA FISH", "experiment_bucket": "raw file", "assay_info": "Chromosomes, GRCm38:18:3004000-5000150 mouse region, Srsf2 mouse protein", "dataset": "FISH for DNA SPRITE", "condition": "Chr18 inactive region + nuclear speckle", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Mitchell Guttman, CALTECH"}}, {"file_size": 1056975712, "@type": ["FileMicroscopy", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/b1391ad2-5eb1-42b2-b89a-498229def4e9/4DNFIJOJG848.r3d", "@id": "/files-microscopy/4DNFIJOJG848/", "file_type_detailed": "z-stack (r3d)", "display_title": "4DNFIJOJG848.r3d", "accession": "4DNFIJOJG848", "uuid": "b1391ad2-5eb1-42b2-b89a-498229def4e9", "file_classification": "raw file", "file_type": "z-stack", "md5sum": "dcc1d1e8ac6cb550e8584ff3cf9e499d", "upload_key": "b1391ad2-5eb1-42b2-b89a-498229def4e9/4DNFIJOJG848.r3d", "href": "/files-microscopy/4DNFIJOJG848/@@download/4DNFIJOJG848.r3d", "status": "released", "lab": {"uuid": "c17e88b5-912a-496a-acc7-28dd71215a7d", "display_title": "Mitchell Guttman, CALTECH", "name": "mitchell-guttman-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/mitchell-guttman-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c17e88b5-912a-496a-acc7-28dd71215a7d"]}}, "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f886118b2c", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "r3d", "file_format": "r3d", "@id": "/file-formats/r3d/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Mitchell Guttman, CALTECH", "experiment_type": "DNA FISH", "experiment_bucket": "raw file", "assay_info": "Chromosomes, GRCm38:18:3004000-5000150 mouse region, Srsf2 mouse protein", "dataset": "FISH for DNA SPRITE", "condition": "Chr18 inactive region + nuclear speckle", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Mitchell Guttman, CALTECH"}}, {"file_size": 1056975712, "@type": ["FileMicroscopy", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/e53b94c9-5b10-4c75-ba99-7f2da17b5c31/4DNFINU1B9DM.r3d", "@id": "/files-microscopy/4DNFINU1B9DM/", "file_type_detailed": "z-stack (r3d)", "display_title": "4DNFINU1B9DM.r3d", "accession": "4DNFINU1B9DM", "uuid": "e53b94c9-5b10-4c75-ba99-7f2da17b5c31", "file_classification": "raw file", "file_type": "z-stack", "md5sum": "fd4165258e156f54b9da35f59281e963", "upload_key": "e53b94c9-5b10-4c75-ba99-7f2da17b5c31/4DNFINU1B9DM.r3d", "href": "/files-microscopy/4DNFINU1B9DM/@@download/4DNFINU1B9DM.r3d", "status": "released", "lab": {"uuid": "c17e88b5-912a-496a-acc7-28dd71215a7d", "display_title": "Mitchell Guttman, CALTECH", "name": "mitchell-guttman-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/mitchell-guttman-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c17e88b5-912a-496a-acc7-28dd71215a7d"]}}, "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f886118b2c", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "r3d", "file_format": "r3d", "@id": "/file-formats/r3d/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Mitchell Guttman, CALTECH", "experiment_type": "DNA FISH", "experiment_bucket": "raw file", "assay_info": "Chromosomes, GRCm38:18:3004000-5000150 mouse region, Srsf2 mouse protein", "dataset": "FISH for DNA SPRITE", "condition": "Chr18 inactive region + nuclear speckle", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Mitchell Guttman, CALTECH"}}, {"file_size": 1056975712, "@type": ["FileMicroscopy", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/4db31265-156d-4f8c-8539-5ea8acfa1d8e/4DNFIQ2PBINN.r3d", "@id": "/files-microscopy/4DNFIQ2PBINN/", "file_type_detailed": "z-stack (r3d)", "display_title": "4DNFIQ2PBINN.r3d", "accession": "4DNFIQ2PBINN", "uuid": "4db31265-156d-4f8c-8539-5ea8acfa1d8e", "file_classification": "raw file", "file_type": "z-stack", "md5sum": "afa8be5a5236f3d59cc0c58d158153d5", "upload_key": "4db31265-156d-4f8c-8539-5ea8acfa1d8e/4DNFIQ2PBINN.r3d", "href": "/files-microscopy/4DNFIQ2PBINN/@@download/4DNFIQ2PBINN.r3d", "status": "released", "lab": {"uuid": "c17e88b5-912a-496a-acc7-28dd71215a7d", "display_title": "Mitchell Guttman, CALTECH", "name": "mitchell-guttman-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/mitchell-guttman-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c17e88b5-912a-496a-acc7-28dd71215a7d"]}}, "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f886118b2c", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "r3d", "file_format": "r3d", "@id": "/file-formats/r3d/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Mitchell Guttman, CALTECH", "experiment_type": "DNA FISH", "experiment_bucket": "raw file", "assay_info": "Chromosomes, GRCm38:18:3004000-5000150 mouse region, Srsf2 mouse protein", "dataset": "FISH for DNA SPRITE", "condition": "Chr18 inactive region + nuclear speckle", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Mitchell Guttman, CALTECH"}}, {"file_size": 1056975712, "@type": ["FileMicroscopy", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/e94f8e93-8ed4-4a60-9838-cb7939e4229f/4DNFIDR7QERN.r3d", "@id": "/files-microscopy/4DNFIDR7QERN/", "file_type_detailed": "z-stack (r3d)", "display_title": "4DNFIDR7QERN.r3d", "accession": "4DNFIDR7QERN", "uuid": "e94f8e93-8ed4-4a60-9838-cb7939e4229f", "file_classification": "raw file", "file_type": "z-stack", "md5sum": "e437f2df3b19168a6bb6629cc710e4a2", "upload_key": "e94f8e93-8ed4-4a60-9838-cb7939e4229f/4DNFIDR7QERN.r3d", "href": "/files-microscopy/4DNFIDR7QERN/@@download/4DNFIDR7QERN.r3d", "status": "released", "lab": {"uuid": "c17e88b5-912a-496a-acc7-28dd71215a7d", "display_title": "Mitchell Guttman, CALTECH", "name": "mitchell-guttman-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/mitchell-guttman-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c17e88b5-912a-496a-acc7-28dd71215a7d"]}}, "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f886118b2c", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "r3d", "file_format": "r3d", "@id": "/file-formats/r3d/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Mitchell Guttman, CALTECH", "experiment_type": "DNA FISH", "experiment_bucket": "raw file", "assay_info": "Chromosomes, GRCm38:18:3004000-5000150 mouse region, Srsf2 mouse protein", "dataset": "FISH for DNA SPRITE", "condition": "Chr18 inactive region + nuclear speckle", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Mitchell Guttman, CALTECH"}}, {"file_size": 1056975712, "@type": ["FileMicroscopy", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/f8550646-e9ac-4d61-9cfd-4bc97819a7b2/4DNFIL74MBGE.r3d", "@id": "/files-microscopy/4DNFIL74MBGE/", "file_type_detailed": "z-stack (r3d)", "display_title": "4DNFIL74MBGE.r3d", "accession": "4DNFIL74MBGE", "uuid": "f8550646-e9ac-4d61-9cfd-4bc97819a7b2", "file_classification": "raw file", "file_type": "z-stack", "md5sum": "b65d8c059c7fcf56230a11390af71118", "upload_key": "f8550646-e9ac-4d61-9cfd-4bc97819a7b2/4DNFIL74MBGE.r3d", "href": "/files-microscopy/4DNFIL74MBGE/@@download/4DNFIL74MBGE.r3d", "status": "released", "lab": {"uuid": "c17e88b5-912a-496a-acc7-28dd71215a7d", "display_title": "Mitchell Guttman, CALTECH", "name": "mitchell-guttman-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/mitchell-guttman-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c17e88b5-912a-496a-acc7-28dd71215a7d"]}}, "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f886118b2c", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "r3d", "file_format": "r3d", "@id": "/file-formats/r3d/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Mitchell Guttman, CALTECH", "experiment_type": "DNA FISH", "experiment_bucket": "raw file", "assay_info": "Chromosomes, GRCm38:18:3004000-5000150 mouse region, Srsf2 mouse protein", "dataset": "FISH for DNA SPRITE", "condition": "Chr18 inactive region + nuclear speckle", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Mitchell Guttman, CALTECH"}}], "@type": ["ExperimentMic", "Experiment", "Item"], "@id": "/experiments-mic/4DNEXNDIAZIG/", "biosample": {"display_title": "4DNBS2F7M7RP", "@type": ["Biosample", "Item"], "status": "released", "treatments_summary": "None", "modifications_summary": "None", "@id": "/biosamples/4DNBS2F7M7RP/", "biosample_type": "stem cells", "accession": "4DNBS2F7M7RP", "uuid": "d79d81be-6cdf-4fdf-a75c-dd4c9f291c90", "biosample_category": ["Mouse stem cell"], "biosource_summary": "F1 2-1 mESC line", "treatments": [], "biosource": [{"display_title": "F1 2-1 mESC line - 4DNSRW5UG3MR", "cell_line_tier": "Unclassified", "status": "released", "biosource_type": "stem cell derived cell line", "@type": ["Biosource", "Item"], "accession": "4DNSRW5UG3MR", "uuid": "4101fd9b-449a-4dc9-913e-944e1038ddf1", "@id": "/biosources/4DNSRW5UG3MR/", "cell_line": {"term_name": "F121-CASTx129", "display_title": "F1 2-1 mESC line", "preferred_name": "F1 2-1 mESC line", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/4DN:0000255/", "status": "released", "term_id": "4DN:0000255", "uuid": "5a7ff7a9-a2af-4137-9229-1e4e328a58da", "slim_terms": [{"uuid": "c57be9f1-b913-43fb-8437-e76960cfab59", "@id": "/ontology-terms/CL:0002322/", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "embryonic stem cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "f9483d7e-4731-47d1-b8e0-1aac05ba2b49", "@id": "/ontology-terms/CLO:0000031/", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "cell line", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"status": "released", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "display_title": "M. musculus", "@id": "/organisms/10090/", "name": "mouse", "@type": ["Organism", "Item"], "scientific_name": "Mus musculus", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"term_id": "CL:0000034", "term_name": "stem cell", "display_title": "stem cell", "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "synonyms": ["animal stem cell"], "@type": ["OntologyTerm", "Item"], "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "status": "released", "slim_terms": [{"@type": ["OntologyTerm", "Item"], "status": "current", "@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample missing doubling_number", "Biosample missing culture_duration", "Biosample missing morphology_image", "Biosample is a stem cell line over 10 passages but missing karyotype"], "badge": {"display_title": "Biosample Metadata Incomplete", "status": "released", "badge_classification": "Warning", "title": "Biosample Metadata Incomplete", "warning": "Biosample Metadata Incomplete", "badge_icon": "/static/img/badges/biosample-icon.svg", "@type": ["Badge", "Item"], "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "@id": "/badges/biosample-metadata-incomplete/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "modifications": [], "cell_culture_details": [{"display_title": "BiosampleCellCulture from 2018-05-04", "@type": ["BiosampleCellCulture", "Item"], "uuid": "f3ab660c-5d9e-44d4-9c18-f6b81f2880fe", "@id": "/biosample-cell-cultures/f3ab660c-5d9e-44d4-9c18-f6b81f2880fe/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"accession": "4DNFIA7L8MS3", "upload_key": "41c4326c-a2ab-4de2-b816-a449d0ef6f77/4DNFIA7L8MS3.csv", "file_type": "locus distances, submitter format", "display_title": "4DNFIA7L8MS3.csv", "genome_assembly": "GRCm38", "file_type_detailed": "locus distances, submitter format (csv)", "file_format": {"@id": "/file-formats/csv/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "status": "released", "display_title": "csv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_size": 402, "href": "/files-processed/4DNFIA7L8MS3/@@download/4DNFIA7L8MS3.csv", "file_classification": "processed file", "uuid": "41c4326c-a2ab-4de2-b816-a449d0ef6f77", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/41c4326c-a2ab-4de2-b816-a449d0ef6f77/4DNFIA7L8MS3.csv", "md5sum": "f0b0ee21fee9644b2edd05a1e00a2af8", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIA7L8MS3/", "status": "released", "lab": {"status": "current", "@id": "/labs/mitchell-guttman-lab/", "display_title": "Mitchell Guttman, CALTECH", "@type": ["Lab", "Item"], "name": "mitchell-guttman-lab", "uuid": "c17e88b5-912a-496a-acc7-28dd71215a7d", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c17e88b5-912a-496a-acc7-28dd71215a7d"]}}, "last_modified": {"date_modified": "2020-05-21T17:05:59.919139+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Mitchell Guttman, CALTECH", "experiment_type": "DNA FISH", "experiment_bucket": "processed file", "assay_info": "Chromosomes, GRCm38:18:3004000-5000150 mouse region, Srsf2 mouse protein", "dataset": "FISH for DNA SPRITE", "condition": "Chr18 inactive region + nuclear speckle", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F1 2-1 mESC line", "lab_name": "Mitchell Guttman, CALTECH"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Target", "value": "Chromosomes, GRCm38:18:3004000-5000150 mouse region, Srsf2 mouse protein", "combined": "Target: Chromosomes, GRCm38:18:3004000-5000150 mouse region, Srsf2 mouse protein"}, "experiment_type": {"title": "DNA FISH", "display_title": "DNA FISH", "assay_subclassification": "Fixed Sample DNA Localization", "status": "released", "uuid": "5761d0ec-35b0-4aa8-8b81-aac94def59b8", "assay_subclass_short": "FISH", "assay_classification": "Fluorescence Localization", "@type": ["ExperimentType", "Item"], "@id": "/experiment-types/dna-fish/", "experiment_category": "Microscopy", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2019-04-24T16:49:04.510381+00:00"}, "external_references": []}], "experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNESCXK9T73/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "a8ce162e-54fc-49c2-b892-4fe8293388ce", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNESCXK9T73", "external_references": [], "produced_in_pub": {"authors": ["Quinodoz SA", "Ollikainen N", "Tabak B", "Palla A", "Schmidt JM", "Detmar E", "Lai MM", "Shishkin AA", "Bhat P", "Takei Y", "Trinh V", "Aznauryan E", "Russell P", "Cheng C", "Jovanovic M", "Chow A", "Cai L", "McDonel P", "Garber M", "Guttman M"], "short_attribution": "Quinodoz SA et al. (2018)", "status": "current", "uuid": "4ab311b1-a442-46b4-ae4f-16c57521f52e", "@type": ["Publication", "Item"], "url": "https://www.ncbi.nlm.nih.gov/pubmed/29887377", "ID": "doi:10.1016/j.cell.2018.05.024", "display_title": "Quinodoz SA et al. (2018) doi:10.1016/j.cell.2018.05.024", "abstract": "Eukaryotic genomes are packaged into a 3-dimensional structure in the nucleus. Current methods for studying genome-wide structure are based on proximity ligation. However, this approach can fail to detect known structures, such as interactions with nuclear bodies, because these DNA regions can be too far apart  to directly ligate. Accordingly, our overall understanding of genome organization remains incomplete. Here, we develop split-pool recognition of interactions by tag extension (SPRITE), a method that enables genome-wide detection of higher-order interactions within the nucleus. Using SPRITE, we recapitulate known structures identified by proximity ligation and identify additional interactions  occurring across larger distances, including two hubs of inter-chromosomal interactions that are arranged around the nucleolus and nuclear speckles. We show that a substantial fraction of the genome exhibits preferential organization relative to these nuclear bodies. Our results generate a global model whereby nuclear bodies act as inter-chromosomal hubs that shape the overall packaging of  DNA in the nucleus.", "title": "Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus.", "journal": "Cell", "@id": "/publications/4ab311b1-a442-46b4-ae4f-16c57521f52e/", "date_published": "2018-06-07", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"status": "current", "display_title": "Quinodoz SA et al. (2018) doi:10.1016/j.cell.2018.05.024", "abstract": "Eukaryotic genomes are packaged into a 3-dimensional structure in the nucleus. Current methods for studying genome-wide structure are based on proximity ligation. However, this approach can fail to detect known structures, such as interactions with nuclear bodies, because these DNA regions can be too far apart  to directly ligate. Accordingly, our overall understanding of genome organization remains incomplete. Here, we develop split-pool recognition of interactions by tag extension (SPRITE), a method that enables genome-wide detection of higher-order interactions within the nucleus. Using SPRITE, we recapitulate known structures identified by proximity ligation and identify additional interactions  occurring across larger distances, including two hubs of inter-chromosomal interactions that are arranged around the nucleolus and nuclear speckles. We show that a substantial fraction of the genome exhibits preferential organization relative to these nuclear bodies. Our results generate a global model whereby nuclear bodies act as inter-chromosomal hubs that shape the overall packaging of  DNA in the nucleus.", "@type": ["Publication", "Item"], "uuid": "4ab311b1-a442-46b4-ae4f-16c57521f52e", "date_published": "2018-06-07", "title": "Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus.", "authors": ["Quinodoz SA", "Ollikainen N", "Tabak B", "Palla A", "Schmidt JM", "Detmar E", "Lai MM", "Shishkin AA", "Bhat P", "Takei Y", "Trinh V", "Aznauryan E", "Russell P", "Cheng C", "Jovanovic M", "Chow A", "Cai L", "McDonel P", "Garber M", "Guttman M"], "@id": "/publications/4ab311b1-a442-46b4-ae4f-16c57521f52e/", "journal": "Cell", "ID": "doi:10.1016/j.cell.2018.05.024", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 1, "imaging_paths": [{"path": {"display_title": "Chromosomes targeted by DAPI", "status": "released", "@type": ["ImagingPath", "Item"], "@id": "/imaging-paths/44903e2c-f725-4cba-b030-e387b8d980d3/", "labeled_probe": "DAPI", "uuid": "44903e2c-f725-4cba-b030-e387b8d980d3", "target": [{"@type": ["BioFeature", "Item"], "display_title": "Chromosomes", "organism_name": "unspecified", "uuid": "655728f9-d4ab-4dd2-971c-1627ab2c8d33", "cellular_structure": "Chromosomes", "status": "released", "@id": "/bio-features/655728f9-d4ab-4dd2-971c-1627ab2c8d33/", "feature_type": {"term_url": "http://purl.obolibrary.org/obo/GO_0005575", "display_title": "cellular_component", "@id": "/ontology-terms/GO:0005575/", "status": "released", "term_name": "cellular_component", "@type": ["OntologyTerm", "Item"], "term_id": "GO:0005575", "uuid": "e47e2bea-bc1e-4989-881c-521fc0b33529", "preferred_name": "cellular_component", "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": {"display_title": "GRCm38:18:3004000-5000150 mouse region targeted by 495/517nm fluorophore-labeled oligo probe set", "status": "released", "@type": ["ImagingPath", "Item"], "@id": "/imaging-paths/e7d08f59-8779-4281-9419-3bfab40d3daf/", "labeled_probe": "oligo probe set", "uuid": "e7d08f59-8779-4281-9419-3bfab40d3daf", "target": [{"@type": ["BioFeature", "Item"], "display_title": "GRCm38:18:3004000-5000150 mouse region", "organism_name": "mouse", "uuid": "22780c81-56b0-460d-aff7-901427c7dfdd", "status": "released", "@id": "/bio-features/22780c81-56b0-460d-aff7-901427c7dfdd/", "genome_location": [{"status": "released", "start_coordinate": 3004000, "uuid": "689dbe9e-4c3f-4c64-a3c8-0ed1adcb7cec", "@type": ["GenomicRegion", "Item"], "@id": "/genomic-regions/689dbe9e-4c3f-4c64-a3c8-0ed1adcb7cec/", "end_coordinate": 5000150, "genome_assembly": "GRCm38", "display_title": "GRCm38:18:3004000-5000150", "chromosome": "18", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "feature_type": {"term_url": "http://purl.obolibrary.org/obo/SO_0000001", "display_title": "region", "@id": "/ontology-terms/SO:0000001/", "status": "released", "term_name": "region", "@type": ["OntologyTerm", "Item"], "term_id": "SO:0000001", "uuid": "41b7a2c5-f2d9-46b4-a49d-51502fe61bb3", "preferred_name": "region", "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": {"display_title": "Srsf2 mouse protein targeted by mouse anti-SC35 antibody (with DyLight650-labeled anti-mouse secondary antibody)", "status": "released", "@type": ["ImagingPath", "Item"], "@id": "/imaging-paths/3d1d5205-9286-49c2-b745-c66bcf2fae06/", "labeled_probe": "anti-mouse secondary antibody", "uuid": "3d1d5205-9286-49c2-b745-c66bcf2fae06", "other_probes": ["mouse anti-SC35 antibody"], "target": [{"@type": ["BioFeature", "Item"], "display_title": "Srsf2 mouse protein", "organism_name": "mouse", "uuid": "93b0f937-9063-4be9-9e71-0bf2475a0e7d", "status": "released", "@id": "/bio-features/93b0f937-9063-4be9-9e71-0bf2475a0e7d/", "relevant_genes": [{"preferred_symbol": "Srsf2", "@type": ["Gene", "Item"], "status": "released", "@id": "/genes/20382/", "geneid": "20382", "display_title": "Srsf2", "uuid": "7c82239e-2af9-46df-b2ed-0b57c2a52849", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "feature_type": {"term_url": "http://purl.obolibrary.org/obo/SO_0000104", "display_title": "protein", "@id": "/ontology-terms/SO:0000104/", "status": "released", "term_name": "polypeptide", "@type": ["OntologyTerm", "Item"], "term_id": "SO:0000104", "uuid": "91f427e6-5246-4992-8123-b4f8fa9eef01", "preferred_name": "protein", "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": "ch02"}], "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBS2F7M7RP/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["Biosample missing doubling_number", "Biosample missing culture_duration", "Biosample missing morphology_image", "Biosample is a stem cell line over 10 passages but missing karyotype"], "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."}}}, {"parent": "/experiment-set-replicates/4DNESCXK9T73/", "embedded_path": "badges", "item": {"messages": ["Replicate set contains only a single biological replicate"], "badge": {"commendation": null, "warning": "Replicate Numbers", "uuid": "24a64a84-3c33-4d76-aaf2-e5ef45eff347", "@id": "/badges/replicate-numbers/", "badge_icon": "/static/img/badges/replicates-orange-circle.svg", "description": "Issues with replicate numbers"}}}]}, "validation-errors": []}