{"lab": {"@type": ["Lab", "Item"], "@id": "/labs/thomas-gregor-lab/", "status": "current", "display_title": "Thomas Gregor, PRINCETON", "title": "Thomas Gregor, PRINCETON", "correspondence": [{"contact_email": "dGcyQHByaW5jZXRvbi5lZHU=", "@id": "/users/e46f310b-2ed3-4b05-8d78-37456688a86d/", "display_title": "Thomas Gregor"}], "uuid": "41cedc04-1e04-423a-8d08-0fc181409ee7", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.41cedc04-1e04-423a-8d08-0fc181409ee7"]}}, "award": {"uuid": "4a3ea2f9-864b-429d-9948-54dbe0d7958d", "@type": ["Award", "Item"], "@id": "/awards/1U01EB021239-01/", "description": "IT: One of the most fundamental problems in modern biology is to understand dynamic gene activity in time and space in the context of native chromosomes in living cells. The goal of the proposed study is to measure the levels of transcription produced by defined long-range chromosomal interactions in living cells. Traditional live imaging methods lack the spatial resolution to accurately determine the dynamics of gene activity, while bulk assays using fixed material strongly limit investigation of temporal dynamics. Here we propose to overcome these limitations by developing new methods of microscopy and computational analysis. Most of the studies will exploit the unique advantages of the early Drosophila embryo for the development of quantitative live cell imaging methods. Previous studies have identified hundreds of such interactions, and we will sample several of these to provide a \"titration\" of varying distances, from tens to hundreds of kilobases, as seen in mammalian systems. There are two specific aims: 1. Develop high-resolution imaging methods and associated computational algorithms for the visualization and quantification of dynamic enhancer-promoter interactions at select endogenous loci in living embryos. 2. Label regulatory regions and associated transcription units of individual genetic loci exhibiting long-range interactions, including trans-homolog associations during transvection at Hox loci, to measure in vivo the effect of chromosome topology on transcriptional activity. We plan to extend this approach to include the visualization of several hundred fluorescent DNA foci in a library of genetically engineered fly lines to establish a general overview of the dynamics of an entire chromosome in a living embryo and its impact on transcription. The successful realization of the proposed studies will greatly augment our current capacity to superimpose whole-genome maps based on fixed tissues onto the dynamic chromosomes of living cells. The resulting technologies will be immediately applied to the visualization of chromosome dynamics in mammalian tissues, particularly multipotent progenitor cells such as mouse hepatoblasts.", "display_title": "IMAGING CHROMOSOME DYNAMICS AND MEASURING ITS IMPACT ON TRANSCRIPTIONAL ACTIVITY", "name": "1U01EB021239-01", "status": "current", "center_title": "IT - Gregor", "project": "4DN", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "pi": {"error": "no view permissions"}}, "md5sum": "6a0971302b0b92e4e243d7aef28b7d9e", "status": "released", "aliases": ["thomas-gregor-lab:fileproc_parS-homie-noPr-PP7_eveMS2"], "filename": "nopromoter.csv", "accession": "4DNFILJ2WX5N", "file_size": 41710326, "file_type": "spt results, submitter format", "description": "Spot localization information from parS-homie-noPr-PP7 embryos (control without promoter). See file format specification for details.", "file_format": {"file_format": "csv", "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "@id": "/file-formats/csv/", "display_title": "csv", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "date_created": "2021-01-13T23:42:22.955987+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-01-25T23:21:25.253472+00:00"}, "content_md5sum": "6a0971302b0b92e4e243d7aef28b7d9e", "public_release": "2021-01-25", "schema_version": "3", "static_headers": [{"lab": {"display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "status": "current", "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "Raw locations from Spot tracking (spot trajectories in time) contain the following information:\n\n1. Name/date of the imaged embryo (embryoName)\n2. Genotype of the embryo (transgeneGenotype)\n3. The developmental time in nc14 of the first frame in trajectoryInfo (devTime)\n4. Time at which the first z-slice of each frame is taken (acquisitionTimeInfo)\n5. Stage z-position for each frame during imaging (zPositionAdjust).\n6. Information of raw spot locations in each nucleus (trajectoryInfo)\n 1. XY positions of the nuclear centers (nucCenterXY)\n 2. Which stripe the nucleus belongs to (stripeInfo)\n 3. XYZ positions and the intensity of the identified red spots (redSpotXYZI)\n 4. XYZ positions and the intensity of the identified green spots (greenSpotXYZI)\n 5. XYZ positions and the intensity of the identified blue spots (blueSpotXYZI)\n 6. Background intensities for each channel (backgroundRGB)\n\n**Notes:**\n\n1. Raw z-positions need to be adjusted using zPostionAdjust in order to get displacement in the axial dimension, \n2. All positions are in pixels. XY pixel size: 107.2 nm; Z pixel size: 335.7 nm. \n3. Background intensities are from the spots tracked from the re-tracking step (see Methods, step III of Spot Tracking). Usually, it's the second brightest spot candidate in the nuclei where a 'real spot' is flagged, or the brightest spot candidate in the nuclei where no 'real spot' is tracked.\n4. Correction for chromatic aberration is needed in order to get distance between spots of different colors.", "name": "custom_format_spt", "award": {"uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "@id": "/awards/2U01CA200059-06/", "@type": ["Award", "Item"], "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "File format specification", "status": "released", "aliases": ["4dn-dcic-lab:static_section_custom_format_spt"], "options": {"filetype": "md", "collapsible": true, "default_open": true}, "date_created": "2021-01-21T00:41:51.902448+00:00", "section_type": "Page Section", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-01-25T23:21:24.321931+00:00"}, "schema_version": "2", "contributing_labs": [{"@id": "/labs/thomas-gregor-lab/", "@type": ["Lab", "Item"], "status": "current", "uuid": "41cedc04-1e04-423a-8d08-0fc181409ee7", "display_title": "Thomas Gregor, PRINCETON", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.41cedc04-1e04-423a-8d08-0fc181409ee7"]}}], "@id": "/static-sections/15e54b9d-05d7-48d9-87ca-125b35e2bf77/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "15e54b9d-05d7-48d9-87ca-125b35e2bf77", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.e4a22298-1da4-4e59-8a65-9e661f47fb48"]}, "display_title": "File format specification", "external_references": [], "content": "Raw locations from Spot tracking (spot trajectories in time) contain the following information:\n\n1. Name/date of the imaged embryo (embryoName)\n2. Genotype of the embryo (transgeneGenotype)\n3. The developmental time in nc14 of the first frame in trajectoryInfo (devTime)\n4. Time at which the first z-slice of each frame is taken (acquisitionTimeInfo)\n5. Stage z-position for each frame during imaging (zPositionAdjust).\n6. Information of raw spot locations in each nucleus (trajectoryInfo)\n 1. XY positions of the nuclear centers (nucCenterXY)\n 2. Which stripe the nucleus belongs to (stripeInfo)\n 3. XYZ positions and the intensity of the identified red spots (redSpotXYZI)\n 4. XYZ positions and the intensity of the identified green spots (greenSpotXYZI)\n 5. XYZ positions and the intensity of the identified blue spots (blueSpotXYZI)\n 6. Background intensities for each channel (backgroundRGB)\n\n**Notes:**\n\n1. Raw z-positions need to be adjusted using zPostionAdjust in order to get displacement in the axial dimension, \n2. All positions are in pixels. XY pixel size: 107.2 nm; Z pixel size: 335.7 nm. \n3. Background intensities are from the spots tracked from the re-tracking step (see Methods, step III of Spot Tracking). Usually, it's the second brightest spot candidate in the nuclei where a 'real spot' is flagged, or the brightest spot candidate in the nuclei where no 'real spot' is tracked.\n4. Correction for chromatic aberration is needed in order to get distance between spots of different colors.", "filetype": "md", "content_as_html": "

Raw locations from Spot tracking (spot trajectories in time) contain the following information:

\n
    \n
  1. Name/date of the imaged embryo (embryoName)
    2. \n
  2. Genotype of the embryo (transgeneGenotype)
    3. \n
  3. The developmental time in nc14 of the first frame in trajectoryInfo (devTime)
    4. \n
  4. Time at which the first z-slice of each frame is taken (acquisitionTimeInfo)
    5. \n
  5. Stage z-position for each frame during imaging (zPositionAdjust).
    6. \n
  6. Information of raw spot locations in each nucleus (trajectoryInfo)
    7. \n
  7. XY positions of the nuclear centers (nucCenterXY)
    8. \n
  8. Which stripe the nucleus belongs to (stripeInfo)
    9. \n
  9. XYZ positions and the intensity of the identified red spots (redSpotXYZI)
    10. \n
  10. XYZ positions and the intensity of the identified green spots (greenSpotXYZI)
    11. \n
  11. XYZ positions and the intensity of the identified blue spots (blueSpotXYZI)
    12. \n
  12. Background intensities for each channel (backgroundRGB)
    13. \n
\n

Notes:

\n
    \n
  1. Raw z-positions need to be adjusted using zPostionAdjust in order to get displacement in the axial dimension,
    2. \n
  2. All positions are in pixels. XY pixel size: 107.2 nm; Z pixel size: 335.7 nm.
    3. \n
  3. Background intensities are from the spots tracked from the re-tracking step (see Methods, step III of Spot Tracking). Usually, it's the second brightest spot candidate in the nuclei where a 'real spot' is flagged, or the brightest spot candidate in the nuclei where no 'real spot' is tracked.
    4. \n
  4. Correction for chromatic aberration is needed in order to get distance between spots of different colors.
    5. \n
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