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--- 4dn:phase2:working_groups:integrating_imaging_omics [2021/01/29 15:39]
chris_frick
+++ 4dn:phase2:working_groups:integrating_imaging_omics [2025/04/22 16:21] (current)
@@ Line 1: / Line 1: @@
-====== WTC 11 ======
+====== Integrating Imaging and Omics (IOWG) ======
-**Point people/organizers:** //Frank Alber, Bing Ren, Yin Shen, Susanne Rafelski//
+**Point people/organizers:** //Frank Alber, Yin Shen, Susanne Rafelski//
 <font inherit/inherit;;#c0392b;;inherit>**4DN Google Drive folder: **</font>[[https://drive.google.com/drive/folders/1sskUxIcdm9Aohp92XeNwv9wt6nNYR3U2?usp=sharing|https://drive.google.com/drive/folders/1sskUxIcdm9Aohp92XeNwv9wt6nNYR3U2?usp=sharing]]
@@ Line 9: / Line 9: @@
 <font inherit/inherit;;#c0392b;;inherit>**Agenda/minutes:**</font> [[https://docs.google.com/document/d/1-cgXP2sBcvZMT-Ap5Z5wzSYteRJnyAvQTsShsu9Wgw0/edit?usp=sharing|https://docs.google.com/document/d/1-cgXP2sBcvZMT-Ap5Z5wzSYteRJnyAvQTsShsu9Wgw0/edit?usp=sharing]]
-<font inherit/inherit;;#c0392b;;inherit>**TEST_for_survey_link:**</font> [[https://docs.google.com/document/d/1-cgXP2sBcvZMT-Ap5Z5wzSYteRJnyAvQTsShsu9Wgw0/edit?usp=sharing|https://docs.google.com/document/d/1-cgXP2sBcvZMT-Ap5Z5wzSYteRJnyAvQTsShsu9Wgw0/edit?usp=sharing]]
+<font inherit/inherit;;#c0392b;;inherit>**Schedule for lightning talks:**</font> [[https://docs.google.com/document/d/1sR0aNxYZIw_0MtHBFaHS_O9fkKiAyNDXow31r-JN6PU/edit?usp=sharing|https://docs.google.com/document/d/1sR0aNxYZIw_0MtHBFaHS_O9fkKiAyNDXow31r-JN6PU/edit?usp=sharing]]
 <font inherit/inherit;;#c0392b;;inherit>**Meeting attendee spreadsheet: **</font>[[https://docs.google.com/spreadsheets/d/1pUjpEu0NoodCX4pHtf4lYxJn2DdhVWxwrThaiHYUy2o/edit?usp=sharing|https://docs.google.com/spreadsheets/d/1pUjpEu0NoodCX4pHtf4lYxJn2DdhVWxwrThaiHYUy2o/edit?usp=sharing]]
-<font inherit/inherit;;#c0392b;;inherit>**Email list:**</font> [[model-mechanism@4dnucleome.org|wtc-11@4dnucleome.org]]
+<font inherit/inherit;;#c0392b;;inherit>**Email list:**</font> <integrating-imaging-omics@4dnucleome.org>
-<font inherit/inherit;;#c0392b;;inherit>**Slack channel:**</font> #wg-wtc11
+<font inherit/inherit;;#c0392b;;inherit>**Slack channel:**</font> #wg-integrating-imaging-omics
-<font inherit/inherit;;#e74c3c;;inherit>**Landing page at the 4DN portal:**</font> [[https://data.4dnucleome.org/4DN-AICS-Collaboration|https://data.4dnucleome.org/4DN-AICS-Collaboration]]
+<font inherit/inherit;;#c0392b;;inherit>**Landing page at the 4DN Data Portal:**</font> [[https://data.4dnucleome.org/4DN-AICS-Collaboration|https://data.4dnucleome.org/4DN-AICS-Collaboration]]
 ===== Mission Statement =====
-Objective: Develop a general approach for studying the dynamic nuclear organization in mammalian cells. Ultimately, this will allow us to learn the general principles of dynamic nuclear organization of cells during the cell cycle, differentiation, and in response to extracellular signals.
+<font inherit/Arial,Helvetica,sans-serif;;inherit;;inherit><font 11pt/inherit;;inherit;;inherit>The working group’s efforts will be devoted to developing an integrative framework for combining imaging modalities with single cell and ensemble genomics data to study the changes in global cellular organization during biological processes, such as cell cycle, differentiation or perturbations.</font></font>
-Goals of the working group:
+<font inherit/Arial,Helvetica,sans-serif;;inherit;;inherit><font 11pt/inherit;;inherit;;inherit>The working group has two main objectives:</font></font>
-) Establish WTC11 as target system for studying the temporal dimension of 3D genome organization. The goal is to understand the principles by which cells reorganize in 3D space as they move from state to state in response to the cell cycle, differentiation, changes in environment, agonists/antagonists, etc. The working group will coordinate efforts across different labs working on WTC11 cells. We will explore synergies and coordinate efforts for data production.
+  - <font inherit/Arial,Helvetica,sans-serif;;inherit;;inherit><font 11pt/inherit;;inherit;;inherit>An explicit goal of this working group is to provide a platform and foster interactions between researchers from different disciplines—imaging, genomics and computational modeling—to work jointly on breaking the barriers in integrating imaging with omics data types. The working group will develop strategies for data integration, discuss common practices and compare different integration strategies. The strategies developed by this objective will be generally useful for a variety of 4DN projects and data types.</font></font>
+  - <font inherit/Arial,Helvetica,sans-serif;;inherit;;inherit><font 11pt/inherit;;inherit;;inherit>The second objective is to coordinate a joint effort in generating a variety of genomics and imaging data sets for a specific target system. Here, we focus on the WTC11 cell line and expand the joint effort of this working group from phase 1 in generating and analyzing a variety of imaging and genomics data. The initial focus on one cell type will guarantee the production of a rich data set, which will be applied to integration strategies developed in objective 1.</font></font>
-) A central component of our efforts will be the integration of imaging with genomics data to study the changes in global cellular organization during cell cycle and differentiation. We continue to explore synergies with the Allen Institute of Cell Science (AICS), which developed a panel of human pluripotent stem cell (hiPSC) lines expressing genetically engineered, EGFP-tagged proteins that can be used to map the dynamic localization of a particular organelle or structure using live cell imaging. The AICS developed segmentation algorithms for quantitative image analyses and label-free simultaneous imaging of cellular structures during cell cycle and differentiation. These images will be integrated with ensemble and single cell genomics data to enable in-depth understanding of dynamic chromatin organization during cell cycle and differentiation in human cells.

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