====== Imaging Approaches to Genomics Subgroup ======

===== OBJECTIVES =====

<font 20px/inherit;;inherit;;inherit>Biological questions to be addressed (From JAWG):</font>

  * How does a loop, TAD, Compartment (From Hi-C definition) look like?
  * How often do these domains appear on a per single cell basis? Are these imaging results compatible with corresponding Hi-C data based on populations? Is there heterogeneity from cell to cell?
  * What are the dynamic properties of these domains? Can we make predictions?

Based on these questions, the Imaging Approaches to Genomics (IAG) will work to define an experimental strategy to generate imaging data that can be correlated to biochemical/sequencing data. In addition, even after image collection we need a common image data analysis format to correlate imaging and omics data (IWG current work).

<font 20px/inherit;;inherit;;inherit>The IAG will address the following points, in order:</font>

  * Determine limitations of labelling approaches: DNA-FISH, CAS-labelling, unspecific labelling (e.g. replication domains). How many discernible labels in a single experiment? What is the smallest unit of DNA that can be realizably labelled and visualized with either DNA-FISH or with CAS-labelling?
  * Determine the spatial and temporal resolution limits of microscopy technique(s): live-cell microscopy, super-resolution microscopy and potentially electron microscopy.
  * Prioritize labelling approaches and microscopy techniques to image loops, TADS and domains, respectively. Each genome organizational layer happens at different spatial scales, is likely going to be best imaged with different microscopy techniques, and likely poses different technical challenges.
  * Prioritize loci to image (From original JAWG list). At least 2 loci for each level (loop, TAD, compartments). Possibly choose loci for which there are already available genetic mutants (CRISPR), and/or whose conformation predictably changes in response to a biological stimulus.
  * Prioritize imaging throughput/dynamics and image analysis choices. How many loci do we need to image for experimental condition (Heterogeneity)? How fast can we image loci in live cells (dynamics)? What kind of data do the omics bioinformaticians want: position, distances, movement (IWG ongoing work)? All three? Is there a fundamental limit in correlating structures from sequencing and imaging?

===== Microscopy Information Tables =====

  * [[https://docs.google.com/spreadsheets/d/1xPUOPXCe2MDif7MuYIB1bhZU5umGoclwjdTOtRbGmmo/edit?usp=sharing|Microscopy Techniques and Labelling Limits]]
  * [[https://docs.google.com/spreadsheets/d/1AZj6ZoT9-l7Ptn4iJbBF4r6NFsoeztAJHFbItvdcSKw/edit?usp=sharing|4DN Microscopy Techniques and Labelling Experts]]
  * [[https://docs.google.com/spreadsheets/d/1dfPG4q5wSJ-WBNZtP0RG-768X-2_9fwBsLI_WH8N_vU/edit#gid=0|Biological Questions Table]]

===== Meetings =====

^Date^Presenters / Topics^Attachments / Links / Minutes|
|5/10/2018|~~TABLE_CELL_WRAP_START~~<WRAP>

  * Initial goals and tasks discussion

</WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>

  * [[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDo3NDkzYTBmZmQxMTAwYWIx|Meeting Notes]]

</WRAP>~~TABLE_CELL_WRAP_STOP~~|
|6/14/2018|~~TABLE_CELL_WRAP_START~~<WRAP>

  * Selection of the JAWG biological questions
  * Discussion on the microscopy/labelling techniques

</WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>

  * [[https://docs.google.com/document/d/1TXFaNPQq_mNod0w2grFNthutzOl5efL6e4bS3Vght1Y/edit?usp=sharing|Meeting Agenda]]
  * [[https://docs.google.com/spreadsheets/d/1xPUOPXCe2MDif7MuYIB1bhZU5umGoclwjdTOtRbGmmo/edit?usp=sharing|Microscopy and Labelling Techniques Table]]
  * [[https://docs.google.com/spreadsheets/d/1urn5n9yK6lYhwkenw6VgzQMVVOU1jjNZs7LYlhrf_9U/edit?usp=sharing|Oligo DNA/RNA FISH Experimental conditions]]
  * [[https://docs.google.com/document/d/1VMcXLPP8J_E5_Hj67et-22BkevrptqJlpfNUoJ6gql4/edit|Meeting Notes]]

</WRAP>~~TABLE_CELL_WRAP_STOP~~|
|7/12/2018|~~TABLE_CELL_WRAP_START~~<WRAP>

  * Elizabeth Finn (Misteli Lab) presentation + discussion
  * Improvements to the table and request for contributions
  * Selection of live cell imaging approaches for the JAWG
  * Selection of measurements needed to compare genome structure as measures by imaging and sequencing: distances, contact frequencies, both, more?

</WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>

  * [[https://docs.google.com/document/d/1DfZ-wgeGnhDbObSxqLbdeP3GHTwXx4_kyQH7IBponDE/edit#|Meeting Agenda]]

</WRAP>~~TABLE_CELL_WRAP_STOP~~|
|8/9/2018|~~TABLE_CELL_WRAP_START~~<WRAP>

  * Johan Gibcus (Dekker Lab) presentation + discussion

</WRAP>~~TABLE_CELL_WRAP_STOP~~|~~CKG_TABLE_NBSP~~|
|9/13/2018|~~TABLE_CELL_WRAP_START~~<WRAP>

  * Long Cai (caltech) presentation + discussion

</WRAP>~~TABLE_CELL_WRAP_STOP~~|~~CKG_TABLE_NBSP~~|
|10/11/2018|~~TABLE_CELL_WRAP_START~~<WRAP>

  * Progress report on microscopy labelling techniques information gathering
  * Discussion of the final deliverables for the group

</WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>

  * [[https://docs.google.com/document/d/1xodUdJk5pPi00abZ8Txko8jDsOhAjOt6eIL86ezoUEM/edit?usp=sharing|Meeting Agenda]]

</WRAP>~~TABLE_CELL_WRAP_STOP~~|

===== Meeting Information =====

<font inherit/inherit;;#e74c3c;;inherit>**2nd Thursday of every month, 9:00 am PT (12pm ET) **</font>

<font inherit/inherit;;#e74c3c;;inherit>**May - Dec 2018**</font>

**Meeting Link:** [[https://4dnucleome.webex.com/4dnucleome/j.php?MTID=m95a4817718db4d2245cb073daf08cac7|https://4dnucleome.webex.com/4dnucleome/j.php?MTID=m95a4817718db4d2245cb073daf08cac7]]

Meeting number: 809 270 065

Meeting password: myMuWqr8

Host key: 116087

Audio Connection: +1-415-655-0002 US TOLL

Access code: 809 270 065

**<font 20px/inherit;;inherit;;inherit>WebEx emergency contact information</font>**

Kate Rivera

858-822-1626 (Office)

619-734-5961 (Cell)

**<font 20px/inherit;;inherit;;inherit>MEMBER: Google Group address: <imaging-to-omics-subgroup@4dnucleome.org></font>**

<font inherit/inherit;;inherit;;#e74c3c>Insert spreadsheet</font>

===== Reference Links =====

  * [[4dn:phase1:working_groups:joint_4d_nucleome_analysis|Joint 4D Nucleome Analysis]]
  * [[https://docs.google.com/spreadsheets/d/1kOW2m_DSKQJaupXnANqImwqJ3BmjUaPYhR8rxG3pgxM/edit#gid=251396676|NOFIC Shared LOCI List]]
  * [[https://docs.google.com/spreadsheets/d/1kOW2m_DSKQJaupXnANqImwqJ3BmjUaPYhR8rxG3pgxM/edit#gid=251396676|Data Generation Plan]]

===== Calendar =====

{{url>https://calendar.google.com/calendar/embed?src=4dnucleome.org_eo4cpha38fkq666i07cecms9po%40group.calendar.google.com&ctz=America%2FLos_Angeles 800,400 noborder|4DN OMICS WG Calendar}}

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{{medialist>4dn:working_groups:imaging_data_standards:imaging_approaches_to_genomics_subgroup:}}