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broadinstitute / cmQTL

High-dimensional phenotyping to define the genetic basis of cellular morphology
BSD 3-Clause "New" or "Revised" License
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Adding Single Cell Data Pilot Analysis #3

Closed gwaybio closed 5 years ago

gwaybio commented 5 years ago

Experiment

Here we assess plate density and plating timepoint conditions to determine optimal conditions to scale up the experiments.

We test conditions using profiles generated from all cells within each well and two additional categories representing two distinct cell populations.

  1. Cells in Colonies: Defined by having 4 or greater neighbors
  2. Isolated Cells: Defined by having exactly zero neighbors

Conclusion

The optimal conditions are 6 hour plating at 10,000 cell density

Data

I add all relevant data as git-lfs files in 0.pilot-determine-conditions/data.

Figures

Kolmogorov-Smirnov Test across Profile Types

condition_pilot_kstest

Replicate Correlation: All Cells In Profile

condition_pilot_all

Replicate Correlation: Colony Cells

condition_pilot_colony

Replicate Correlation: Isolated Cells

condition_pilot_isolated

gwaybio commented 5 years ago

cc @TiffanyAmariuta