The LINCS MCF10A_SS1 experiment was performed with MCF10A cells grown in 8 8-well plates. The analyzed endpoints include DAPI, phalloidin, CellMask and mitoTracker. Color images of the cells at each spot were gathered on a Nikon automated microscope.
Intensity, position and morphology data are gathered for each cell, merged with the experiment metadata, normalized with RUVLoessResiduals, filtered and summarized.
The spot cell count analysis identifies MEPs with extreme population sizes. The normalized spot cell counts in the plot below are summarized by the median and standard error of their replicates. Hovering over the the interactive plot below shows the MEP identities. Clicking and dragging over a section of the plot will zoom into the selected location. Double clicking on the zooomed plot will restore the original plot.
The interactive heatmaps below are arranged by unsupervised clustering of the rows and columns and colored by the normalized spot cell count. Clicking and dragging across any subsection will zoom in on that section. Double clicking on the zoomed image will return to the full heatmap.
All cells are stained with DAPI and autogated as DNA 2N or 4N. The proportion of 2N and 4N cells at each spot is calculated and will always sum to 1. The proportions are logit transformed then RUV and loess normalized then back transfomred to a proportion. Lower normalized values have smaller 2N populations and therefore larger 4N populations.
The interactive heatmaps below are arranged by unsupervised clustering of the rows and columns and colored by the normalized DNA 2N proportions. Clicking and dragging across any subsection will zoom in on that section. Double clicking on the zoomed image will return to the full heatmap.
This staining set includes MitoTracker which stains mitochondria.
A PCA dimension reduction is performed on the 52 normalized features that have non-zero variance. Hovering over the datapoints will show the MEP values.
A tSNE dimension reduction is performed on the 52 normalized features that have non-zero variance. Hovering over the datapoints will show the MEP values.