Fig. 1

Principal component analysis of the TMM-normalized reads in the 160 samples. The loadings of the first two principal components are plotted against each other for each sample. The type of treatment is indicated by the shape of the markers (circles for CTR, triangles for ATE and squares for ISO), while the filling of the markers refers to the strains (see legend on the right). Biological replicates (same shape and filling) tend to cluster together. For any given strain the markers corresponding to CTR and ATE are usually not far apart, while those for ISO tend to be more distal with smaller loadings on both principal components. This effect is visualized by the ellipsoids, whose centers and major axes reflect the first two moments of the respective distributions (see legend on top)