Figure 1.

Genetic Background Defines the Transcriptional Profile of Naive mESCs

(A) Graphical representation of mESC ground state lines showing differentiation toward different defined lineages.

(B) Representative bright-field images of cells growing in 2iL. Number in brackets indicates the specific line shown.

(C) Representative flow cytometry plots for Oct4 in cells growing in 2iL. Number in brackets indicates the specific line shown.

(D) Quantitation of flow cytometry for Oct4 in cells growing in 2iL. Data shown represent a minimum of five samples from each genetic background, two lines per background. Error bars represent the standard error of the means.

(E) Heatmap of selected markers generated from RNA-seq data. Data shown are from three independently derived lines for each genetic background.

(F) Principal-component analysis plot of transcriptome data. Data shown are from three independently derived lines for each genetic background.

(G) UMAP plot generated from single-cell data. Strains are partitioned into four clusters (Louvain method).

(H) UMAP plot showing log-normalized gene expression of selected markers.