Degust analysis of RNA-seq data of LSK cells obtained from Zeb1, Zeb2, Zeb1/2 DKO, or single Zeb2 allele rescue.

(A) PCA of DEGs showing clustering of samples based upon genotype. Zeb1 Δ/Δ Zeb2 +/+ samples (yellow) cluster more closely together with Zeb1 Δ/Δ Zeb2 Δ/+ samples (blue). Zeb1 Δ/Δ Zeb2 Δ/Δ DKO (red) and Zeb1 +/+ Zeb2 Δ/Δ (green) samples cluster father apart because they are more genetically diverse. (B) Gene expression heatmap showing that Zeb1/2 DKO samples have many genes that become up-regulated compared to either Zeb1 or Zeb2 single deletion alone and these genes appear to be normalized if even a single Zeb2 allele is present in Zeb1 Δ/Δ Zeb2 Δ/+ samples. (C) Volcano plot of DEGs highlighting differences in gene expression between Zeb1 Δ/Δ Zeb2 +/+ and Zeb1 Δ/Δ Zeb2 Δ/Δ DKO samples. Highlighted are 3 genes known to be repressed by Zeb2 including Ctse , Id2 , and Epcam . Moreover, Zeb2 is highlighted as being down-regulated between the 2 samples. (D) Volcano plot showing how maintained presence of single Zeb2 allele in Zeb1 Δ/Δ Zeb2 Δ/+ samples can lead to repression or normalization of up-regulated genes observed in Zeb1/2 DKO samples. FDR rates for (C) and (D) was 0.05. (E) Highlighted Zeb2 DEGs and rough grouping of biological processes associated with each gene. Raw data behind plots are included in S2 Table . DEG, differentially expressed gene; DKO, double knockout; FDR, false discovery rate; LSK, Lin − Sca1 + cKit + ; PCA, principle component analysis. (TIFF)