Figure S3. Pcgf6 loss does not affect Myc-dependent transcription.

RNA-seq profiles were generated from tumor (T) samples of either Pcgf6 genotype (WT and KO). (A) Pearson correlation between tumor samples, based on their RNA-seq profiles. (B) Comparison of the differentially expressed genes (DEGs) called in T-WT (Y-axis) and T-KO (X-axis), both relative to C-WT (P_adj < 0.05 and |log₂FC > 0.5|). The DEGs are colored based on the call in the X-axis. (C) Same as Fig 3B, showing the DEGs called between the T-KO and T-WT samples. (D) Representative RNA-seq profiles at the Pcgf6 locus (UCSC Genome Browser) for the indicated WT and KO tumor samples. Note the absence of reads in the targeted exon 2–3 region in the KO sample. (D, E) Gene Ontology analysis (category C5) of the DEGs called in panel (D); GOBP, Gene Ontology Biological Processes; GOMF, Gene Ontology Molecular Function; GOCC, Gene Ontology Cellular Component. (F) Cdkn2a mRNA levels, as measured by RNA-seq, normalized to the C-WT samples. The data show means and s.d.; n ≥ 3.