RNA sequencing (RNAseq) profiling of metabolism-related genes in CD40- and BCR-stimulated CLL cells. RNAseq was performed from CLL cells stimulated by BCR (n = 12; 6 hours) or CD40 (n = 4; 48 hours). Log2 fold change (FC) in the expression of selected genes was calculated relative to the corresponding unstimulated controls with differential gene expression analysis by DESeq2. The FC in expression of the same genes in LNs compared with PB was calculated from a previously published microarray data set (n = 17)⁴⁴ with differential gene expression analysis by R2 software (https://r2.amc.nl). Additionally, the FC of gene expression in 1-month (n = 18) and 6-month (n = 17) IBR-treated patient samples compared with baseline samples was calculated from a previously published data set³⁰ with differential gene expression analysis by DESeq2. Gene expression data were compiled and analyzed according the scheme in supplemental Figure 3A and depicted as log2 FC compared with the reference data sets: PB vs LNs, unstimulated vs BCR or CD40, and baseline vs IBR for 1 or 6 months. The PB/LN data set derived from micorarrays⁴⁴ was scaled differently (shown next to each heat map) than the RNAseq data. The heat map shows the log2 FCs of gene expressions in the 3 groups in overlapping metabolic pathways of CD40 and BCR stimulation, including purinosome, glutamate-cysteine ligase, glutathione S-transferases and glutathione peroxidases (A), glutamine metabolism (B), glycolysis (C), and OXPHOS-related genes (D). (E) MYC and MYC target genes. (F) Scale for all the heat maps of RNAseq data sets.