Additional file 9: of A map of gene expression in neutrophil-like cell lines

Nutridoma affects gene expression during differentiation subtly, but consistently in HL-60 and PLB-985 cells. (a) PLB-985 cells were differentiated into a neutrophil-like state by culturing in media supplemented with 1.3% DMSO, 2% Nutridoma and 0.5% FBS. At the indicated days post-differentiation, cells were harvested and processed for RNA-seq analysis or stained with FLPEP. Shown are the expression level of FPR1 at the mRNA level (from our RNA-seq data) and at the surface of the cells (FLPEP staining). Values for undifferentiated cells and for cell differentiated with 1.3% DMSO and 9% FBS are shown for comparison. Values were normalized by the values for the sample differentiated with only DMSO. (b) Density-colored scatter plots of expression values (normalized FPKM on a log10 scale) for protein-coding genes for HL-60 (left) or PLB-985 cells (right) cells differentiated with DMSO + Nutridoma versus those differentiated with DMSO. These data represent the averages of two replicate experiments. (c) Density-colored scatter plots of log10 fold-changes between the two protocols (subtracting DMSO values from DMSO + Nutridoma) comparing each of our two replicates of the RNA-Seq experiments for HL-60 (left) or PLB-985 (right) cells. To avoid noise from lowly expressed genes, only protein-coding genes with a mean log10 normalized expression value of − 1 or higher were included. The Pearson’s (R) and Spearman’s correlation coefficients are shown. (PDF 417 kb