Fig. 3

Higher gDNA contamination affects Ribo-Zero to a greater extent than Poly (A) Selection. a) Different library preparation methods clustered separately; and Poly (A) Selection mutually clustered, while Ribo-Zero gDNA clustered closely by the treatments. For Poly (A) Selection, different treatments clustered together regardless of gDNA concentrations, except for no-DNase treatment, while closely clustered by gDNA concentrations particularly at high gDNA concentrations for Ribo-Zero. b) PCA showed results similar to those shown in panel a). Different library preparation methods separately clustered. For Poly (A) selection, different gDNA contamination treatments tightly clustered, which reflected that gDNA exerted a small amount of influence on gene expression levels. For Ribo-Zero, different treatments tightly clustered on PC1 and sporadically on PC2, which reflects the different extents of influence of gDNA on gene expression levels. c) More genes were affected by gDNA, indicated by changes in their expression levels in Ribo-Zero compared with Poly (A) Selection. These samples were enriched in genes expressed at low expressed in Ribo-Zero (See Supplementary Figure S1, Additional File 2). Each line represents the mean expression level of one gene from three replicates at different contaminating gDNA concentrations. The x-axis represents different amounts of gDNA contamination, and the y-axis represents the gene expression value. The light red line represents gene expression levels that significantly correlated with gDNA contamination, and the gray line represents gene expression levels that did not. Left (Ribo-Zero), right (Poly (A) Selection)