Fig. 4

BRB-seq multiplexing experiment and comparison with TruSeq. a Venn diagram showing the protein-coding genes detected (at least one read) across all 60 (TruSeq A) or 53 (TruSeq B) LCL samples after downsampling to 1M reads. b Distribution of counts per millions (CPM) of genes taken from every subset (corresponding color) of the Venn diagram shown in panel a. c Pearson’s correlations of log2 expressions, calculated sample by sample, i.e., of the same sample taken from two different dataset combinations (TruSeq A and B and BRB-seq). d Correlation heatmap showing in greater detail the individual LCL sample correlations between all three datasets (BRB-seq, TruSeq A, and TruSeq B). Highlighted in black are the three main clusters, showing, as expected, a clear separation by protocol (BRB-seq vs. TruSeq) or sequencing run (TruSeq A vs. B), overriding the relatively modest biological differences between 60 LCL samples, while maintaining an overall high correlation (Pearson’s r > 0.8). In all panels, all libraries were randomly downsampled to one million single-end reads for an unbiased comparison (see the “Methods” section)