Fig. 2

Depletion performance of five LNAs targeting the most abundant contaminants. (a) Heatmap visualization of undepleted samples and samples that were supplemented with an LNA mixture during library amplification. The LNA mix contained five probes at 1 µM each, targeting the most abundant contaminants identified across all tested growth conditions. The shortest common sequence of each contaminant group is indicated on the y-axis; LNA target sequences are marked with an asterisk. Tile color represents the percentage of that group in relation to the total reads in the sample. Cumulative percentages for all displayed contaminants are summarized at the top of each column. (b) Comparison between the amount of mRNA reads in undepleted and LNA-depleted samples. Percentages in relation to total read count per sample are indicated at the top of each bar. (c) Correlation of averaged gene-level read counts between undepleted and depleted samples. Counts were regularized log-transformed using the “rlog” function from the DESeq2 R package. Libraries were processed with the ORFik toolkit¹⁶, filtering for reads over 20 nt and removing reads that mapped to non-coding RNAs. Pearson correlation coefficient is denoted in the top left corner.