Fig. 6

Different library types detect different sets of LPS-inducible transcripts, although a greater number can be captured when merging datasets. Counts are of the number of protein-coding genes with >1 TPM both pre- and post-LPS stimulation (0 and 7 h, respectively) and a log₂ fold change in expression >2. Data was creating either by (a) quantifying expression against the complete Oar v3.1 transcriptome, and (b) employing a filtered reference transcriptome for quantifying expression (restricted only to protein-coding genes, excluding those genes not expressed in BMDMs and adding de novo assembled transcripts), and then applying a ratio-based correction to TPM estimates from ribo-minus libraries. After this process of filtering and correction, the number of LPS-inducible genes in the intersection of all sets is doubled. P = polyA+, R = ribo-minus. Figure created using Venny 2.1 [88]