Fig. 3. Dual RNA-Seq strategy for enriching mycobacterial transcripts from necrotic granulomas.

(A) Diagram depicting the oligo(dT) bead-based host mRNA depletion strategy to enrich M. marinum transcripts from zebrafish necrotic granulomas. The figure was created with BioRender.com. (B) Bar plot showing enrichment of M. marinum transcripts in WT and Rac2D57N samples using the dual RNA-Seq approach. For each experiment, ~250 granulomas from 8 WT/12 Rac2D57N fish were used to isolate total RNA. n = 4 independent experiments for the WT and 3 independent experiments for the Rac2D57N fish. (C) Table showing total reads (* filtered for low-quality reads) and the number of rRNA and mRNA reads for zebrafish and M. marinum, before and after enrichment.