Ribosomal RNA-depletion provides an efficient method for successful dual RNA-Seq expression profiling of a marine sponge holobiont

To determine the optimal RNA-Seq approach for animal host-bacterial symbiont analysis, we compared transcriptome bias, depth and coverage achieved by two different mRNA capture and sequencing strategies applied to the marine demosponge Amphimedon queenslandica holobiont, for which genomes of the animal host and three most abundant bacterial symbionts are available. Overall design: The two strategies were: (i) poly(A) captured mRNA-Seq (Poly(A)-RNA-Seq); and (ii) ribosomal RNA depleted RNA-Seq (rRNA-depleted-RNA-Seq). Please note that each processed data was generated from all three replicates and is linked to the *A and *D sample records.