Lymph node tissue was taken from mule deer in several geographical regions. The Bonner pool consisted of tissue from four mule deer (167, 191, 196, 200) Preparation of genomic DNA, total RNA, poly(A) + RNA and cDNA Lymph node tissue cores were dissected into small pieces and further disrupted, lysed and homogenized using a TissueLyser with steel beads (Qiagen, Germany). Genomic DNA was isolated from lymph nodes of four individual Mule deer (MD 72360, MD 80228, MD 84709, and MD 84730) using either the Genomic DNA Buffer Set with 20/G Genomic-tips (Qiagen, Germany) or the AllPrep DNA/RNA Mini Kit (Qiagen, Germany). Total RNA was isolated using the RNAqueous-Midi Kit (Applied Biosystems, Ambion, CA). For the Bonner-and OCT-pools, equal quantities of total RNA from lymph nodes of four or eight individual Mule Deer, respectively, were combined. Poly(A) + RNA was enriched from total RNA using the MicroPoly(A) Purist Kit (Applied Biosystems, Ambion, CA). Poly(A) + RNA (0.9-5.0 mg each) was used for cDNA synthesis (Just cDNA Double-Stranded cDNA Synthesis Kit, Stratagene, CA) after elimination of residual contaminating genomic DNA using the Turbo DNA-free Kit (Applied Biosystems, Ambion, CA). In one case we explored an alternative empirical approach to enrich for rare microbial transcripts, using total RNA of the MD OCT-pool. Reverse transcription and amplification of cDNA was done as described by Cheung and coworkers [59] and included a normalization step, which effectively decreased overexpressed reads. The data resulting from this approach are included in the MD OCT-pool data.