Trichostatin A inhibits the expression of innate immune genes in macrophages. BMDMs were preincubated for 1 hour with or without TSA (100nM) before exposure (C-D, 4 hours) to LPS (100 ng/mL) or Pam₃CSK₄ (100 ng/mL). Transcriptome was analyzed with Agilent Mouse Development Oligoarrays (A-B) or Mouse Oligo Microarray Kit V2 (C-D). (A) Number of genes either up-regulated or down-regulated by LPS and Pam₃CSK₄ without preincubation with TSA (fold change > 2 vs medium). (B) Effect of 1-hour preincubation with TSA on genes (expressed in percentage) either up-regulated or down-regulated by LPS or Pam₃CSK₄ (fold change > 2 vs medium). White represents no change; red, inhibition; and green, increase by TSA compared with stimulation with LPS or Pam₃CSK₄ alone. (C) Heat map of selected pattern recognition molecules (medium, TSA, LPS and Pam₃CSK₄: 4 hours of incubation, LPS + TSA and Pam₃CSK₄ + TSA; 1-hour preincubation with TSA followed by 4-hour incubation with LPS and Pam₃CSK₄). (D) Effect of 1-hour preincubation with TSA (fold changes were calculated vs LPS or Pam₃CSK₄ alone) on a selection of genes up-regulated by LPS or Pam₃CSK₄ and grouped into various categories based on their biologic functions (microbial sensing and killing; adhesion; cytokine, growth factor and receptors; signaling; antigen processing and presentation). White represents no change; red, inhibition; and green, increase by TSA compared with stimulation with LPS or Pam₃CSK₄ alone. (E) Tlr1-9, Md-2, Cd14, and Cd36 mRNA copy number was determined by RT-PCR and expressed relative to that of GAPDH. Data are representative of 2 independent experiments.