Verification of DEGs at the protein level using a proteomic procedure.

<p>Equal amounts of protein from macrophages at different activation statuses were stained with either red or green fluorescent dyes and co-resolved using a 2D-DIGE procedure (Applied Biomics, Inc., Hayward, CA) to isolate protein spots that significantly increased in macrophages at certain activation statuses and to further identify the isolated proteins by nano LC-MS/MS. Of 16 significantly increased protein spots randomly selected across four activation statuses (black bars) compared with the M0-PBS status (the white bars), 12 (75%) protein spots (WARS, PLEK, RAN, CKB, PLOD3, RNF114, HNRNPU, ATP6V1E1, CANX, MX1, MX2, H2B3A) also showed significant up-regulation at the RNA level, with the other four (SND1, ANXA1, UBE2D3 and MPP5) showing a significant increase only at the protein level. *, FDR ≤0.001 of gene expression and protein ratio ≥2. The number before each gene symbol along the X-axis indicates the protein spot mapped in the gel shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087613#pone.0087613.s002" target="_blank">Figure S2</a>. Gene symbol abbreviations: SND1, staphylococcal nuclease domain-containing protein 1; WARS, tryptophanyl-tRNA synthetase; PLEK, pleckstrin; RAN, Ras-related GTP binding C; CKB, creatine kinase B-type; PLOD3, procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3; RNF114, RING finger protein 114; HNRNPU, heterogeneous nuclear ribonucleoprotein U; ANXA1, annexin A1; ATP6V1E1, v-type proton ATPase subunit E 1; UBE2D3, ubiquitin-conjugating enzyme E2 D3; CANX, calnexin; MX, myxovirus resistance gene; H2B3A, histone H2B3A; MPP5, membrane protein palmitoylated 5.