Ge et al. BMC Genomics 2010, 11:456 http://www.biomedcentral.com/1471-2164/11/456 helper plasmid pKOBEGA is a low-copy-number plas- mid that contains an ampicillin resistance gene, a tem- perature-sensitive origin of replication and the Red system, including three genes expressing the Exo, Bet and Gam functions of phage l, which helps allelic exchanges between linear DNA and the corresponding region on the chromosome [74]. The Salmonella strains carrying the l Red helper plasmid were made electro- competent as described above. PCR linear DNA frag- ments were generated with specific hybrid primers and high-fidelity thermophilic DNA polymerase (Dynazyme Ext; Finnzymes). The primer pairs shown in Table 4 were used. PCR products were purified with a QIAquick PCR Purification kit (QIAGEN) and 5 μg of purified product (5-10 μl) was electroporated (25 μF, 200 Ω, 2.5 kV) into 50 μl of eletrocompetent cells according to the manufacturer’s instructions (Bio-Rad), then 950 μl of LB broth was added to the shocked cells and the solution was transferred into clear eppendorf tubes and incu- bated for 2 h at 37°C, and then spread on to LB agar Km to select Km transformants after overnight growth at 37°C. Selected antibiotic resistance colonies were then grown on LB broth Km at 43°C for 24 h and then spread on LB agar Km or Amp at 37°C to check the loss of the helper plasmid. The mutated genes were con- firmed by PCR using the primers shown in Table 4, which are external to the site of mutagenesis with the internal deletion replaced by the kanamycin cassette. Additional material Additional file 1: Supplemental Tables S1- 6 - Global gene expression of S. Enteritidis PT4 in HLA-B27- or HLA-A2-transfected cells using microarray assay. The Supplemental Tables S1-6 contain gene expression profiles of S. Enteritidis PT4 strain during infection of U937 cells (Table S1), genes up- or down-regulated more than two-fold in HLA-A2-transfected U937 cells compared to LB culture at 2 h after infection (Tables S2-1, -2), in HLA-B27-transfected cells compared to LB culture at 2 h after infection (Table S3-1,-2), in HLA-A2-transfected U937 cells compared to LB culture at 8 h after infection (Tables S4-1, -2), in HLA-B27-transfected cells compared to LB culture at 8 h after infection (Table S5-1,-2) and in HLA-B27-transfected cells compared to HLA-A2- transfected cells at 8 h after infection (Tables S6-1, -2). Additional file 2: Supplemental Tables S7 and S8 - The correlation analysis between PT-PCR and array data and the expression of the gene rfaH in different conditions. The Supplemental Tables S7 and S8 contain the correlation analysis between PT-PCR and array data (Table S7) and the expression of the gene rfaH in different conditions (Table S8). Acknowledgements We are grateful for useful discussions and advice from Jari Jalava, Yangyang Wang, Sanna Vähämiko, Anna Sahlberg, Isabelle Hautefort and Arthur Thompson. We thank Tuija Turjas, Tuula Rantasalo, Päivi Haaranen, and Erkki Nieminen for their technical assistance. We also thank Anja Siitonen for typing our S. Enteritidis strain, Joel D. Taurog for providing the HLA-B27 and HLA-A2 genomic DNA, and Jean-Marc Ghigo and Iñigo Lasa for providing E. Page 11 of 13 coli MC4100 ybeW::Km, plasmid pKOBEGA and bacteriophage P22. Biomedes is acknowledged for copyediting of the manuscript. This study was supported by grants from the Academy of Finland and the Sigrid Jusélius Foundation to Kaisa Granfors and the BBSRC core strategic grant to Jay C. D. Hinton and the DEFRA VTRI VT104 grant to Vittoria Danino. Author details 1Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, Turku, Finland. 2Molecular Microbiology Group, Institute of Food Research, Colney, Norwich, UK. Authors’ contributions SCG designed and carried out the experiments, and wrote the manuscript. VD performed the microarray tests and analyzed the data. QSH designed the experiments and analyzed the data. JCDH conceived and designed the experiments. KG conceived and designed the experiments, and wrote the manuscript. All authors reviewed the manuscript. Received: 3 December 2009 Accepted: 30 July 2010 Published: 30 July 2010 References 1. Fierer J, Guiney DG: Diverse virulence traits underlying different clinical outcomes of Salmonella infection. J Clin Invest 2001, 107:775-780. 2. Mishu B, Koehler J, Lee LA, Rodrigue DF, Brenner H, et al: Outbreaks of S. Enteritidis infections in the United States, 1985-1991. J Infect Dis 1994, 169:547-552. 3. 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