Todorčević et al. BMC Genomics 2010, 11:39 http://www.biomedcentral.com/1471-2164/11/39 Table 1 Primers used for real-time qPCR analyses Gene Tumor necrosis factor alpha (TNFa) Tumor necrosis factor (TNF) decoy Arachidonate 5-lipoxygenase-activating protein (FLAP) Tyrosine-protein kinase 1 (Jak1) Programmed death ligand 1 (PD-L1) Interleukin 13 receptor alpha 2 (IL13Ra2) Leukocyte cell-derived chemotaxin 2 (LECT2) Complement component 5 (C5) Proliferator-activated receptor gamma (PPARg) Bone morphogenic protein 4 (BMP4) Myogenic factor D (MyoD) CCAAT-enhancer-binding protein beta (C/EBPb) CCAAT-enhancer-binding protein delta (C/EBPδ) CCAAT-enhancer-binding protein alpha (C/EBPa) Hexokinase (HK) Glucose-6-phosphate dehydrogenase (G6PD) Phosphofructokinase (PFK) Pyruvate kinase (PK) Malate dehydrogenase cytoplasmic (MDHC) Cytosolic phosphoenolpyruvate carboxykinase (PEPCKC) 6-phosphogluconate dehydrogenase (PGD) Transketolase (TKT) Peroxiredoxin 1 (PRDX1) Glutathione peroxidase 2 (GPX2) Activating transcription factor 6 (ATF6) X-box binding protein 1 (XBP1) Microsomal triglyceride transfer protein (MTP) 78 kDa glucose-regulated protein (GRP78) Cluster of differentiation 36 (CD36) ATP-binding cassette transporter 2 Lipoprotein lipase (LPL) Fatty acid(FAS) 18S Elongation factor 1A (EF1A) Eukaryotic translation initiation factor 3 subunit 6 Page 14 of 17 Indirect cDNA Labelling System (Invitrogen, Carlsbad, CA, USA). The cDNA synthesis was performed at 46°C for 3 h in a 20 μl reaction volume, following RNA degradation with 0.2 M NaOH at 37°C for 15 min and alkaline neutralization with 0.6 M Hepes. Labelled cDNA was purified with Microcon YM30 (Millipore, Bedford, MA, USA). The slides were pretreated with 1% BSA fraction V, 5 × SSC, 0.1% SDS (30 min at 50°C) and washed with 2 × SSC (3 min) and 0.2 × SSC (3 min) and hybridized overnight at 60°C in a cocktail con- taining 1.3 × Denhardt’s, 3 × SSC 0.3% SDS, 0.67 μg/μl polyadenylate and 1.4 μg/μl yeast tRNA. After hybridization slides were washed at room temperature in 0.5 × SSC and 0.1% SDS (15 min), 0.5 × SSC and 0.01% SDS (15 min), and twice in 0.06 × SSC (2 and 1 min, respectively). Scanning was performed with Axon GenePix 4100A and images were processed with Gene- Pix 6.0 (Molecular Devices, Sunnyvale, CA, USA). The spots were filtered by criterion (I-B)/(SI+SB) ≥ 0.6, where I and B are the mean signal and background intensities and SI, SB are the standard deviations. Low quality spots were excluded from analysis and genes presented with less than three high quality spots on a slide were discarded. After subtraction of median Forward primer (5’-3’) AGGTTGGCTATGGAGGCTGT TCTCCTGGTATTTGCGCTCTGTGGT TCTGAGTCATGCTGTCCGTAGTGGT Reverse primer (5’-3’) Accession number TCTGCTTCAATGTATGGTGGG AF321836 TATAAGTCGGTGTGTGAGCGCCTGA CA351440 CCTCCCTCTCTACCTTCGTTGCAAA CA369467 GAGGAGTTTGTCCAGTTCGGTCCGT CATGCACCAGCTTCTTATCCTCCAG CA368994 TCAACGACTCTGGGGTGTACCGATG TCCACCTCATCTCCACCACGTCTC CA366631 TCTCTGAGCCGCTCAACCTGTCAT CGTTCCACGACAGCTTTATACGGA CA348044 CTGTGTTGTCAGAGTGCGAGATGGT TACACACAATGTCCAGGCCCTGA EXOB2 AGAACTCTTCCGAGTTGGCATGGT AGTGATGCTGGGATCCATCTCTGA CA364804 CGTGTATCAAGACGCCAGCT TTGCAGCCCTCACAGACATG EU655708 TCAAGTTGCCCATAGTCAGT CACCTGAACTCTACCAACCA FJ195610 CCGCAACACGAAGCAACTATTACAGC GGAACCCTCCTGGCCTGATAACAC AJ557150 CAAACTACATTACCAGGC GTTATGTGTTGCCAGTTG EU668996 TTGGGCGGTGGAGCCTAT TTTCCTCGCCCGTGTCAT EU668997 AGACCTCGGCGAGATTTGT TGTGGAATAGATCAGCCAGGAA EU668995 GCTGAAGACCAGAGGCATCTTTGA GCTGCATACCTCCTTGACGATGAT AY864082 TGGTGCAGAACCTCATGGTCCTCA ATCCCGGATGATTCCAAAGTCGTC BT044902 AATCCATCGGCGTTCTGACAAGC GCCCGTACAGCAGCATTCATACCTT BT059256 TGCCTTCATTCAGACGCAGCA CAGATGATTCCGGTGTTGCGA BT043851 AGACGTCCACCACTGCAAGGTCAA TTAACAGCGTCGAAGCAGGCCA BT043497 AGGGCATGGACCAGGAACTCC GGGCTCTCCATCCTGGGATGT BT072418 CCAATGAGGCTAAAGGCACCAAGA TGCCATCTCCGAGAGCAACATC CACTGCTGTGGTGGATGGACAGTT TGTACCTCAAGGAGAAGCTGCCGT CTCACACCATCAAAGCTACAGCGA CGACTCAAATTCGACAACTGGGC CAAAGACCAGCGTCAACAACAA GTGCAGCATGACATCAAGTA GGATGAACTCCCTGCATGTGA AGCGGGGGAAACAGTAGCAGGA TGCTGGTAGCGGAGAAAGACAT TGCCTCAGCACCCTACTCTG TGTGCCGCTAGAGGTGAAATT TGCCCCTCCAGGATGTCTAC GTCGCCGTACCAGCAGGTGATT CCAGCTTGTCGATGAAGTCATCCA BT050391 CCGTGGGAATGGCTCTGAACAT BT059642 CCAGCGGGTAGAAGAAGAACACCA est02b08 ATTAAGGCCATGGGATCGTCGC est04e05 GTGTCGCCTCGTCGATTTAACTCA CA367172 TTTCTGTCTCTGGCTGTCTGGGCT CA385697 CGCCTCTGTCTCAAAGCTCACT CA042356 CTCTTCTTCTCGATAACCTT CA368961 TGAGGCCAAAGTACTCGTCGA AY606034 GCCTGGTCTTGAGATTGTGGGTGT CA343913 CTGACCACCAGGAAGACACCAT BI468076 GCTTTACAACCTCAGGATTGGC BT048827 GCAAATGCTTTCGCTTTCG AJ427629 CACGGCCCACAGGTACTG BG933853 CGTGGGCCATCTTCTTCTCGA CX040383