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Table 2 Validation of array data by real-time PCR

From: Identification of novel transcriptional regulators involved in macrophage differentiation and activation in U937 cells

   Illumina array fold change Real time PCR
      Ct   RQ fold *  
Ref.Seq Gene Symbol PMA24 LPS VitD3 Cont PMA24 LPS VitD3
Cytokines and Chemokines
NM_002983 CCL3 7.1 197.3 1.4 26 27.9 776 1.6
NM_000594 TNFa 3 121.4 1.6 29 13.9 119.4 1.1
NM_000584 IL8 3.7 82.9 2.3 25 1.2 222.9 3.2
NM_000575 IL1A 1.1 98.7 -1 35 5.7 2195 2.3
NM_000576 IL1B 2.9 75.2 1.1 26 2.5 415.9 0.7
NM_004591 CCL20 -1 47.6 1.1 30 2.1 724.1 0.9
NM_000600 IL6 3.7 29.9 2.1 28 4.6 157.6 3.5
NM_001565 IP10 7.5 23.4 -1 30 97 222.9 0.7
NM_002089 CXCL2 1.2 16.5 1.1 28 0.4 48.5 1.7
NM_002984 CCL4 1.1 1.7 1.1 35 52 80,000 1.9
Surface molecules
NM_004233 CD83 1.8 10.4 -1.1 23 3.2 9.8 0.6
NM_001781 CD69 1.4 4.1 -1.4 21 3.2 4.9 0.9
NM_000632 CD11b 3.3 3.1 2.7 24 7.5 3 2.6
NM_000591 CD14 -1 1.2 22.4 29 1.1 1.1 45.3
Signaling and effector molecules
NM_002423 MMP7 29.9 36.5 -1.4 28 512 181 0.6
NM_002658 PLAU 1.3 19.9 -1 28 1.1 5.3 0.6
NM_000265 NCF1 18.6 17.8 3.8 29 32 39.4 2.6
NM_005627 SGK 7.5 13 -1 22 10.6 52 1.6
NM_000389 p21 6.1 11.8 1.3 25 42.2 42.2 1.1
NM_000014 A2M 10.4 11.5 1.1 30 52 32 3.2
NM_004994 MMP9 8.4 8.3 -1.2 30 21.1 9.2 1.1
NM_000228 LAMB3 2.9 6.5 8.5 28 32 19.7 64
NM_002468 MYD88 4.5 4.2 1.4 27 27.9 7.5 1.5
NM_000064 C3 1.8 2.3 -1 27 119.4 42.2 1.2
NM_003264 TLR2 1.4 1.6 1.1 31 11.3 3.2 2
NM_000215 JAK3 1.5 1.7 1.1 18 5.7 4.9 1.4
NM_004345 LL37 -1.2 -1.3 32.1 30 1.3 0.8 84.4
NM_001775 CD38 -1.9 -2 5.9 22 1.1 0.2 7.5
NM_001911 CTSG -3.4 -4.8 -1.3 21 0.03 0.01 0.6
NM_006573 TNFSF13B -4.3 -5.1 -1.2 22 0.3 0.1 1.9
NM_000250 MPO -8.3 -9.6 -1.1 17 0.1 0.03 1.1
Transcription factors/Histone modifiers
NM_005384 NFIL3 3.1 4.9 -1.3 27 9.8 78.8 3.2
NM_000321 RB1 2.2 1.8 1 19 3 1.1 -0.2
NM_005461 MAFB 3.3 35.8 1.2 27 17.1 18.4 -1.1
NM_005587 MEF2A 4 4.4 1.1 19 9.2 4.3 1.1
NM_002397 MEF2C 1.8 1.9 -1.2 19 8 4.3 1.6
NM_005920 MEF2D 2.1 7.9 -1.1 26 1.1 3 0.5
NM_021958 HLX1 2.2 2.3 -1 23 10.6 3.5 1.2
NM_021999 BRI 2.6 2.2 -1.2 22 8.6 3.7 1.2
NM_005474 HDAC5 NA    24 4.9 4 0.8
NM_012412 H2AV NA    19 2.6 1 1.3
NM_173158 Nur77 1.2 11.7 1.1 35 1.1 2.3 1
NM_001706 BCL6 7.6 19.5 1.6 25 78.8 34.3 8
NM_001964 EGR1 4.2 13.6 1.1 27 14.9 1.2 1.4
NM_005252 FOS 2.4 3.3 -1.5 26 32 2.6 0.9
NM_002167 ID3 11.9 38.9 2.7 30 13 18.4 8
NM_006084 IRF9 2.5 2.8 1 25 214.5 5.3 1.4
NM_000399 EGR2 5.3 27.3 1.1 28 5.3 4.3 2.5
NM_016270 KLF2 13.9 9.8 -1.3 26 32 97 0.5
NM_021784 FOXA2 4.9 2.9 -1 30 73.5 16 0.3
NM_005524 HES1 2.8 2.8 1.2 32 27.9 64 0.8
NM_004235 KLF4 1.5 1.7 -1 27 3.7 3 1.9
NM_002698 OCT2 2.1 3.3 -1.2 26 14.9 7 0.4
NM_030756 TCF7L2 3 2.8 -1.2 21 8.6 5.3 0.5
NM_004030 IRF7 2.2 2.6 -1.3 26 13 4.6 1.2
NM_014707 HDAC7 3.2 2.5 -1.2 22 29.9 16 0.7
NM_003884 PCAF 2 1.8 -1.2 25 3.7 1.4 0.8
NM_005919 MEF2B 1.3 1.4 1.3 27 6.5 0.4 0.8
  1. 58 genes representative of cytokines, chemokines, signaling molecules, transcription factors and histone modifiers were selected. NA (none applicable) denotes data not available from array experiment. *RQ = 2-ddCt in which ddCt = dCt(samples) - dCt(control U937 cells). dCt denotes Ct value normalized to GAPDH.
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