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. 2012 Jun 6;18:1484–1504.

Table 2. Comparison of microarray data and real-time PCR data.

 
 CNTF(-SM)
 FBS(-SM)
 CNTF(-FBS)
Gene Microarray qPCR Confirmed? Microarray qPCR Confirmed? Microarray qPCR Confirmed?
Immature Markers:
Nestin
 −4.85*
 −2.58*
 ✓
 −1.37
 −1.53*
 ✓
 −3.54*
 −1.68*
 ✓
SRY (sex determining region Y)-box 2 (Sox2)
  
 2.12*
  
  
 1.17*
  
  
 1.82*
  
Vimentin
 −1.19
 −1.51*
 ✓
 −1.02
 1.01*
 ?
 1.04
 −1.52*
 ?
c-myc
 −1.61
 −1.03
 X
 −1.37
 −1.69*
 ✓
 −1.18
 1.63*
 X
Kruppel-like factor 4 (KLF4)
 −3.42*
 −3.63*
 ✓
 −1.33
 −3.86*
 ✓
 −2.57*
 1.06
 X
Ki-67
 1.09
 1.49*
 ✓
 1.08
 −1.05*
 X
 1.05
 1.56*
 ✓
C-X-C chemokine receptor type 4 (CXCR4)
 1.05
 3.52*
 ✓
 −1.02
 1.93
 ?
 1.07
 1.82*
 ✓
Differentiation Markers:
Janus kinase 1 (Jak1)
 1.33
 2.56*
 ✓
 −1.31
 1.75*
 X
 −1.15
 1.46*
 X
STAT1
 1.35
 2.24*
 ✓
 2.32*
 3.06*
 ✓
 −1.72
 −1.37*
 ✓
STAT3
 1.22
 2.28*
 ✓
 1.12
 1.48*
 ✓
 1.02
 1.54*
 ?
β-3 Tubulin
 2.08*
 1.27
 X
 2.07*
 −1.27*
 X
 1
 1.56*
 ?
Microtubule-associated protein 2 (Map2)
 1.47
 2.84*
 ✓
 1.16
 1.2
 ✓
 1.27
 1.33*
 ✓
Glial fibrillary acidic protein (GFAP)
 5.05*
 10.87*
 ✓
 7.13*
 11.90*
 ✓
 −1.41
 −1.10*
 ✓
Myelin basic protein (MBP)
 8.81*
 16.84*
 ✓
 1.26
 1.09*
 ✓
 6.96*
 15.41*
 ✓
Claudin 11 (CLDN11) 16.33* 7.92* ✓ 1.43 1.52 ✓ 11.44* 5.22* ✓

Microarray and real-time PCR data from CNTF treated cells were normalized to SM treated cells; data from FBS treated cells were normalized to SM, and data from CNTF treated cells were normalized to FBS. Noted differentiation and proliferation marker genes listed were compared in both the microarray and real-time PCR data, with blank cells in the microarray signifying no known gene annotation in the Affymetrix probe list. The real-time PCR data are from the day 5 time point only. * indicates significant gene (microarray: |fold change| > 2, FDR α<0.05; real-time PCR: p<0.05, fold change ≠ 1) ✓ indicates similar fold change direction between microarray and real-time PCR X indicates differing direction of fold change between microarray and real-time PCR or lack of PCR significance ? indicates no clear correlation between the fold change of microarray and real-time PCR.