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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.