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Table 2 RT-qPCR results

From: A comparison between whole transcript and 3’ RNA sequencing methods using Kapa and Lexogen library preparation methods

Gene name

Primer set used

RT-qPCR fold change

Trad-KAPA fold change

3’-LEXO fold change

RT-qPCR result match which RNA-Seq method

Group

Adnp

mAdnp-ex2–3

0.83

1.15

5.02

Trad-KAPA

Trad-KAPA only

Cd7a

mCd7a-ex3–4

0.69

0.79

5.11

Trad-KAPA

Trad-KAPA only

Fv1

mFv1-F169

0.55

0.54

10.48

Trad-KAPA

Trad-KAPA only

Mid1

mMid1ex4–5

0.77

0.53

5.12

Trad-KAPA

Trad-KAPA only

Mid1

mMid1ex8–9

0.83

0.53

5.12

Trad-KAPA

Trad-KAPA only

Mmp28

mMmp28ex2–3

3.24

4.52

8.55

Trad-KAPA

Trad-KAPA only

Unkl

mUnkl-ex5–6

0.75

1.11

5.12

Trad-KAPA

Trad-KAPA only

Unkl

mUnkl-ex2–3

0.90

1.11

5.12

Trad-KAPA

Trad-KAPA only

Zfp647

mZfp647-204ex4–5

0.55

0.42

8.46

Trad-KAPA

Trad-KAPA only

Zfp647

mZfp647-201ex3–4

0.59

0.42

8.46

Trad-KAPA

Trad-KAPA only

Bcl2a1b

mBcl2a1bEx1–2

2.91

1.44

5.76

In between

3’-LEXO only

Hist4h4

mHist4h4

1.83

0.26

0.27

Neither

3’-LEXO only

Mir5136

mMir5136

1.47

5.07

0.88

3’-LEXO

3’-LEXO only

Mt-Tq

mMt-Tq

1.09

0.95

0.30

Trad-KAPA

3’-LEXO only

Rps27rt

mRps27rt

1.27

0.27

1.40

3’-LEXO

3’-LEXO only

S100a4

mS100a4ex1–2

1.93

1.42

2.31

3’-LEXO

3’-LEXO only

S100a4

mS100a4ex2–3

2.06

1.42

2.31

3’-LEXO

3’-LEXO only

Schip1

mSchip1ex7–8

0.85

0.51

0.90

3’-LEXO

3’-LEXO only

Snord118

mSnord118

0.46

0.26

0.60

3’-LEXO

3’-LEXO only

Snord13

mSnord13

0.92

0.98

0.48

Trad-KAPA

3’-LEXO only

Spink1

mSpink1ex3–4

9.49

2.66

8.28

3’-LEXO

3’-LEXO only

Tceal5

mTceal5ex3–4

5.82

10.48

30.09

Trad-KAPA

3’-LEXO only

Tceal5

mTceal5ex1–2

6.07

10.48

30.09

Trad-KAPA

3’-LEXO only

Atoh8

mAtoh8

3.97

3.10

3.19

Both

Iron metabolism

Bdh2

mBdh2

0.28

0.35

0.39

Both

Iron metabolism

Bmp6

mBmp6

4.83

6.01

6.20

Both

Iron metabolism

Cp

mCp

1.77

1.88

1.94

Both

Iron metabolism

Ftl1

mFtl1

1.75

0.98

3.26

In between

Iron metabolism

Hamp1

mHamp1

5.75

5.19

5.73

Both

Iron metabolism

Hamp2

mHamp2

0.26

0.28

0.33

Both

Iron metabolism

Hfe2

mHfe2

0.61

0.66

0.67

Both

Iron metabolism

Id1

mId1F205&200

4.05

3.43

3.19

Both

Iron metabolism

Lcn2

mLcn2

2.91

2.92

2.25

Both

Iron metabolism

Slc11a2

mSlc11a2

0.66

0.80

0.73

Both

Iron metabolism

Smad7

mSmad7

3.33

3.85

2.91

In between

Iron metabolism

Tfrc

mTfrc

1.16

1.26

1.32

Both

Iron metabolism

  1. Column 3–5 give the log2 fold difference in expression between the iron loaded and control samples by RT-qPCR, Trad-KAPA, and 3’-LEXO. Column 6 indicates if the RT-qPCR results matched better to one RNA-Seq method. Column 7 denotes the group of the genes: detected only in Trad-KAPA (Trad-KAPA only), detected only in 3’-LEXO (3’-LEXO only) or iron metabolism related (Iron metabolism)