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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)