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Table 2 Comparison of qPCR versus RNA-seq of 23 selected DEGs in BEAS-2B cells exposed to diesel UFP. Numbers represent fold changes of separate experiments (n = 3) for each time point. Fold changes for both qPCR and RNA-seq are calculated considering exposed cells versus control cells after normalization. Pearson correlation between qPCR and RNA-seq FC for 4, 8, 16 and 20 h resulted in 0.759, 0.772, 0.715 and 0.774 respectively

From: Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles

Gene symbol qPCR (FC) RNAseq (FC) Biological annotations (GSEAe)
4 h 8 h 16 h 20 h 4 h 8 h 16 h 20 h
ALDH3A1 3.49 6.79 6.40 3.74 4.64 4.95 4.65 4.14 Enzyme
CCL5 1.78 1.78 −1.04 −1.71 1.85 1.19 1.63 −1.16 Secreted protein (NFK; INF)
CDKN1A 1.68 1.51 1.29 1.41 1.56 1.62 1.27 1.34 Transcription factor (NFK; INF)
CXCL2 a −1.52 −1.04 2.01 3.24 1.28 1.37 1.26 2.09 Secreted protein (NFK; INF)
EPGN b 6.50 6.04 5.19 4.09 5.92 6.94 8.52 6.06 Secreted protein
FOSL1 1.37 1.87 1.94 1.27 1.29 1.75 1.70 1.98 Transcription factor (NFK)
GREM1 b 1.66 2.38 3.50 2.64 1.22 1.97 2.61 2.76 Secreted protein (EMT)
HES1 3.56 1.21 1.47 2.34 2.15 −1.19 1.26 1.28 Transcription factor (NFK)
HMOX1 b 3.70 2.95 2.51 2.34 3.46 2.48 1.16 1.35 Enzyme (XEN)
IER3 1.88 1.54 2.15 1.63 1.22 1.89 1.85 2.04 Secreted (NFK)
IGFBP1 4.20 2.86 3.73 1.95 4.21 4.73 3.82 3.71 Transcription factor (XEN)
IL1A 2.47 1.71 2.32 2.08 2.57 1.79 2.25 1.91 Secreted protein (NFK;INF)
IL1B 2.10 2.60 3.70 5.30 2.16 1.83 3.73 3.49 Secreted protein (NFK;INF)
LIF c 1.86 1.72 1.98 1.74 1.36 1.69 1.84 2.25 Secreted protein (NFK)
MAFF c 1.41 1.41 1.96 1.67 1.52 1.29 1.79 1.45 Transcription factor (NFK)
NFE2L2 −1.76 −1.08 1.26 1.94 1.64 1.26 1.28 1.13 Transcription factor (NFK)
PPP1R15A d 3.39 1.51 −1.12 1.07 2.24 1.88 1.18 1.17 ENZYME (NFK)
SLC16A6 3.86 1.58 1.05 2.09 4.09 1.78 1.37 1.29 Solute carrier (NFK)
SLC7A5 1.57 2.28 −1.08 2.90 1.25 1.82 1.77 1.98 Solute carrier
STC2 a 3.54 2.25 1.60 1.48 1.94 2.03 1.60 1.53 Secreted factor
TGIF1 2.37 1.41 1.15 1.18 1.77 1.23 1.34 1.34 Transcription factor (NFK)
TNFAIP3 a −1.12 1.22 2.33 2.26 1.01 1.72 1.76 1.48 Transcription factor (NFK;INF)
TXNRD1 b −1.04 1.92 1.57 2.14 1.43 1.54 1.51 1.55 Enzyme
  1. Gene included in next-maSigPro cluster analysis: acluster 2; bcluster 9; ccluster 8;dcluster 3
  2. eGSEA hallmarks gene set legend: NFK TNF-α signaling via NF-kB, INF inflammatory response, XEN, xenobiotic metabolism, EMT, epithelial mesenchymal transition