Table 2.
Quantitative real time PCR (qRT-PCR) validation of RNA-seq data
| Official gene | RNA Type | Log2 FC | Log2FC | p-value | p-value |
| symbol | qRT-PCR | RNA-seq | qRT-PCR | RNA-seq | |
| UBC | protein_coding | 4.8 | 0.37 | 0.01 | 0.16 |
| SSTR5 | protein_coding | –2.06 | –2.27 | 0.02 | 2.3E-08 |
| MAPK11 | protein_coding | –1.09 | 2.20 | 0.5 | 5.26E-12 |
| PTPRC | protein_coding | –1.75 | –1.84 | 0.18 | 9.37E-09 |
| PARK7 | protein_coding | –1.97 | 0.14 | 0.17 | 0.99 |
| NDUFV2 | protein_coding | –0.76 | –2.22 | 0.06 | 2.73E-12 |
| LRRK2 | protein_coding | –2.01 | –0.1 | 0.33 | 0.49 |
| LPAR1 | protein_coding | –1.23 | –1.74 | 0.14 | 2.32E-08 |
| EZH2 | protein_coding | 2.29 | 1.72 | 0.03 | 3.32E-06 |
| DNMT1 | protein_coding | –1.38 | 1.14 | 0.01 | 0.000255726 |
| CCR3 | protein_coding | –1.2 | –4.47 | 0.05 | 1.34E-30 |
| BMP7 | protein_coding | –1.84 | –2.79 | 0.01 | 1.68E-29 |
| AL356309.1 | miRNA | 0.37 | –2.62 | 0.72 | 1.35E-13 |
| AC010127.3 | antisense | –1.52 | –2.31 | 0.08 | 3.81E-12 |
| RP3-467N11.1 | antisense | –0.95 | –3.24 | 0.56 | 9.08E-18 |
| RP5-1051H14.2 | lincRNA | 1.36 | 2.68 | 0.4 | 1.5E-12 |
| CTD-2066L21.2 | lincRNA | –1.2 | –2.7 | 0.13 | 4.03E-14 |
We successfully confirmed the results of RNA-seq by qRT-PCR validation; the trend of fold changes (FC) in the two groups showed a 76% correlation between RNA-seq and qRT-PCR findings. Log2 fold changes (Log2FC) in qRT-PCR correlated with Log2FC in RNA-seq (p = 0.01, r2 = 0.65). The qRT-PCR and RNA-seq fold changes for four genes: PARK7, DNMT1, MAPK11 and AL356309.2 were not validated.