Table 1 qPCR validation of differential expression (sarcoma vs. skin) of five genes detected as differentially expressed by mRNA-seq. Abbreviations are as follows: n.s., not significant at p ≤ 0.05; ΔCt, average of the two differences between the cycle time for the indicated gene and the average of the cycle times for two endogenous normalizer genes (ATE1 and SHOC2); ΔΔCt,difference between the average ΔCt value for the sarcoma samples and the average ΔCt value for the normal skin samples. Column "Gene" contains the HGNC official gene symbol
Gene | RNA-seq log2(sarcoma/skin) | TaqMan assay | ΔΔCt | qPCR log2(sarcoma/skin) |
|---|---|---|---|---|
BARX1 | 5.29 | Hs01026253_g1 | 436.6 | 8.77 |
BARX2 | −7.08 | Hs01573160_m1 | 0.0003 | −11.76 |
FBN2 | 4.99 | Cf02646808_mH | 83.67 | 6.39 |
GAPDH | −3.86 | Cf04419463_gH | 0.5663 | −0.82 |
ITM2B | −3.31 | Hs00222753_m1 | 0.0303 | −1.72 |
LATS1 | 0.815 | custom (see Methods) | 0.8697 | −0.20 |
LEF1 | −2.17 | Hs00212390_m1 | 0.0689 | −3.86 |
MMP13 | 5.91 | Cf02741638_m1 | 84.62 | 6.40 |
ATE1 | n.s. | Cf02638583_m1 | n/a (endogenous normalizers) | |
SHOC2 | n.s. | Cf02707128_m1 | ||