Noise levels for the measurements of known quantities of mRNA from Rps29, Chgb, Ins2, Gfap, Nes and Sox2. (a) The measured noise strength (η2 = SD2/mean2) for Rps29 (blue circles), Chgb (red squares) Ins2 (black triangles), Gfap (green triangles), Nes (cyan stars) and Sox2 (magenta diamonds) with corresponding fits (lines) obtained using non-linear regression for the mathematical model presented in Additional file 2. The model estimates the RT-efficiency and the results are reasonable for five of the six genes. For Ins2 the efficiency is much lower than expected. The poor curve fit for the Ins2 gene results from the fact that the Ins2 data was generated for much higher copy numbers whereas our model for the PCR-noise was adapted for the low abundances of tge five other genes. (b) The proportion of the total noise for the PCR (filled symbols) and RT reactions (open symbols). Circles, squares and triangles are designated as in (a). The PCR and RT components do not have to add up to 1; the noise stemming from the dilution corresponds to the remaining noise. For Rps29, Chgb and Gfap, the PCR noise clearly dominates for all concentrations. For Ins2 and Sox2, the estimated RT efficiency is very low which means that this reaction will add a larger contribution to the total noise. Nes has an intermediate efficiency and for low copy numbers the RT noise dominates but it becomes smaller than the qPCR nosie when more transcripts are analyzed. Furthermore, the copy numbers are relatively high for Ins2 which deflates the PCR noise.
Bengtsson et al. BMC Molecular Biology 2008 9:63 doi:10.1186/1471-2199-9-63