Correct. Quantitative PCR was used to compare transcript abundance
If you are using or have used something for the express purpose for which it was designed then you should always use “use”. Utilised only gets used when you are repurposing something.
There seems to be a trend toward trying to use “fancier” versions of the same word, presumably in an attempt to sound cleverer. You should always aim to deliver the message in the clearest way possible, especially when the more complex term isn’t right anyway!
“Shopping bags were initially used to carry shopping. Shopping bags were then utilised as makeshift umbrellas during the storm.
“A modified form of the assay was utilised to assess transcriptional activity over time, SPSS was then used to perform statistical analyses.”
Affect / Effect