I want to see if specific genes are up/down regulated under colony biofilm conditions. So far, I tested 5 housekeeping genes, but all of them seem to be less expressed under biofilm condition, thus may not be used as "housekeeping" genes for analysis.

I troubleshot, thinking that results might be due to different concentration\RT efficiency. I tried both - using same 500 ng of RNA for RT reaction (quantified by Qubit) and later also measured cDNA with ssDNA Qubit kit - adjusted concentration a bit, but still no consistency within putative housekeeping genes.

RNA is of height 8.0 to 9.