I carried out an experiment in which I fed marine larvae with bacteria expressing dsRNA of a particular gene under different treatments and timepoints. I extracted RNA for qPCR and fixed samples for ISH. I have done the two approaches and there is a phenotype (reduction of the expression of my gene) based on ISH. However, the qPCR does not show any statistical significant differences based on the Relative Quantification of my samples. My housekeeping is good and the CT values of this reference gene are consistent across samples. What do you suggest to do? Is it something related to expression levels of the gene? or maybe the qPCR does not detect the reduction of this gene if it is lowly expressed. Any suggestions?
Are you absolutely sure the genomic DNA is removed? Do the qPCR amplicon and ISH probe overlap? Is it possible that qPCR amplifies something else? Try to sequence the amplicon, maybe? Can you try different dsRNAs and see if that helps?