I am getting a very low yield of RNA from Macrophages infected with pathogen Mtb. In fact I noticed the cells detached lot from Wells. Potentially an insufficient amount of cells in the well is the problem here.
I guess you have to check a) cell numbers, b) intergrity of your RNA. Macrophages have the tendency to destroy their own RNA very fast when they die. Immediate shock-freezing of shock-freezing in eg Trizol might help