Which gene would you recommend as reference in those types of cells? Until now, I was working with HPRT but it's not efficient for me anymore. Thank you for all of the answers!
Our gold standard was gapdh. There are limitations, but we used it on lung samples and purified immune cells from mice
I would always say "See it for yourself". As per MIQE guidelines of qRTPCR, it is always recommended to see for yourself from a set of common housekeeping genes (GAPDH, B-Actin, UBC, 16srRNA etc) in your samples, using your enzymes and all reaction conditions. For me, who uses some sample, and some set of enzymes, the same housekeeping would never work for you. What I always prefer doing is take a sample each of a pool of mouse epithelial and mouse macrophages and extract good quality RNA. Label each as sample 1 and sample 2 (you may pool several RNA from each group for the standardization purpose). And run qRTPCR using each housekeeping gene (preferably in a single run in triplicates). Analyse the Ct value that comes out from each triplicate and also the mean value. The mean values should not exceed 30 cycles (for a good housekeeping 13-20 cycle would be best). Examine the coefficient of variance (CV) in the triplicates. The ideal CV should be less than 5%. Then examine the melt curves. There should be single peaks. I know this looks tedious, but trust me it will always work for you once you standardize and the results would always be reproducible in your set of conditions. It would consume a maximum of one single 96 well plate and if you do it in a micro PCR plate, the reagents consumed will also be very less.
for macrophages which do not proliferate (primary tissue macrophages) it is absolutely fine to use GAPDH, for cells that do proliferate I would also use Beta-Actin.
I never worked with mouse macrophages and epithelial cells but I used beta actin for renal cells. I will suggest you do a literature search and check the reference genes commonly used for mouse macrophages and epithelial cells. Try to go for articles published in highly ranked journals. All the best.