To assess the cellular and subcellular localization of specific TFs, we used a CLARITY protocol modified to work on 200-µM-thick slices of brain (Chung et al. 2013 (link)). Briefly, male animals were transcardially perfused, and then brains were extracted and fixed in the perfusion solution before being sectioned in 200-µm slices on a vibrating microtome. Sections were embedded in hydrogel and then cleared overnight using electrophoretic tissue clearing. After washing, tissue was incubated with primary antibodies (ERR-alpha: Santa Cruz sc-66882; CNPase: Millipore no. MAB326) for 3 d. After three more washes, cleared tissues were incubated with fluorescent secondary for 3 d before being washed. The final wash included the nuclear counterstain Hoechst 33342. The tissue slices were then cleared in RIMS made from 70% Histodenz (Sigma no. D2158) in PBS with Triton-X100 and mounted on lifter slides before being imaged on a Zeiss LSM 710 confocal microscope. Detailed methods used for thick slice CLARITY are reported in Supplemental Methods.