Cells were fixed either with 4% paraformaldehyde (PFA) for 20 min or with cold methanol for 5 min at -20°C for proper axoneme proteins detection [22 (link)]. They were then washed and incubated for 30 min in blocking buffer (10% FCS in PBS) followed by incubation with primary antibodies diluted in blocking buffer supplemented with 0.05% saponin for 1 h at room temperature or overnight at 4°C. Cells were washed 3 times, and then incubated for 1 h with fluorescent Alexa-Fluor secondary antibodies. After washing, 150 μl of DAPI-Fluoromount were added into the Luer chamber (Southern Biotech). Images were acquired with a Zeiss Apotome.2 fluorescence microscope equipped with a 63x oil immersion fluorescence objective. Number of ciliated cells and length of cilia were quantified using Zen Software (Zeiss) or Imaris Software (Bitplane). The following antibodies were used for immunofluo-rescence: mouse-anti-LC3B (MBL, Cat# M152-3); rabbit-anti-FLCN (Cell signaling, Cat#3697); mouse-anti-ARL13B (C-5) (Santa Cruz, Cat#515784); rabbit-anti-ATG16 (MBL, Cat#PM040); rabbit-anti IFT20 (Proteintech, Cat#13615-1-AP); rabbit-anti-p-AMPK (T172) (Cell signaling, Cat#2535); Phalloidin (Cat# A34055); Alexa Fluor-conjugated secondary anti-bodies (donkey anti-mouse IgG and donkey anti-Rabbit IgG, Life Technologies).
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