A combination of rabbit polyclonal anti-HDAC2 (Thermo Scientific, PA1-861) at 1:3000 and mouse monoclonal anti-β-Tubulin (DSHB, E7) at 1:2000 was used as positive controls for the nuclear and cytoplasmic fractions, respectively. A combination of mouse monoclonal anti-GFP (Clontech, 632381) at 1:2000 and rabbit polyclonal anti-MAP1LC3B (Novus, NB100-2220) at 1:5000 was used to analyze the IP fractions. For validation of the MudPIT results, Western blots were probed with either mouse monoclonal anti-SQSTM1 (BD, 610832) at 1:2000 dilution or goat polyclonal anti-MAP1B (Santa Cruz, sc-8970) at 1:100 dilution in combination with rabbit polyclonal anti-MAP1LC3B (Novus, NB100-2220) at 1:5000.
Secondary antibodies used for Western blotting included goat anti-rabbit IRDye-800CW (LI-COR, 926-32211), goat anti mouse IRDye 680 LT (LI-COR, 926-68020), donkey anti-goat IRDye-800CW (926-32214), donkey anti-rabbit IRDye 680 LT (926-68023).