Atg16l1

Briefly, lysis was performed with NP40 lysis buffer. The lysates were electrophoresed on 4–12% NuPAGE Bis-Tris gels in MOPS SDS running buffer and transferred onto nitrocellulose membranes (Invitrogen) overnight. The membranes were blocked in 3% BSA and incubated with indicated primary antibodies where specified for: mouse CLEC16A, PINK1 (Abgent), GFP, Nrdp1 (Novus Biologicals), TOM20 (ProteinTech), Parkin, p62/SQSTM1, LC3 I/II, ATG16L1, cytochrome c, caspase-9, p-ERK1/2 and EK1/2 (Santa Cruz), cleaved Caspase-3, p-Akt (ser473), p-Akt (Ser308) and total Akt (Cell signaling). The membranes were washed and incubated with a respective mouse/rabbit secondary antibody and bound antibody was detected with WesternBright ECL kit (Advansta). Membranes were stripped and re-probed for β-actin as loading control.

Cells were lysed in buffer (10 mM HEPES pH 7.4, 50 mM NaPyrophosphate, 50 mM NaF, 50 mM NaCl, 5 mM EDTA, 5 mM EGTA, 100 µM Na₃VO₄, 0.1% Triton X-100) and Western blotting was conducted using the following primary antibodies: LC3B (Novus Biologicals, NB100-2220), β-actin (ACTB, Sigma-Aldrich, A5316), ATG5 (Santa Cruz, sc-33210), FIP200 (Cell Signaling Technology, D10D11), BECN1 (Santa Cruz, sc-48341), PIK3C3 (Santa Cruz, sc365404), WIPI2 (Cell Signaling Technology, #8567), ATG13 (Cell Signaling Technology, D4P1K), ATG9A (Cell Signaling Technology, D4O9D), ULK1 (Santa Cruz, sc-390904), ULK2 (GeneTex, GTX111476), UVRAG (Santa Cruz, sc-293268), ATG14 (Cell Signaling Technology, #5504), ATG16L1 (Santa Cruz, sc-393274), cleaved-caspase 3 (Cell Signaling Technology, #9661), viral capsid protein 1 (VP1, Dako, M706401-1), FLAG (Sigma, F1804), PI4KIIIβ (Sigma 06578), and PIKfyve (Santa Cruz, sc-100408). Blots were cropped to improve clarity and conciseness. Uncropped blots are provided in Supplemental Figure 2.