REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit Anti-ATG13 Monoclonal Antibody	Cell Signaling	Cat#13468; RRID: AB_2797419
Rabbit Anti-ATG16L1 Monoclonal Antibody	Cell Signaling	Cat#8089; RRID: AB_10950320
Anti-GAPDH Antibody	Abcam	Cat#ab9484; ab9484, RRID: AB_307274
Mouse Anti-GFP Monoclonal Antibody	Sigma	Cat#11814460001; RRID: AB_390913
Anti-M2 Antibody	Abcam	Cat#ab5416; RRID: AB_304873
Goat Anti-Rabbit IgG HRP Conjugated Antibody	Cell Signaling	Cat#7074; RRID: AB_2099233
Goat Anti-Mouse IgG HRP Conjugated Antibody	Cell Signaling	Cat#7076; RRID: AB_330924
Rabbit Anti-GABARAPL2 Polyclonal Antibody	In house	N/A
Rat Anti-HA Monoclonal Antibody	Roche	Cat#11867423001; RRID: AB_390918
Rabbit Anti-ATG4D Polyclonal Antibody	Proteintech	Cat#16924-1-AP; RRID: AB_2062024
Rabbit Anti-ATG4B Polyclonal Antibody	Cell Signaling	Cat#5299; RRID: AB_10622184
Bacterial and virus strains
Influenza A Virus PR8 (strain A/Puerto Rico/9/1934)	Fletcher et al., 2018	N/A
BL21-Gold (DE3) E. coli.	Agilent	Cat#230132
Chemicals, peptides, and recombinant proteins
Bafilomycin A1	Tocris	Cat#1334
PP242	Tocris	Cat#4257
Monensin	Sigma	Cat#M5273
DAPI	Sigma	Cat#D9542
Human IgG	Sigma	Cat#I4506
Murine IFNγ	Peprotech	Cat#315-05
GFP-TRAP beads	Chromotek	Cat#gtma-20
Control magnetic agarose beads	Chromotek	Cat#bmab-20
Magnetic 3-micron beads	Bangs Lanoratories	Cat#PMA3N
Latex 3-micron beads	Polysciences	Cat#17134-15
Zymosan	Sigma	Cat#Z4250
Human serum	Sigma	Cat#P2918
DMEM	Thermofisher	Cat#41966-029
DMEM F/12	Thermofisher	Cat#11320074
Pen/Strep	Thermofisher	Cat#15140-122
N-Ethylmaleimide (NEM)	Sigma	Cat#E3876
Puromycin	Sigma	Cat#P8833
Blasticidin	Sigma	Cat#15205
Protease inhibitor cocktail III	Sigma	Cat#P8340
Phosphatase inhibitor	Sigma	Cat#P0044
EGF	Peprotech	Cat#AF-100-15
Hydrocortisone	Sigma	Cat#H0888
Cholera toxin	Sigma	Cat#C8052
Insulin	Sigma	Cat#I9278
2x LDS buffer	Thermofisher	Cat#NP0008
Imperial Stain	Thermofisher	Cat#24615
AspN protease	Sigma	Cat#11420488001
Gold anti-fade	Thermofisher	Cat#P36930
Anti-HA Agarose beads	Sigma	Cat#A2095
Recombinant His-tagged human ATG4B	Abcam	Cat#ab188707
Deposited data
https://data.mendeley.com/datasets/f5kjfmnf2p/1	N/A	N/A
Experimental models: cell lines
HCT116 GFP-rLC3B	Fletcher et al., 2018	N/A
HCT116 ATG16L1−/− GFP-rLC3B	Fletcher et al., 2018	N/A
HCT116 GFP-rLC3B WT clone A	Ulferts et al., 2020 (BioRxiV)	N/A
HCT116 GFP-rLC3B ATG4D−/−	Ulferts et al., 2020 (BioRxiV)	N/A
MCF10A GFP-hLC3A	Florey et al., 2011	N/A
MCF10A ATG13−/− GFP-hLC3A	Jacquin et al., 2017	N/A
MCF10A ATG13−/− GFP-hLC3B	This manuscript	N/A
MCF10A ATG13−/− GFP-hLC3C	This manuscript	N/A
MCF10A ATG13−/− GFP-hGABARAP	This manuscript	N/A
MCF10A ATG13−/− GFP-hGABARAPL1	This manuscript	N/A
MCF10A ATG13−/− GFP-hGABARAPL2	This manuscript	N/A
J774.1A GFP-hLC3A	Florey et al., 2011	N/A
RAW264.7 GFP-hLC3A	This manuscript	N/A
RAW264.7 ATG16L1−/−	Lystad et al., 2019	N/A
RAW264.7 ATG16L1−/− GFP-hLC3A + WT FlagS-ATG16L1	This manuscript	N/A
RAW264.7 ATG16L1−/− GFP-hLC3A + K490A FlagS-ATG16L1	This manuscript	N/A
HeLa GFP-hLC3B.G120	Agrotis et al., 2019	N/A
HeLa ATG4B−/− GFP-hLC3B.G120	Agrotis et al., 2019	N/A
HEK293 FT	ATCC	ATCC Cat# PTA-5077, RRID:CVCL_6911
Oligonucleotides
ATG4D guide 1	ggcgggacacaaagucccgc	N/A
ATG4D guide 2	gggacuuugugucccgccug	N/A
ATG4D guide 3	ccggcgguaugugagccac	N/A
Recombinant DNA
pBabe-Puro GFP-GABARAP	MRC-PPU	DU36756
pBabe-Puro GFP-GABARAPL1	MRC-PPU	DU36757
pBabe-Puro GFP-GABARAPL2	MRC-PPU	DU40072
pBabe-Puro GFP-LC3B	MRC-PPU	DU40253
pBabe-Puro GFP-LC3C	MRC-PPU	DU40860
mRFP-Lact-C2	Addgene	Addgene plasmid Cat#74061