REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
LAMP1	Abcam	Cat# ab25630, RRID: AB_470708
TGN46	Novus	Cat# NBP1-49643, RRID: AB_10011762
alpha Tubulin	Abcama	Cat# ab15246, RRID: AB_301787
β-Tubulin	Sigma-Aldrich	Cat# T4026, RRID: AB_477577
MSF	Abcam	Cat# ab114099, RRID: AB_10863530
Rab7	Cell Signaling Technology	Cat# 9367, RRID: AB_1904103
GM130	BD Biosciences	Cat# 610822, RRID: AB_398141
p62/SQSTM1	Sigma-Aldrich	Cat# P0068, RRID: AB_1841066
LC3B	Sigma-Aldrich	Cat# L7543, RRID: AB_796155
V5 tag	Abcam	Cat# ab9116, RRID: AB_307024
V5 tag	Abcam	Cat# ab27671, RRID: AB_471093
FLAG	Sigma-Aldrich	Cat# F7425, RRID: AB_439687
FLAG	Sigma-Aldrich	Cat# F3165, RRID: AB_259529
MTMR3	Santa Cruz Biotechnology	sc-398353
Mouse IgG HRP-linked whole Ab	Sigma-Aldrich	NA931V
Rabbit IgG HRP Linked Whole Ab	Sigma-Aldrich	NA934V
Alexa Fluor® 488	Thermo Fisher Scientific	Cat# A-11001, RRID: AB_2534069
Alexa Fluor® 488	Thermo Fisher Scientific	Cat# A-11008, RRID: AB_143165
Alexa Fluor® 546	Thermo Fisher Scientific	Cat# A10040, RRID: AB_2534016
Alexa Fluor® 546	Thermo Fisher Scientific	Cat# A-11003, RRID: AB_2534071
Streptavidin, Alexa Fluor™ 488 Conjugate	Thermo Fisher Scientific	S322354
Chemicals, peptides, and recombinant proteins
LysoTracker™ Red DND-99	Thermo Fisher	L7528
BODIPY™ 493/503	Thermo Fisher	D3922
Sodium oleate	Sigma-Aldrich	O7501
Bafilomycin A1 Ready Made	Sigma-Aldrich	SML1661-1ML
Albumin, Bovine Serum, Fraction V, Fatty Acid-Free	Sigma-Aldrich	126575
Nocodazole	Sigma-Aldrich	487928
Paclitaxel	Sigma-Aldrich	T7191
BODIPY™ 576/589	Thermo Fisher	D2225
PI(5)P diC8	Echelon	P-5008
PI(3,5)P2	Echelon	P-3508
Hoechst 33342	Thermo Fisher	H3570
Critical commercial assays
RNeasy Mini Kit	QIAGEN	74104
RevertAid First Strand cDNA Synthesis Kit	Thermo Fisher	K1621
X-tremeGENE™ 9 DNA Transfection Reagent	Roche	6365779001
X-tremeGENE™ siRNA Transfection Reagent	Roche	4476093001
QuantiTect SYBR® Green PCR Kits	QIAGEN	204141
Experimental Models: Cell Lines
Huh7	ATCC	NA
Oligonucleotides
LIPA Forward CTGACAAAGGTCCCAAACCAG LIPA Reverse GCAAGAATGAAGCCCAGGC	This paper	Invitrogen
GNS Forward CCCATTTTGAGAGGTGCCAGT GNS Reverse TGACGTTACGGCCTTCTCCTT	This paper	Invitrogen
GBA Forward GGGCAAAGGTGGTACTGACAG GBA Reverse GCATGGTGTTGGGGAACAG	This paper	Invitrogen
MCOLN1 Forward TTGCTCTCTGCCAGCGGTACTA MCOLN1 Reverse GCAGTCAGTAACCACCATCGGA	This paper	Invitrogen
TMEM55B Forward GTTCGATGCCCCTGTAACTGTC TMEM55B Reverse CCCAGGTTGATGATTCTTTTGC	This paper	Invitrogen
ATP6V1E1 Forward AAAGGTCGGCTTGTGCAAACCC ATP6V1E1 Reverse GGTCATCTCTTGCTCTGAGGAC	This paper	Invitrogen
GAPDH Forward CCACATCGCTCAGACACCAT GAPDH Reverse CCAGGCGCCCAATACG	This paper	Invitrogen
LAMP1 Forward ACGTTACAGCGTCCAGCTCAT LAMP1 Reverse TCTTTGGAGCTCGCATTGG	This paper	Invitrogen
Recombinant DNA
cDNA GFP-Rab7	Dr Goud	Institute Curie, PSL Research University, CNRS UMR 144, Paris, France
cDNA MTMR3	Dr Tronchère	INSERM U1048, I2MC and Université Paul Sabatier, 31432 Toulouse, France.
cDNA septin 9 isoform 1	Dr Russell	CCRCB, Queens University Belfast
Software and algorithms
G:BOX Chemi	SYNGENE	https://www.syngene.com/software/
LAS X	Leica	https://www.leica-microsystems.com/products/microscope-software/
LightCycler® 96 SW 1.1	Roche	https://lifescience.roche.com/en_fr/products/lightcycler-software-4-1.html
FIJI	ImageJ	https://imagej.net/software/fiji/