REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse monoclonal anti-β-actin (clone C4), HRP-conjugated	Santa Cruz Biotechnology	Cat# sc-47778 HRP, RRID: AB_2714189
Mouse monoclonal anti-ds DNA (clone HYB331-01)	Abcam	Cat# ab27156, RRID: AB_470907
Rabbit polyclonal anti-cathepsin D	Santa Cruz Biotechnology	Cat# sc-6487, RRID: AB_2292414
Mouse monoclonal anti-DDK (clone OTI4C5)	OriGene	Cat# TA50011-100, RRID:AB_2622345
Goat polyclonal anti-EEA1	Santa Cruz Biotechnology	Cat# sc-6415, RRID: AB_2096822
Mouse monoclonal anti-EGF-R (clone 6F1)	MBL International	Cat# MI-12-1
Rabbit polyclonal anti-FYCO1	Sigma-Aldrich	Cat# HPA035526, RRID: AB_10672867
Mouse Anti-GM130 Monoclonal Antibody (clone 35/GM130)	BD Biosciences	Cat# 610822, RRID: AB_10015242
Mouse monoclonal anti-HA-Tag (clone HA.C5)	Applied Biological Materials	Cat# G036, RRID: AB_2616604
Mouse monoclonal anti-LAMP-1 (clone 1D4B)	BD Biosciences	Cat# 553792, RRID: AB_2134499
Rabbit monoclonal anti-HA-Tag (clone C29F4)	Cell signaling Technology	Cat# 3724S
Rabbit monoclonal anti-LAMP1 (clone D2D11)	Cell signaling Technology	Cat# 9091S
Mouse monoclonal anti-LAMP2 (clone H4B4)	Santa Cruz Biotechnology	Cat# sc-18822, RRID:AB_626858
Rabbit monoclonal anti-TFAM (clone D5C8)	Cell signaling Technology	Cat# 8076S
Rabbit polyclonal anti-LC3	MBL International	Cat# PM036, RRID: AB 2274121
Mouse monoclonal anti-LC3 (clone 5F10)	Nanotools	Cat# 0231-100/LC3-5F10, RRID: AB_2722733
Mouse monoclonal anti-Myc (clone 9E10)	OriGene	Cat# TA150121, RRID:AB_2622266
Mouse monoclonal anti-PDI (clone C-2)	Santa Cruz Biotechnology	Cat# sc-74551, RRID: AB_2156462
Rabbit polyclonal antibody anti-lipin1	Cell Signaling Technology	Cat# 5195S, RRID: AB_10694491
Mouse monoclonal 8OHDG (clone 15A3)	Santa Cruz Biotechnology	Cat# sc-66036, RRID: AB_832272
Mouse monoclonal anti-PI3P	Echelon Biosciences	Cat# Z-P003, RRID: AB_427221
Mouse monoclonal anti-PI34P2	Echelon Biosciences	Cat# Z-P034B, RRID: AB_427223
Mouse monoclonal anti-PI35P2	Echelon Biosciences	Cat# Z-P035, RRID: AB_427224
Mouse monoclonal anti- SQSTM1 (Clone 2C11)	Abnova Corporation	Cat# H00008878-M01, RRID: AB_437085
Rabbit monoclonal anti-Rab7 (clone D95F2)	Cell Signaling	Cat# 9367S, RRID: AB_1904103)
Mouse monoclonal anti-Rab7 (clone Rab7-117)	Abcam	Cat# ab50533, RRID: AB_882241
Rabbit polyclonal anti-STX6	Proteintech Group	Cat# 10841-1-AP, RRID: AB_2196506
Mouse monoclonal anti-TOMM20 (clone 29)	Santa Cruz Biotechnology	Cat# sc-136211, RRID: AB_2207538
Mouse monoclonal anti-CD14 conjugated to microbeads	Miltenyi Biotec	Cat# 130-050-201, RRID: AB_2665482
Mouse monoclonal anti-CD56 conjugated to microbeads (clone AF12-7H3)	Miltenyi Biotec	Cat# 130-050-401, RRID: AB_244333
Mouse monoclonal anti-CD56 Allophycocyanin Conjugated (clone B159)	BD Biosciences	Cat# 555518, RRID: AB_398601
Mouse monoclonal anti-CD83 Phycoerythrin Conjugated (clone HB15e)	BD Biosciences	Cat# 556855, RRID: AB_396526
Goat Anti-Mouse polyclonal IgG, Human ads-HRP antibody	Southern Biotech	Cat# 1030-05, RRID: AB_2619742
Goat Anti-Mouse IgG (H+L) secondary antibody Alexa Fluor 488	Thermo Fisher Scientific	Cat# A32723, RRID: AB_2633275
Goat anti-Rabbit IgG (H+L) secondary Antibody, Alexa Fluor 488	Thermo Fisher Scientific	Cat# A-11008, RRID: AB_143165
Donkey anti-Goat IgG (H+L) secondary Antibody, Alexa Fluor 488	Thermo Fisher Scientific	Cat# A-11055, RRID: AB_2534102
Goat anti-Mouse IgG (H+L) secondary Antibody, Alexa Fluor 594	Thermo Fisher Scientific	Cat# A-11032, RRID: AB_2534091
Goat anti-Rabbit IgG (H+L) secondary Antibody, Alexa Fluor 594	Thermo Fisher Scientific	Cat# A-11037, RRID: AB_2534095
Goat anti-Mouse IgG (H+L secondary Antibody, Alexa Fluor Plus 647	Thermo Fisher Scientific	Cat# A32728, RRID: AB_2633277
Goat anti-Rabbit IgG (H+L) secondary Antibody, Alexa Fluor Plus 647	Thermo Fisher Scientific	Cat# A32733, RRID: AB_2633282)
Bacterial and virus strains
LPIN1 - Human shRNA lentiviral particle	OriGene	Cat# TL303494V
Biological samples
Human primary myoblasts from healthy individuals and patients	Department of biology and molecular genetics, Cochin Hospital, Paris, France	N/A
Human immortalized myoblasts from healthy donor	MYOBANK-AFM (Myology institute BB-0033), Paris, France	N/A
Blood samples from healthy individuals and patients	Department of Inherited Metabolic Diseases, Necker Hospital, Paris, France	N/A
Chemicals, peptides, and recombinant proteins
Recombinant human IL-4	Miltenyi Biotec	Cat# 130-095-915
Recombinant human GM-CSF	Miltenyi Biotec	Cat# 130-093-372
Animal-Free Recombinant Human EGF	Peprotec	Cat# AF-100-15
Pam3CSK4	Invivogen	Cat# tlr-pms
Poly(I:C) (HMW)	Invivogen	Cat# tlr-pic
LPS-B5 (LPS from E. coli 055:B5)	Invivogen	Cat# tlr-b5lps
FLA-BS, standard flagellin from B. subtilis	Invivogen	Cat# tlr-bsfla
Imiquimod (R837)	Invivogen	Cat# tlr-imqs
CpG-A (ODN2216)	Invivogen	Cat# tlr-2216
TLR9 antagonist ODN TTAGGG (A151)	Invivogen	Cat# tlr-ttag151
Calcium indicator Fluo-4 AM	Thermo Fisher Scientific	Cat# F14201
DAPI (4’,6-diamidino-2-phenylindole)	Thermo Fisher Scientific	Cat# D1306
DQ-Ovalbumin	Thermo Fisher Scientific	Cat# D12053
Dulbecco’s Modified Eagle’s Medium - high glucose	Sigma-Aldrich	Cat# D6546
Dulbecco’s Modified Eagle’s Medium - low glucose	Sigma-Aldrich	Cat# D5546
Earle’s Balanced Salt Solution, EBSS, calcium, magnesium, phenol red	Thermo Fisher Scientific	Cat# 24010043
Fetal Bovine Serum	Thermo Fisher Scientific	Cat# 16000044
Fluoromount-G	Thermo Fisher Scientific	Cat# 00-4958-02
Ham’s F-10 Nutrient Mix	Thermo Fisher Scientific	Cat# 11550043
Image-iT TMRM Reagent (mitochondrial membrane potential indicator)	Thermo Fisher Scientific	Cat# I34361
LysoTracker Deep Red	Thermo Fisher Scientific	Cat# L12492
MitoSpy Orange CMTMRos	Biolegend	Cat# 424804
MitoTracker Green FM	Thermo Fisher Scientific	Cat# M22425
Penicillin-Streptomycin (10,000 U/mL)	Thermo Fisher Scientific	Cat# 15140122
Phosphate-Buffered Saline, PBS, pH 7.4	Thermo Fisher Scientific	Cat# 10010023
Puromycin	Thermo Fisher Scientific	Cat# A1113802
Recombinant Cholera Toxin subunit B Alexa Fluor 594	Thermo Fisher Scientific	Cat# C34777
Bovine Serum Albumin	Sigma-Aldrich	Cat# A2153; CAS Number: 9048-46-8
Carbonyl cyanide 3-chlorophenylhydrazone, CCCP	Sigma-Aldrich	Cat# C2759; CAS Number: 555-60-2
Dexamethasone	Sigma-Aldrich	Cat# D4902; CAS Number: 50-02-2
Etidium bromide	Sigma-Aldrich	Cat# E7637; CAS Number: 1239-45-8
Hexadimethrine bromide, Polybrene	Sigma-Aldrich	Cat# H9268; CAS Number: 28728-55-4
Paraformaldehyde	Sigma-Aldrich	Cat# P6148; CAS Number 30525-89-4
RIPA Buffer	Sigma-Aldrich	Cat# R0278
Saponin	Sigma-Aldrich	Cat# 47036; CAS Number: 8047-15-2
Sodium pyruvate	Sigma-Aldrich	Cat# P5280; CAS Number: 113-24-6
Staurosporin	Sigma-Aldrich	Cat# S4400; CAS Number: 62996-74-1
Uridine	Sigma-Aldrich	Cat# U3003; CAS Number 58-96-8
Propidium Iodide Solution	Biolegend	Cat# 421301
7-AAD Viability Staining Solution	Biolegend	Cat# 420404
Critical commercial assays
Caspase 3/7 assay	Thermo Fisher Scientific	Cat# R37111
Click-iT® EdU Alexa Fluor® 647 Flow Cytometry Assay Kit, 50 assays	Thermo Fisher Scientific	Cat# C10424
Human Inflammatory Cytokine Kit	BD Bioscience	Cat# 551811
ELISA MAX Deluxe Set Human IL-6	Biolegend	Cat# 430504
Cell ROS flow cytometry assay kit	Thermo Fisher Scientific	Cat# C100491
Seahorse XFp cell mito stress test kit	Seahorse Bioscience	Cat#103010-10
JetPrime Transfection assay	Polyplus transfection	Cat# 114-07
Cell Fractionation Kit standard	Abcam	Cat# ab109719
Oligonucleotides
12S-forward 5′-TAGCCCTAAACCTCAACAGT-3′; reverse 5′-TGCGCTTACTTTGTAGCCTTCAT-3′	Eurofins Genomics	N/A
BACTIN-forward 5′-CAGCGGAACCGCTCATTGCCAATGG-3′; reverse 5′-TCACCCACACTGTGCCCATCTACGA-3′	Eurofins Genomics	N/A
DLOOP-forward 5′-ACCTGTGATCCATCGTGATGT-3′; reverse 5′-GCCCATAACACTTGGGGGTA-3′	Eurofins Genomics	N/A
GAPDH-Hs03929097_g1	Thermo Fisher Scientific	N/A
IFI27-Hs01086370_m1	Thermo Fisher Scientific	N/A
IFI44-Hs00199115_ m1	Thermo Fisher Scientific	N/A
IFIT1-Hs01675197_m1	Thermo Fisher Scientific	N/A
IFNA-forward 5′-GAAGAATCTCTCCTTTCTCCTGCC-3′; reverse 5′-ATGGAGGACAGAGATGGCTTG-3′	Eurofins Genomics	N/A
IFNB-forward 5′-CAGCAATTTTCAGTGTCAGAAGC-3′; reverse 5′-TCATCCTGTCCTTGAGGCAGT-3′	Eurofins Genomics	N/A
ISG15- Hs01921425_s1	Thermo Fisher Scientific	N/A
LPIN1-forward 5′-CCTTCTATGCTGCTTTTGGGAACC-3′; reverse 5′-CTGATCGACCACTTCGCAGAGC-3′	Eurofins Genomics	N/A
RSAD2-Hs00369813_m1	Thermo Fisher Scientific	N/A
SIGLEC1-Hs00988063_m1	Thermo Fisher Scientific	N/A
Recombinant DNA
pGFP-2XFYVE	Ketel et al., 201666	N/A
pRFP-GFP-LC3	Kimura et al., 200767	N/A
pRFP-RILP	Jongsma et al., 202068	N/A
pRFP-ARMUS	Carroll et al., 201331	N/A
pTLR9-HA	Invivogen	Cat# puno1ha-htlr9a
LPIN1 (Myc-DDK-tagged)-Human lipin1 (LPIN1) ORF clone (NM_145693)	OriGene	Cat# RC207138
Software and algorithms
FIJI v2.00	https://fiji.sc	RRID: SCR_002285
FlowJo v9.3.0 (Mac)	https://www.flowjo.com/solutions/flowjo	RRID: SCR_008520
Image Reader LAS-1000 v2.3	http://www.imb.sinica.edu.tw/core/publicfacilities/pdf/LAS-1000plus_om_e_ver2.pdf	RRID: SCR_014585
GraphPad Prism v6.0	https://www.graphpad.com/	RRID: SCR_002798
Icy v1.9.5.1	http://icy.bioimageanalysis.org/	RRID: SCR_010587
Imaris v8.4.2	https://imaris.oxinst.com/packages	RRID: SCR_007370
Soft Flow v3.00	http://softflow.com/	RRID: SCR_002599
System Detector System (SDS) v2.3	https://www.thermofisher.com/order/catalog/product/4444202	RRID: SCR_015806
Other
3 Well Chamber, removable microscopy glass slide, sterilized	Ibidi	Cat# 80381