REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
mouse anti-β-actin	Cell Signaling Technology	Cat#3700; RRID: AB_2242334
rabbit anti-LC3	Cell Signaling Technology	Cat#3868; RRID: AB_2137707
rabbit anti-NPC1	Abcam	Cat#ab134113; RRID:AB_2734695
rat anti-LAMP1	Abcam	Cat#ab25245; RRID:AB_449893
HRP goat anti-rabbit IgG	Abclone	AS014
HRP goat anti-mouse IgG	Abclone	AS003
Alexa Fluor 594-labeled goat anti-rat IgG	Antgene	ANT035
Alexa Fluor 488-labeled goat anti-rabbit IgG	Antgene	ANT024
Bacterial and virus strains
M. tuberculosis H37Rv	ATCC	ATCC 27294
BCG Tokyo strain	ATCC	ATCC 35737
M. tuberculosis H37RvΔphoP	This paper	N/A
M. tuberculosis H37RvΔ0818	This paper	N/A
M. tuberculosis H37RvΔ3220c	This paper	N/A
M. tuberculosis H37RvΔ3143	This paper	N/A
M. tuberculosis H37RvΔ1759c	This paper	N/A
Chemicals, peptides, and recombinant proteins
7H11 agar media	Difco	212203
7H9 agar media	Difco	271310
Baf-A1	Selleck	S1413
DAPI	Beyotime	C1005
OADC	Difco	212352
Glycerol	Sigma Aldrich	G5516
Tween 80	Sigma Aldrich	P8074
RPMI-1640	Gibco	31800022
DMEM	Gibco	12800017
HiPerFect Transfection Reagent	Qiagen	301705
PMA	Sigma Aldrich	79346
TRIzol	Life Technologies	15596026
Lipofectamine™ 2000 Transfection Reagent	Invitrogen	11668019
RIPA lysis buffer	Beyotime	P0013B
Critical commercial assays
RNeasy minikit	Qiagen	217004
miRcute Plus miRNA First-Strand cDNA Synthesis Kit	Tiangen	KR21
miRNA using miRcute Plus miRNA qPCR Detection Kit (SYBR Green)	Tiangen	FP411
HiScript II Q Select RT SuperMix for qPCR(+gDNA wiper)	Vazyme	R233
AceQ qPCR SYBR Green Master Mix	Vazyme	Q111
Dual-Luciferase® Reporter (DLR™) Assay System	PROMOGA	E1910
Deposited data
Raw and analyzed data	This paper	GSE184660
Experimental models: Cell lines
THP-1	ATCC	TIB-202
293T	ATCC	CRL-3216
Experimental models: Organisms/strains
MiR-25−/− mice	BIOCYTOGEN	N/A
C57BL/6 mice	Charles River Labs	N/A
Oligonucleotides
MiR-25 mimic CAUUGCACUUGUCUCGGUCUCUGA	GenePharma	B02003
control mimic UUCUCCGAACGUGUCACGUTT	GenePharma	B04002
miR-25 inhibitor UCAGACCGAGACAAGUGCAAUG	GenePharma	B03001
inhibitor control CAGUACUUUUGUGUAGUACAA	GenePharma	B04001
NPC1 siRNA GAGGUACAAUUGCGAAUAUTT	GenePharma	A01001
NFKBIZ siRNA GCCCGAUUCGUUGUCUGAUTT	GenePharma	A01001
control siRNA UUCUCCGAACGUGUCACGUTT	GenePharma	B04002
Primers for qPCR see Table S1	This paper	N/A
Recombinant DNA
pmirGLO	PROMOGA	E1330
psPAX2	Addgene	12260
pMD2.G	Addgene	12259
pLVX-shRNA1	HedgehogBio	HH-shRNA-044
PLVX-puro	HedgehogBio	HH-LV-048
Software and algorithms
TargetScan	http://www.targetscan.org/	N/A
miRDB	http://www.mirdb.org/miRDB/	N/A
miRanda	http://www.microrna.org/microrna/home.do	N/A
GraphPad Prism 8	https://www.scienceplus.com/nl/prism-commercieel.html	N/A
Image Lab Software	https://www.bio-rad.com/fr-fr/product/image-lab-software?ID=KRE6P5E8Z	N/A
ZEN	https://www.zeiss.com/microscopy/int/products/microscope-software/zen-lite.html	N/A
UCSC	http://genome.ucsc.edu/	N/A