REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-mouse PECAM-1 (clone 390)	Thermo Fisher Scientific	Cat#16-0311-85; RRID: AB_468933
Blocking anti-mouse PECAM-1 (clone Mec12.3)	Biolegend	Cat#102502; RRID: AB_312909
Anti-mouse IgG2a, κ isotype control (clone RTK2758)	Biolegend	Cat#400502; RRID: AB_2736919
Anti-mouse CD102 (clone 3C4)	Biolegend	Cat#105602; RRID: AB_313195
Anti-mouse CD45 (clone 30-F11)	Biolegend	Cat#103102; RRID: AB_312967
Anti-mouse ICAM-1 (clone YN1)	Biolegend	Cat#116102; RRID: AB_313693
Anti-mouse Ly6G (clone 18A)	Biolegend	Cat#127602; RRID: AB_1089180
Anti-mouse MRP14 (clone 2B10)	Gift from Dr N. Hogg (The Francis Crick Institute, UK) (Hobbs et al., 2003)	N/A
Anti-mouse CD144 (clone BV14)	Thermo Fisher Scientific	Cat#14-1442-82; RRID: AB_891369
Polyclonal anti-mouse GFP	Abcam	Cat#ab6662; RRID: AB_305635
Anti-mouse JAM-C (clone 114.2)	Gift from Dr M. Aurrand-Lions (INSERM, France) (Lamagna et al., 2005)	N/A
Polyclonal anti-mouse LC3	Thermo Fisher Scientific	Cat#PA1-16930; RRID: AB_2281384
Anti-mouse WIPI2	Gift from Dr S. Tooze (The Francis Crick Institute, UK) (Dooley et al., 2014)	N/A
Anti-mouse F4/80 (clone BM8)	Biolegend	Cat#123102; RRID: AB_893506
Anti-mouse Ly6C (clone HK1.4)	Biolegend	Cat#128002; RRID: AB_1134214
Anti-mouse SiglecF (clone S17007L)	Biolegend	Cat#155502; RRID: AB_2810420
Anti-mouse CD11b (clone M1/70)	Biolegend	Cat#1012020; RRID: AB_312785
Anti-mouse neutrophil (clone 7/4)	Abcam	Cat#ab53453; RRID: AB_881408
Anti-mouse CD16/CD32 (CLONE 2.4G2)	BDBiosciences	Cat#553141; RRID: AB_394656
Anti-human PECAM-1 (clone WM59)	Thermo Fisher Scientific	Cat#14-0319-82; RRID: AB_467204
Blocking anti-human PECAM-1	Generated in the lab of Dr W. A. Muller (Feinberg School of Medicine, Chicago, IL, USA) (Mamdouh et al., 2003)	N/A
Polyclonal anti-human LC3	Cell Signaling Technology	Cat#2775; RRID: AB_915950
Anti-human Atg5 (clone D5F5U)	Cell Signaling Technology	Cat#12994; RRID: AB_2630393
Anti-human β-Actin (clone AC-15)	Sigma-Aldrich	Cat#A5441; RRID: AB_476744
Anti-human VE-Cadherin (F-8)	Santa Cruz Biotechnology	Cat#sc-9989 RRID: AB_2077957
Chemicals, peptides, and recombinant proteins
LPS	Sigma-Aldrich	Cat#A9543
Peptidoglican G from Staphylococcus aureus	Sigma-Aldrich	Cat#77410-10mg
Zymosan A	Sigma-Aldrich	Cat#Z4250
Muramydipeptide (MDP, L-D isomer, active)	InvivoGen	Cat#tlrl-mdp
IL1β	R&D	Cat#201-LB-010
M199 medium	GIBCO-BRL	Cat#11150059
DMEM	GIBCO-BRL	Cat#21068028
Fetal Bovine Serum (FBS)	Sigma-Aldrich	Cat#F9665
Heparin	Sigma-Aldrich	Cat#H3393
Endothelial Cell Growth Supplement (ECGS)	Sigma-Aldrich	Cat#E2759
Fetal Calf Serum (FCS)	Thermo Fisher Scientific	Cat# 26010074
Paraformaldehyde (PFA)	Sigma-Aldrich	Cat#158127
EZ-Link Sulfo-NHS-Biotin	Thermo Fisher Scientific	Cat#21217
Pierce NeutrAvidin Agarose	Thermo Fisher Scientific	Cat#29201
Triton X-100	Sigma-Aldrich	Cat#9002-93-1
Bovine Serum Albumin (BSA)	Sigma-Aldrich	Cat#A9543
Tyrode’s solution	Sigma-Aldrich	Cat#T1788
Bafilomycin A1	AlfaAesar (Avocado Research Chemicals)	Cat# J67193
Pig Skin Gelatin	Sigma-Aldrich	Cat#9000-70-8
EDTA	Sigma-Aldrich	Cat#EDS
Halt Protease and phosphatase inhibitors	Thermo Fisher Scientific	Cat#78440
3,3′,5,5′-tetramethylbenzidine	Invitrogen	Cat#N301
2X Laemmli Sample Buffer	Bio-Rad	Cat#1610737
Type I Collagenase	GIBCO	Cat#10114532
Tat-Beclin 1 D11 Autophagy Inducing Peptide - Retroinverso form	Bio-techne	Cat#NBP2-49888
Tat-Beclin 1 L11S Peptide - Scrambled Control	Bio-techne	Cat#NBP2-49887
Propidium Iodide	Sigma-Aldrich	Cat#P4864
Critical commercial assays
Alexa Fluor 488 Antibody Labeling Kit	Thermo Fisher Scientific	Cat#A20181
Alexa Fluor 555 Antibody Labeling Kit	Thermo Fisher Scientific	Cat#A20187
Alexa Fluor 647 Antibody Labeling Kit	Thermo Fisher Scientific	Cat#A20186
DyLight 405 antibody Labeling Kit	Thermo Fisher Scientific	Cat#53021
Yellow Zombie Fixable Viability Kit	Biolegend	Cat#423103
RNeasy Micro Kit	QIAGEN	Cat#74004
iScript cDNA Synthesis Kit	Bio-Rad	Cat#4106228
iQ SYBR Green Supermix	Bio-Rad	Cat#1708880
Experimental models: Cell lines
Human umbilical vein endothelial cells (HUVECs)	PromoCell	Cat#C-14008
Experimental models: Organisms/strains
Mouse, GFP-LC3TG/+	Generated in the lab of Prof. N. Mizushima (RIKEN BRC through the National Bio-Resource Project of the MEXT, Japan) (Mizushima et al., 2004)	N/A
Mouse, Cdh5-Cre; Atg5fl/fl	Generated in the lab of Dr C.Boulanger (INSERM, France) (Vion et al., 2017)	N/A
Mouse, Rosa26CAG-loxP-STOP-loxP-tdTomato/ CAG-loxP-STOP-loxP-tdTomato	The Jackson Laboratory	JAX 007905
Mouse,Cdh5-CreERT2 (Cdh5(BAC)-CreERT2; Rosa26tdTomato/tdTomato)	Generated in the lab of Prof. Y. Kubota (Keio University School of Medicine, Japan) (Okabe et al., 2014)	N/A
Mouse, Lyz2-EGFP-ki	Gift from Dr M. Sperandio (Ludwig Maximilians University of Munich, Germany) (Faust et al., 2000)	N/A
Mouse, Atg16l1E230/E230	Generated in the lab of Prof T. Wileman (Quadram Institute, UK) (Rai et al., 2019)	N/A
Oligonucleotides
Atg5 ON-TARGETplus siRNA SMARTpooL 5′-GGCAUU AUCCAAUUGGUUU-3′ 5′-GCAGAACCAUACUAUUU GC-3′, 5′-UGACAGAUUUGACCAGUUU-3′ 5′-ACAAA GAUGUGCUUCGAGA-3′	Dharmacon Inc; Horizon Discovery	Cat# L-004374-00-0005
Luciferase ON-TARGETplus siRNA 5′-CGUACGC GGAAUACUUCGA-3′	Dharmacon Inc; Horizon Discovery	Cat#D-002050-01-20
Real-time PCR primer: Gapdh Forward 5′- TCGTGG ATCTGACGTGCCGCCTG-3′	This paper	N/A
Real-time PCR primer: Gapdh Reverse 5′- CACCAC CCTGTTGCTGTAGCCGTA-3′	This paper	N/A
Real-time PCR primer: Pecam-1 Forward 5′- AGGTGG AACAAGCACAGATG-3′	This paper	N/A
Real-time PCR primer: Pecam-1 Reverse 5′- TTGCTG ATGGCACCATCTTC-3′	This paper	N/A
Real-time PCR primer: Cdh5 Forward 5′-CAGCCC AAAGTGTGTGAGAA-3′	This paper	N/A
Real-time PCR primer: Cdh5 Reverse 5′- GAACTTC ACGTTTCGTGGTG-3′	This paper	N/A
Real-time PCR primer: Atg5 Forward 5′- GCAGTAG GCTTGAGTGAACT-3′	This paper	N/A
Real-time PCR primer: Atg5 Reverse 5′- CTAGGG CATTGTAGGCTTGA-3′	This paper	N/A
Real-time PCR primer: TdTomato Forward 5′- CAAGC TGGACCATCACCTCC-3′	This paper	N/A
Real-time PCR primer: TdTomato Reverse 5′- TGCCC GTACAGGAACAGGTG-3′	This paper	N/A
Real-time PCR primer: E-selectin Forward 5′- AGCTA CCCATGGAACACGAC −3′	This paper	N/A
Real-time PCR primer: E-selectin Reverse 5′- ACGCAA GTTCTCCAGCTGTT-3′	This paper	N/A
Real-time PCR primer: Icam-1 Forward 5′- GTGCAA TCATGGTTCAGTGC −3′	This paper	N/A
Real-time PCR primer: Icam-1 Reverse 5′- GTGTGG TGTTGTGAGCCTAT −3′	This paper	N/A
Real-time PCR primer: Icam-2 Forward 5′- ATCAAC TGCAGCACCAACTG −3′	This paper	N/A
Real-time PCR primer: Icam-2 Reverse 5′- ACTTGA GCTGGAGGCTGGTA-3′	This paper	N/A
Real-time PCR primer: Vcam-1 Forward 5′- TCTTGG GAGCCTCAACGGTA −3′	This paper	N/A
Real-time PCR primer: Vcam-1 Reverse 5′- CAAGTG AGGGCCATGGAGTC −3′	This paper	N/A
Real-time PCR primer: Cxcl1 Forward 5′- CCGAAG TCATAGCCACACTCAA −3′	This paper	N/A
Real-time PCR primer: Cxcl1 Reverse 5′- GCAGTC TGTCTTCTTTCTCCGTTA −3′	This paper	N/A
Real-time PCR primer: TnfRI Forward 5′- CAGTCT GCAGGGAGTGTGAA-3′	This paper	N/A
Real-time PCR primer: TnfRI Reverse 5′- CACGCA CTGGAAGTGTGTCT −3′	This paper	N/A
Real-time PCR primer: TnfRII Forward 5′- TACCAA GGGTGGCATCTCTC-3′	This paper	N/A
Real-time PCR primer: TnfRII Reverse 5′- TCCTGG GATTTCTCATCAGG −3′	This paper	N/A
Recombinant DNA
pEGFP-LC3 plasmid	Gift from Dr T Yoshimori (Osaka University, Japan) (Kabeya et al., 2000)	N/A
Software and algorithms
FlowJo v10.2	Tree Star	https://www.flowjo.com/
ImageJ v2.0	NIH	https://imagej.nih.gov/ij/
Imaris v9.2	Bitplane	https://imaris.oxinst.com/
Prism v8.4	GraphPad	https://www.graphpad.com/scientific-software/prism/
IMOD	University of Colorado	https://bio3d.colorado.edu/imod/
Other
123cound eBeads counting beads	Thermo Fisher Scientific	Cat#01-1234-42
Staurosporine	Abcam	Cat#120056