|
Antibodies
|
| Anti-mouse MAC3 (clone M3/84) |
BD Biosciences |
Ref#: 550292 |
| Anti-mouse ATG5 |
Novus Biologicals |
Ref#: NBP2-54702 |
| Biotinylated goat-anti-rat IgG (H+L) |
VectorLabs |
Ref#: BA-9401-.5 |
| HRP-conjugated goat ant-mouse C3 |
MP BioMedicals |
Ref#: 0855557 |
| Donkey anti-rabbit IgG (H+L) AlexaFluor 647 |
Thermo Fisher Scientific |
Ref#: A-31573 |
| Anti-mouse MAC1/CD11b (Clone M1/70) |
R&D Systems |
Ref#: MLDP5 |
| Anti-mouse CD16/32 (clone 90) |
Thermo Fisher Scientific |
Ref#: 14-0161-85 |
| Anti-mouse CD11 b APC (clone M1/70) |
Thermo Fisher Scientific |
Ref#: 17-0112-82 |
| Anti-mouse Ly6C FITC (clone HK1.4) |
BioLegend |
Ref#: 128006 |
| Anti-mouse Ly6G PE (clone 1A8) |
BioLegend |
Ref#: 127608 |
| Anti-mouse F4/80 PerCP-Cy5.5 (clone BM8) |
BioLegend |
Ref#: 123128 |
| Anti-mouse CD45R (B220) PerCP-Cy5.5 (clone RA3–6B2) |
Thermo Fisher Scientific |
Ref#: 45-0452-82 |
| Anti-mouse CD43 PE (clone S7) |
BD Biosciences |
Ref#: 553271 |
| Anti-mouse CD23 FITC (clone B3B4) |
BD Biosciences |
Ref#: 11-0232-82 |
| Biotinylated anti-mouse CD21/35 (clone 7E9) |
BioLegend |
Ref#: 123406 |
| Anti-mouse CD3e PE (clone 145–2C11) |
Thermo Fisher Scientific |
Ref#: 12-0031-82 |
| Anti-mouse CD8a APC (clone 53–6.7) |
Thermo Fisher Scientific |
Ref#: 17-0081-82 |
| Anti-mouse C5aR1 PE-Cy7 (clone 20/70) |
BioLegend |
Ref#: 135809 |
| Anti-mouse C5aR2 AlexaFluor 700 (clone 468705) |
R&D Systems |
Ref#: IC4729N |
| Anti-mouse C3aR (clone 14D4) |
Hycult Biotech |
Ref#: HM1123 |
| Anti-mouse C3/C3b/iC3b/C3c (clone 3/26) |
Hycult Biotech |
Ref#: HM1078 |
| Anti-mouse C3a (clone mAb 3/11) |
Hycult Biotech |
Ref#: HM1072 |
| Anti-mouse CD16/32 APC (clone 93) |
Thermo Fisher Scientific |
Ref#: 17-0161-82 |
| Anti-mouse TIM4 PE (clone 54, RM14– 54) |
Thermo Fisher Scientific |
Ref#: 12-5866-80 |
| Anti-mouse VSIG4 PE-Cy7 (clone NLA14) |
Thermo Fisher Scientific |
Ref#: 25-5752-80 |
| Anti-mouse MHCII AlexaFluor 700 (clone M5/114.15.2) |
Thermo Fisher Scientific |
Ref#: 56-5231-82 |
| FITC-labelled hematopoietic lineage cocktail |
Thermo Fisher Scientific |
Ref#: 22-7770-72 |
| Anti-mouse C-kit (CD117) APC-eFluor780 (clone 2B8) |
Thermo Fisher Scientific |
Ref#: 47-1171-80 |
| Anti-mouse Sca1 (Ly6A/E) PE-Cy7 (clone J43) |
Thermo Fisher Scientific |
Ref#: 25-5981-81 |
| Anti-mouse CD34 eFluor 450 (clone RAM34) |
Thermo Fisher Scientific |
Ref#: 48-0341-80 |
| Anti-mouse CD135 (Flt3) PerCP-eFlour 710 (clone A2F10) |
Thermo Fisher Scientific |
Ref#: 46-1351-80 |
| Anti-mouse IL7R (CD127) PE (clone A7R34) |
Thermo Fisher Scientific |
Ref#: 12-1271-82 |
| Anti-human CFH (clone OX-24) |
Cedarlane Laboratories |
Ref#: AM20110PU-N |
| Anti-mouse IgG1 kappa APC (clone P3.6.2.8.1) |
Thermo Fisher Scientific |
Ref#: 17-4714-82 |
| Monoclonal anti-mouse CFH |
R&D Systems |
Ref#: MAB4999 |
| Polyclonal anti-mouse CFH |
R&D Systemnc |
Ref#: AF4999 |
| Anti-human C3 FITC |
MP BioMedicals |
Ref#: 0855500 |
| Anti-mouse LC3 |
GeneTex |
Ref#: GTX127375 |
|
Chemicals, peptides, and recombinant proteins
|
| Thioglycollate |
Thermo Fisher Scientific |
Ref#: CM0173B |
| Zymosan |
Sigma Aldrich |
Ref#: Z4250 |
| Bafilomycin A1 |
Eubio |
Ref#: BV1-0252-C100 |
| 4’,6-Diamidino-2-Phenylindole (DAPI) |
Sigma Aldrich |
Ref#: D1306 |
| Cell Tracker Green CMFDA |
Thermo Fisher Scientific |
Ref#: C7025 |
| Citrate buffer ph6.0, 10x |
Sigma Aldrich |
Ref#: C9999 |
| Recombinant mouse CFH |
R&D Systems |
Ref#: 4999-FH |
| pHrodo Red, succinimidyl ester |
Invitrogen |
Ref#: P36600
|
| Purified mouse complement C3 |
Ĉomplement Technology Înc |
Ref#: M113 |
|
Critical commercial assays
|
| In Situ Cell Death Detection Kit TMR-Red |
Roche Diagnostics |
Ref#: 12156792910 |
| Alexa Fluor 488 Antibody Labeling Kit |
Thermo Fisher Scientific |
Ref#: A20181 |
| Foxp3/ Transcription Factor Staining Buffer set |
Thermo Fisher Scientific |
Ref#: 00-5523-00 |
| Annexin V and 7-AAD viability solution kit |
BioLegend |
Ref#: 640934 |
| Mouse C3 ELISA kit |
Abcam |
Ref#: ab263884 |
| Mouse C5 ELISA kit |
Abcam |
Ref#: ab264609 |
| Mouse C3a ELISA kit |
MyBioSource |
Ref#: MBS2701721 |
| Pierce BCA Protein Assay Kit |
Thermo Fisher Scientific |
Ref#: 23225 |
| IL-1 beta Mouse Uncoated ELISA Kit |
Thermo Fisher Scientific |
Ref#: 88-7013-88 |
| High Capacity cDNA Reverse Transcription Kit |
Thermo Fisher Scientific |
Ref#: 4368814 |
| Kapa SYBR Fast Bio-Rad iCycler with ROX dye |
Roche Diagnostics |
Ref#: KK4602 |
| RNeasy mini kit |
Qiagen |
Ref#:74004 |
| TruSeq Stranded mRNA LT sample preparation kit |
Illumina |
https://illumina.com
|
| Takara’s SMART-Seq v4 Ultra Low Input RNA Kit |
Takara |
Ref#:634894 |
|
Deposited data
|
| scRnAseq and bulk RNAseq datasets |
This paper |
?? |
|
|
|
|
Experimental models: Cell lines
|
| THP-1 human monocytic cell line |
ATCC |
TIB-202 |
| RAW 264.7 murine macrophage cell line |
ATCC |
TIB-71 |
|
|
|
|
Experimental models: Organisms/strains
|
| Mouse: C57BL/6J |
Jackson Laboratory |
Strain code: 000664 |
| Mouse: C57BL/6J Cfh-/-
|
In-house |
Pickering et al. 2002
|
| Mouse: B6.12957-Ldlrtm1Her/J |
Jackson Laboratory |
Strain code: 002207 |
| Mouse: B6.12954-C3tm1Crr/J |
Jackson Laboratory |
Strain code: 029661 |
| Mouse: C57BL/6J Cfh-/-C3-/-
|
In-house |
n.a. |
| Mouse: C57BL/6J Cfh-/-Ldlr-/-
|
In-house |
n.a. |
| Mouse: C57BL/6J C3-/-Ldlr-/-
|
In-house |
n.a. |
| Mouse: C57BL/6J Cfh-/-C3-/-Ldlr-/-
|
In-house |
n.a. |
| Mouse: C57BL/6Tg(UBC-GFP)30Scha/J |
Jackson Laboratory |
Strain code: 004353 |
| Mouse:C57BL/6J Cfh-/-UBC-GFP |
In-house |
n.a. |
| Mouse: B6.SJL-Ptprca Pepcb/BoyJ |
Jackson Laboratory |
Strain code: 002014 |
|
|
Oligonucleotides
|
| Primers, see Table S2
|
|
|
|
|
|
|
Software and algorithms
|
| FlowJo (version 10) |
BD Biosciences |
https://www.flowjo.com
|
| GraphPad Prism (version 8.0) |
Dotmatics |
https://www.graphpad.com
|
| CellRanger (v2.1.0.) |
10x Genomics |
https://10xgenomics.com/
|
| Seurat (v3) |
10x Genomics |
https://satijalab.org/seurat
|
| Harmony |
Broad Institute |
Korsunksy et al., 2019) |
| AxioVision |
Carl Zeiss AG |
https://www.zeiss.com
|
| Adobe Photoshop CS5 |
Adobe Inc. |
https://www.adobe.com
|
| Star 2.5.0a |
Gensoft Pasteur |
https://gensoft.pasteur.fr
|
| Image Lab 4.1 |
Bio-Rad Laboratories |
https://www.bio-rad.com
|
| Loupe Cell Browser 3.1.1 |
10x Genomics |
https://www.10xgenomics.com
|
| ACT-1 v2.63 |
Nikon |
https://www.nikon.com
|
| RTA software |
Illumina |
https://www.illumina.com
|
| TopHat2 v2.1.1 |
CCB at Johns Hopkins |
https://ccb.jhu.edu
|
| Tuxedo Suite |
Illumina |
https://www.illumina.com
|
| Bowtie2 |
Langmead and Salzberg8
|
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
|
| ACT-1 v2.63 |
Nikon |
https://www.nikon.com
|
| Image J |
NIH |
https://imagej.nih.gov
|
| R (version 4.0) |
The R Foundation |
https://www.r-project.org
|
|
Diets
|
| Rodent chow |
LASvendi |
https://www.lasvendi.com
|
| Western-type diet |
Ssniff Spezialdiäten |
https://www.ssniff.com
|
|
|
|
