|
Antibodies
|
| Anti-F4/80 – FITC |
BioLegend |
(BioLegend Cat# 123108, RRID:AB_893502) |
| Anti-MGL2(CD310b) – PE-Cy7 |
BioLegend |
(BioLegend Cat# 146807, RRID:AB_2563389) |
| Anti-MRC1(CD206) – APC |
BioLegend |
(BioLegend Cat# 141708, RRID:AB_10900231) |
| Anti-RETNLA(RELMa) - Unconjugated |
PeproTech |
(PeproTech Cat# 500-P214-50ug, RRID:AB_1268843) |
| Anti-CD16/CD32 |
eBioscience |
RRID:AB_467133 |
| Anti-F4/80 – APC |
BioLegend |
(BioLegend Cat# 123108, RRID:AB_ 893493) |
| Anti-Cd11c – PE |
BD Bioscience |
(BD Biosciences Cat# 553802, RRID:AB_395061) |
| RNAPII-pS2 |
Abcam |
Abcam Cat# ab5095, RRID:AB_304749 |
|
Biological samples
|
|
|
| Mouse bone marrow samples |
Stanford University |
N/A |
| Mouse bronchoalveolar lavage samples |
University of Debrecen |
N/A |
|
Chemicals, peptides, and recombinant proteins
|
| Mouse IL-4 |
PeproTech |
214-14 |
| Mouse IFNG |
PeproTech |
315-05 |
| Mouse M-CSF |
PeproTech |
315-02 |
| Ribociclib |
Selleck Chemicals |
S7440 |
| Artesunate |
Tocris |
6827 |
| Ragweed pollen extract |
Greer Laboratories |
XP56D3A2.5 |
| Alum Adjuvant |
Thermo Fisher Scientific |
77161 |
| Cas9 Nuclease V3 |
IDT |
N/A |
| Red Stain Reagent |
ELITech Biomedical Systems |
SS-035C-EU |
| Blue Stain Reagent |
ELITech Biomedical Systems |
SS-035/049B-EU |
| Rinse |
ELITech Biomedical Systems |
SS-035A-EU |
| Aerofix Additive |
ELITech Biomedical Systems |
SS-148-EU |
| Disuccinimidyl Glutarate (DSG) |
ProteoChem |
C1104 |
| Formaldehyde |
Thermo Scientific |
28906 |
| Trizol |
Thermo Fisher Scientific |
15596018 |
|
Critical commercial assays
|
| Ovation Ultralow System 2 |
Tecan |
0344NB-A01 |
| Ovation RNA-seq System V2 |
Tecan |
7102-32 |
| 10x scRNA-seq (v1.1 chemistry) |
10x Genomics |
1000165 |
| 10X scATAC-seq (v1 chemistry) |
10x Genomics |
1000175 |
| pHrodo Red S. Aureus |
Thermo Fisher Scientific |
A10010 |
| pHrodo Green E. coli |
Thermo Fisher Scientific |
P35366 |
| Vybrant DyeCycle Violet Stain |
Thermo Scientific |
V35003 |
| P3 Primary Cell 4D X Kit S (32 RCT) |
Lonza |
V4XP-3024 |
| Zenon APC Rabbit IgG labeling kit |
Thermo Fisher Scientific |
Z25303 |
| FOXP3 transcription factor staining buffer set |
eBioscience |
00-5523-00 |
| Live/dead Fixable Aqua Dead Cell Stain Kit |
Thermo Fisher Scientific |
L34957 |
| LIVE/DEAD Fixable Green Dead Cell Stain Kit |
Thermo Fisher Scientific |
L23101 |
| High-Capacity cDNA Reverse Transcription Kit |
Thermo Fisher Scientific |
4368814 |
| SsoAdvanced Universal SYBR Green Supermix |
BioRad |
1725274 |
| MinElute PCR Purification Kit |
Qiagen |
28006 |
|
Deposited data
|
| Raw and analyzed data. |
This paper. |
GEO: GSE178526
|
| Original code |
This paper. |
DOI: 10.5281/zenodo.7332328
|
|
Experimental models: Cell lines
|
| Primary bone marrow-derived macrophages (BMDMs) |
Female C57BL/J6 |
N/A |
| Primary alveolar macrophages |
Female C57BL/J6 |
N/A |
|
Experimental models: Organisms/strains
|
| Mouse: C57BL/J6 |
The Jackson Laboratory |
IMSR_JAX:000664 |
|
Oligonucleotides
|
| Guide RNA sequences, see Table
|
This paper. IDT |
Table 10
|
| Primer sequences, see Table
|
This paper. IDT |
Table 10
|
| TracrRNA |
IDT |
1072533 |
|
Software and algorithms
|
| BD FACSDiva Software |
BD Biosciences |
RRID:SCR_001456 |
| FlowJo |
BD Biosciences |
RRID:SCR_008520 |
| GraphPad Prism |
SciCrunch Registry |
RRID:SCR_002798 |
| Seurat |
Hao et al,65
|
https://satijalab.org/seurat/index.html
|
| Cellranger |
10X Genomics |
https://support.10xgenomics.com/singlecell-gene-expression/software/pipelines/latest/using/count
|
| ArchR |
Granja et al,32
|
ArchR (RRID:SCR_020982) |
| Bioconductor |
SciCrunch Registry |
Bioconductor (RRID:SCR_006442) |
| DESeq2 |
SciCrunch Registry |
DESeq (RRID:SCR_000154) |
| Kallisto |
SciCrunch Registry |
kallisto (RRID:SCR_016582) |
| Tximport |
SciCrunch Registry |
tximport (RRID:SCR_016752) |
| ChromVAR |
Schep et al,61
|
https://bioconductor.org/packages/release/bioc/html/chromVAR.html
|
| Magic |
Van Dijk et al,62
|
https://github.com/KrishnaswamyLab/MAGIC
|
| Scrublet |
SciCrunch Registry |
Scrublet (RRID:SCR_018098) |
| Harmony |
SciCrunch Registry |
Harmony (RRID:SCR_022206) |
| Fastp |
SciCrunch Registry |
fastp (RRID:SCR_016962) |
| Hisat2 |
SciCrunch Registry |
HISAT2 (RRID:SCR_015530) |
| MACS2 |
SciCrunch Registry |
MACS (RRID:SCR_013291) |
| BEDTools |
SciCrunch Registry |
BEDTools (RRID:SCR_006646) |
| Bestus Bioinformaticus Tools |
SciCrunch Registry |
Bestus Bioinformaticus Tools (RRID:SCR_016968) |
