|
Antibodies
|
| Brilliant Violet 711™ anti-mouse CD45 clone 30-F11 |
BioLegend |
Cat# 103147 |
| PE anti-mouse CD45.1 clone A20 |
BioLegend |
Cat# 110707 |
| PE/Cyanine7 anti-mouse CD45.2 clone 104 |
BioLegend |
Cat# 109829 |
| PE anti-mouse CD3 clone 17A2 |
BioLegend |
Cat# 100206 |
| PE anti-mouse CD90.2 clone 3O-H12 |
BioLegend |
Cat# 105308 |
| PE anti-mouse CD19 clone 6D5 |
BioLegend |
Cat# 115508 |
| PE anti-mouse B220 clone RA3-6B2 |
BD Biosciences |
Cat# 553089 |
| PE anti-mouse NK-1.1 clone PK136 |
BioLegend |
Cat# 108708 |
| APC anti-mouse Ly-6G clone 1A8 |
BioLegend |
Cat# 127614 |
| FITC anti-mouse Ly-6C clone HK1.4 |
BioLegend |
Cat# 128006 |
| Alexa Fluor® 700 anti-mouse I-A/I-E clone M5/114.15.2 |
BioLegend |
Cat# 107602 |
| APC/Fire™ 810 anti-mouse F4/80 clone BM8 |
BioLegend |
Cat# 123166 |
| APC/Cyanine7 anti-mouse/human CD11b clone M1/70 |
BioLegend |
Cat# 101226 |
| Brilliant Violet 605™ anti-mouse CD115 clone AFS98 |
BioLegend |
Cat# 135517 |
| PE anti-mouse TER-119 clone TER-119 |
BioLegend |
Cat# 116208 |
| FITC anti-mouse CD34 clone RAM34 |
ThermoFisher |
Cat# 11-0341-85 |
| APC anti-mouse CD11c clone N418 |
BioLegend |
Cat# 117310 |
| PE anti-mouse CD127 clone SB/199 |
BioLegend |
Cat# 121112 |
| PerCP/Cyanine5.5 anti-mouse CD16/32 clone 93 |
BioLegend |
Cat# 101324 |
| PerCP/Cyanine5.5 anti-mouse CD150 |
BioLegend |
Cat# 115922 |
| APC anti-mouse CD135 clone A2F10 |
BioLegend |
Cat# 135310 |
| Alexa Fluor® 700 anti-mouse CD48 clone HM48-1 |
BioLegend |
Cat# 103426 |
| PE/Cyanine7 anti-mouse CD117 (c-Kit) clone 2B8 |
BioLegend |
Cat# 105814 |
| APC/Cyanine7 anti-mouse Ly-6A/E (Sca-1) clone D7 |
BioLegend |
Cat# 108126 |
| APC anti-mouse CD8a clone 53-6.7 |
BD Biosciences |
Cat# 553035 |
| Pacific Blue™ anti-mouse CD4 clone GK1.5 |
BioLegend |
Cat# 100428 |
| PE anti-mouse Siglec-F clone E50-2440 |
BD Biosciences |
Cat# 562068 |
| PE anti-mouse CXCR4 clone 2B11 |
ThermoFisher |
Cat# 12-9991-82 |
| PE/Cyanine7 anti-mouse CX3CR1 clone SA011F11 |
BioLegend |
Cat# 149016 |
| PE/Cyanine7 anti-mouse TNF-α clone MP6-XT22 |
BioLegend |
Cat# 506324 |
| PE/Dazzle™ 594 anti-mouse CD64 clone X54-5/7.1 |
BioLegend |
Cat# 139320 |
| AF647™ anti-BrdU clone MoBU-1 |
ThermoFisher |
Cat# B35133
|
| Brilliant Violet 650™ anti-mouse CD192 (CCR2) |
BioLegend |
Cat# 150613 |
|
Bacterial and virus strains
|
| Pseudomonas aeruginosa, Strain Boston 41501 |
ATCC |
ATCC# 27853 |
|
Chemicals, peptides, and recombinant proteins
|
| Corticosterone: HBC complex |
Sigma-Aldrich |
Cat# C174 |
| pHrodo™ Red Phagocytosis Particle Labeling Kit for Flow Cytometry |
Thermo Fisher |
Cat# A10026 |
| pHrodo™ Red E. coli BioParticles™ Conjugate for Phagocytosis |
Thermo Fisher |
Cat# P35361
|
|
Critical commercial assays
|
| RNeasy Mini Kit |
Qiagen |
Cat# 74104 |
| High-Capacity cDNA Reverse Transcription Kit |
Thermo Fisher |
Cat# 4368814 |
| Corticosterone ELISA kit |
Abcam |
Cat# ab108821 |
| Mouse YM1/Chitinase 3-like 3 DuoSet ELISA |
R&D Systems |
Cat# DY2446 |
| Mouse IL-6 Quantikine ELISA Kit |
R&D Systems |
Cat# M6000B |
| Mouse TNF-alpha Quantikine ELISA Kit |
R&D Systems |
Cat# MTA00B |
| Free Fatty Acid Quantitation Kit |
Sigma-Aldrich |
Cat# MAK044 |
| Click-iT™ Plus EdU Pacific Blue™ Flow Cytometry Assay Kit |
Thermo Fisher |
Cat# C10636
|
|
Deposited data
|
| Single cell RNA sequencing data |
Gene Expression Omnibus |
|
| Bulk RNA sequencing data |
Gene Expression Omnibus |
|
|
Experimental models: Organisms/strains
|
| C57BL/6J |
The Jackson Laboratory |
Strain 000664 |
| C57BL/6-Tg(UBC-GFP)30Scha/J |
The Jackson Laboratory |
Strain 004353 |
| B6.129P2-Lyz2tm1(cre)Ifo/J |
The Jackson Laboratory |
Strain 004781 |
| B6.129P2-Cxcr4tm2Yzo/J |
The Jackson Laboratory |
Strain 008767 |
| B6.Cg-Nr3c1tm1.1Jda/J |
The Jackson Laboratory |
Strain 021021 |
| STOCK Prkaa1tm1.1Sjm/J |
The Jackson Laboratory |
Strain 014141 |
| B6.129S4(Cg)-Arntltm1Weit/J |
The Jackson Laboratory |
Strain 007668 |
| STOCK Slc2a1tm1.1Stma/AbelJ |
The Jackson Laboratory |
Strain 031871 |
| B6.FVB(129X1)-Tg(Sim1Cre)1Lowl/J |
The Jackson Laboratory |
Strain 006451 |
| B6.129S4(Cg)-Crhtm2.1 Maj/J |
The Jackson Laboratory |
Strain 030110 |
| B6.129S4-Ccr2tm1Ifc/J |
The Jackson Laboratory |
Strain 004999 |
| C.129S7(B6)-Itgb2tm2Bay/AbhmJ |
The Jackson Laboratory |
Strain 027003 |
| B6.129P2(Cg)-Cx3cr1tm1Litt/J |
The Jackson Laboratory |
Strain 005582 |
| B6.129S7-Rag1tm1Mom/J |
The Jackson Laboratory |
Strain 002216 |
| BALB/cJ |
The Jackson Laboratory |
Strain 000651 |
|
Oligonucleotides
|
| Mouse GAPD Mm99999915_g1 |
Thermo Fisher |
Cat# 4331182 |
| Mouse ACTB Mm00607939_s1 |
Thermo Fisher |
Cat# 4331182 |
| Mouse Clock Mm00455950_m1 |
Thermo Fisher |
Cat# 4331182 |
| Mouse Arntl Mm00500226_m1 |
Thermo Fisher |
Cat# 4331182 |
| Mouse Nr1d2 Mm01310356_g1 |
Thermo Fisher |
Cat# 4331182 |
| Mouse Per1 Mm00501813_m1 |
Thermo Fisher |
Cat# 4331182 |
| Mouse Cry1 Mm00514392_m1 |
Thermo Fisher |
Cat# 4331182 |
| Mouse Selplg Mm01204601_m1 |
Thermo Fisher |
Cat# 4331182 |
| Mouse Cd44 Mm01277161_m1 |
Thermo Fisher |
Cat# 4331182 |
| Mouse Itgal Mm00801807_m1 |
Thermo Fisher |
Cat# 4331182 |
| Mouse Itgam Mm00434455_m1 |
Thermo Fisher |
Cat# 4331182 |
| Mouse Itgb1 Mm01253230_m1 |
Thermo Fisher |
Cat# 4331182 |
| Mouse Itgb2 Mm00434513_m1 |
Thermo Fisher |
Cat# 4331182 |
| Mouse Itga4 Mm01277951_m1 |
Thermo Fisher |
Cat# 4331182 |
| Mouse Itga5 Mm00439797_m1 |
Thermo Fisher |
Cat# 4331182 |
| Mouse Itga6 Mm00434375_m1 |
Thermo Fisher |
Cat# 4331182 |
| Mouse Ccr1 Mm00438260_s1 |
Thermo Fisher |
Cat# 4331182 |
| Mouse Cxcr3 Mm9999054_s1 |
Thermo Fisher |
Cat# 4331182 |
| Mouse Cxcr4 Mm01996749_s1 |
Thermo Fisher |
Cat# 4331182 |
| Mouse Cx3cr1 Mm02620111_s1 |
Thermo Fisher |
Cat# 4331182 |
| Mouse Ilb1 Mm00434228_m1 |
Thermo Fisher |
Cat# 4331182 |
| Mouse Tnf Mm00443258_m1 |
Thermo Fisher |
Cat# 4331182 |
| Mouse Ccr2 Mm99999051_gH |
Thermo Fisher |
Cat# 4331182 |
|
Software and algorithms
|
| FlowJo v10 |
FlowJo |
https://www.flowjo.com/
|
| GraphPad Prism v9 |
GraphPad Software |
https://www.graphpad.com/
|
| BioRender |
BioRender |
https://biorender.com
|
|
R Differential gene expression analysis:
|
|
|
| R version 4.2.1, Platform: aarch64-apple-darwin20 (64-bit); OS: macOS Monterey 12.6.1 |
aarch64-apple-darwin20 (64-bit) |
N/A |
| scales_1.2.1 |
CRAN/BiocManager |
N/A |
| clusterProfiler_4.6.0 |
CRAN/BiocManager |
N/A |
| tidyr_1.2.1 |
CRAN/BiocManager |
N/A |
| dplyr_1.0.10 |
CRAN/BiocManager |
N/A |
| ggplot2_3.3.6 |
CRAN/BiocManager |
N/A |
| GenomicRanges_1.50.0 |
CRAN/BiocManager |
N/A |
| MatrixGenerics_1.10.0 |
CRAN/BiocManager |
N/A |
| ggthemes_4.2.4 |
CRAN/BiocManager |
N/A |
| org.Hs.eg.db_3.16.0 |
CRAN/BiocManager |
N/A |
| immunarch_0.8.0 |
CRAN/BiocManager |
N/A |
| EnhancedVolcano_1.16.0 |
CRAN/BiocManager |
N/A |
| genefilter_1.80.0 |
CRAN/BiocManager |
N/A |
| GenomeInfoDb_1.34.0 |
CRAN/BiocManager |
N/A |
| matrixStats_0.62.0 |
CRAN/BiocManager |
N/A |
| msigdbr_7.5.1 |
CRAN/BiocManager |
N/A |
| org.Mm.eg.db_3.16.0 |
CRAN/BiocManager |
N/A |
| patchwork_1.1.2 |
CRAN/BiocManager |
N/A |
| ggrepel_0.9.1 |
CRAN/BiocManager |
N/A |
| DESeq2_1.38.0 |
CRAN/BiocManager |
N/A |
| IRanges_2.32.0 |
CRAN/BiocManager |
N/A |
| glmpca_0.2.0 |
CRAN/BiocManager |
N/A |
| pathview_1.38.0 |
CRAN/BiocManager |
N/A |
| AnnotationDbi_1.60.0 |
CRAN/BiocManager |
N/A |
| data.table_1.14.4 |
CRAN/BiocManager |
N/A |
| glmGamPoi_1.10.0 |
CRAN/BiocManager |
N/A |
| SummarizedExperiment_1.28.0 |
CRAN/BiocManager |
N/A |
| S4Vectors_0.36.0 |
CRAN/BiocManager |
N/A |
| RColorBrewer_1.1-3 |
CRAN/BiocManager |
N/A |
| enrichplot_1.18.0 |
CRAN/BiocManager |
N/A |
| gridExtra_2.3 |
CRAN/BiocManager |
N/A |
| dtplyr_1.2.2 |
CRAN/BiocManager |
N/A |
| ggbeeswarm_0.6.0 |
CRAN/BiocManager |
N/A |
| Biobase_2.58.0 |
CRAN/BiocManager |
N/A |
| BiocGenerics_0.44.0 |
CRAN/BiocManager |
N/A |
| pheatmap_1.0.12 |
CRAN/BiocManager |
N/A |
|
R scRNA analysis:
|
|
|
| monocle3_1.2.9 |
GitHub |
N/A |
| IRanges_2.32.0 |
CRAN/BiocManager |
N/A |
| BiocGenerics_0.44.0 |
CRAN/BiocManager |
N/A |
| SeuratObject_4.1.2 |
GitHub |
N/A |
| SingleCellExperiment_1.20.0 |
CRAN/BiocManager |
N/A |
| S4Vectors_0.36.0 |
CRAN/BiocManager |
N/A |
| SeuratDisk_0.0.0.9020 |
GitHub |
N/A |
| Seurat_4.2.0 |
GitHub |
N/A |
| SummarizedExperiment_1.28.0 |
CRAN/BiocManager |
N/A |
| MatrixGenerics_1.10.0 |
GitHub |
N/A |
| SeuratWrappers_0.3.1 |
GitHub |
N/A |
| magrittr_2.0.3 |
CRAN/BiocManager |
N/A |
| GenomicRanges_1.50.0 |
CRAN/BiocManager |
N/A |
| matrixStats_0.62.0 |
CRAN/BiocManager |
N/A |
| SeuratData_0.2.2 |
GitHub |
N/A |
| patchwork_1.1.2 |
CRAN/BiocManager |
N/A |
| GenomeInfoDb_1.34.0 |
CRAN/BiocManager |
N/A |
| Biobase_2.58.0 |
CRAN/BiocManager |
N/A |
| sp_1.5-0 |
CRAN/BiocManager |
N/A |
| ggplot2_3.3.6 |
CRAN/BiocManager |
N/A |
