| Antibodies |
|
|
|
| Anti-mouse B220 (RA3–6B2, APC-eF780) |
Invitrogen |
Cat# 47–0452-82; RRID:AB_1518810 |
| Anti-mouse CD3 (145–2C11, PerCP-Cy5.5) |
BioLegend |
Cat# 100328; RRID:AB_893318 |
| Anti-mouse CD3 (UCHT1, APC-eF780) |
Invitrogen |
Cat# 47–0038-42; RRID:AB_1272042 |
| Anti-mouse CD4 (GK1.5, AF700) |
BioLegend |
Cat# 100430; RRID:AB_493699 |
| Anti-mouse CD8a (53–6.7, BV605) |
BioLegend |
Cat# 100744; RRID:AB_2561352 |
| Anti-mouse CD11a (M17/4, PE-Cy7) |
BioLegend |
Cat# 101122; RRID:AB_2562781 |
| Anti-mouse CD11b (M1/70, BV421) |
BioLegend |
Cat# 101236; RRID:AB_10897942 |
| Anti-mouse CD11b (M1/70, APC-eF780) |
eBioscience |
Cat# 47–0112-82; RRID:AB_1603193 |
| Anti-mouse CD11c (N418, APC-eF780) |
eBioscience |
Cat# 47–0114-82; RRID:AB_1548652 |
| Anti-mouse CD16/32 (S17011E, PE-Cy7) |
BioLegend |
Cat# 156610; RRID:AB_2800707 |
| Anti-mouse CD16/32 (FC receptor block) |
eBioscience |
Cat# 14–0161-85; RRID:AB_467134 |
| Anti-mouse CD19 (6D5, BV711) |
BioLegend |
Cat# 115555; RRID:AB_2565970 |
| Anti-mouse CD19 Biotin (1D3) |
Cytek |
Cat# 30–0193; RRID:AB_2621641 |
| Anti-mouse CD34 (RAM34, BV711) |
BD |
Cat# 751621; RRID:AB_2875614 |
| Anti-mouse CD45.2 (104, BV650) |
BioLegend |
Cat# 109835; RRID:AB_2563065 |
| Anti-mouse CD48/Blast (HM48–1, PE) |
BioLegend |
Cat# 103405; RRID:AB_313020 |
| Anti-mouse CD49d (R1–2, PE) |
BioLegend |
Cat# 103608; RRID:AB_313038 |
| Anti-mouse CD64 (X54–5/7.1, PE-Cy7) |
BioLegend |
Cat# 139314; RRID:AB_2563904 |
| Anti-mouse CD115 (AFS98, PE) |
BioLegend |
Cat# 135506; RRID:AB_1937253 |
| Anti-mouse CD117/c-kit (ACK2, BV605) |
BioLegend |
Cat# 135120; RRID:AB_2650925 |
| Anti-mouse CD150/Slam (TC15–12F12.2, APC) |
BioLegend |
Cat# 115909; RRID:AB_493461 |
| Anti-mouse CCR2 (TG5, APC) |
BioLegend |
Cat# 150628; RRID:AB_2810415 |
| Anti-mouse FLT-3/CD135 (A2F10, BV421) |
BioLegend |
Cat# 135314; RRID:AB_2562339 |
| Anti-mouse GR1(RB6–8C5, APC-eF780) |
eBioscience |
Cat# 47–5931-82; RRID:AB_1518804 |
| Anti-mouse Ly6C (HK1.4, PerCP-Cy5.5) |
BioLegend |
Cat# 128012; RRID:AB_1659241 |
| Anti-mouse Ly6G (1A8, FITC) |
BioLegend |
Cat# 127606; RRID:AB_1236494 |
| Anti-mouse Ly6G (RB6–8C5, APC-eF780) |
eBioscience |
Cat# 47–5931-82; RRID:AB_1518804 |
| Anti-mouse myeloperoxidase (2D4, FITC) |
Abcam |
Cat# ab90812; RRID:AB_2050025 |
| Anti-mouse NK1.1 (PK136, APC) |
Cytek |
Cat# 20–5941; RRID:AB_2621611 |
| Anti-mouse NK1.1 (SI7016D, PE-Fire 700) |
BioLegend |
Cat# 156528; RRID:AB_2910320 |
| Anti-mouse Sca-1/Ly6A (E13–161.7, PE-Dazzle 594) |
BioLegend |
Cat# 122528; RRID:AB_2687355 |
| Anti-mouse Ter119 (TER-119, APC-eF780) |
eBioscience |
Cat# 47–5921-82; RRID:AB_1548786 |
| Anti-mouse TNFα (APC, MP6-XT22) |
BioLegend |
Cat# 506308; RRID:AB_315429 |
| Anti-rat IgG2a (2A3) |
BioXCell |
Cat# BE0089; RRID:AB_1107769 |
| Anti-mouse CD4 (GK1.5) |
BioXCell |
Cat# BE0003–1; RRID:AB_1107636 |
| Anti-mouse CD8b (53–5.8) |
BioXCell |
Cat# BE0223; RRID:AB_2687706 |
| Anti-mouse CSF1R (CD115, AFS98) |
BioXCell |
Cat# BE0213; Cat# BE0213 |
| Anti-mouse 90.2 (53–2.1, BUV395) |
BD Biosciences |
Cat# 565257; RRID:AB_2739136 |
| Ghost Dye UV 450 Fixable Viability Dye |
Cell Signaling |
Cat# 80862 |
| Ghost Dye V510 Fixable Viability Dye |
Cell Signaling |
Cat# 59863 |
|
Ex vivo LPS stimulation solution tubes |
Dr. Mark Hall (Nationwide Children’s Hospital, Columbus, OH) |
N/A |
|
| Bacterial and virus strains |
|
| RFP+ kanamycin-resistant uropathogenic E. coli UPEC |
Strain UT189-kan-RFP |
N/A |
| Virulent Listeria monocytogenes |
Dr. Sarah Hamilton-Hart (University of Minnesota, Minneapolis, MN) |
N/A |
|
| Chemicals, peptides, and recombinant proteins |
|
| LPS-EB (LPS from E. coli 011:B4) |
Invivogen |
Cat# Tlrl-eblps |
| Brefeldin A |
BioLegend |
Cat# 420601 |
| Kanamycin |
Gold Bio |
Cat# K-120–5 |
| IGEPAL |
Sigma |
Cat# 542334 |
| RPMI-1640 |
HyClone |
Cat# SH30027.01 |
| Fetal bovine serum |
Atlanta Biologicals |
Cat#S11550 |
| Penicillin 10,000 U/ml - Streptomycin 10,000 μg/ml |
HyClone |
Cat#SV30010 |
| Sodium pyruvate 100mM |
HyClone |
Cat# SH30239.01 |
| HEPES 1M |
HyClone |
Cat# SH30237.01 |
| MEM Non-Essential Amino Acids 100X |
HyClone |
Cat# SH30238.01 |
| 2-Mercaptoethanol solution 50 mM |
Gibco |
21985–023) |
|
| Critical commercial assays |
|
| Mouse Custom ProcartaPlex 20-plex (CCL2, CCL3, CCL4, CCL5, CCL7, CCL11, CXCL1, CXCL2, CXCL10, GM-CSF, IFNγ, IL-1β, IL-2, IL-4, IL-5, IL-6, IL-12p70, IL-13, IL-18, TNFα) |
Thermo Fisher Scientific |
PPX-20 |
| ELISA MAX standard set mouse TNFα |
BioLegend |
Cat# 430901 |
| Cytofix/cytoperm fixation/permeabilization solution kid |
BD Biosciences |
Cat# 554714 |
| EasySep Mouse 90.2 positive selection kit II |
STEMCELL Technologies |
Cat# 18951CA |
| FITC BrdU flow kit |
BD Pharmingen |
Cat# 559619 |
|
| Deposited data |
|
| SPF and CoH murine CD115+ monocytes RNA-seq (bulk) |
This study |
GEO: GSE237883
|
|
| Experimental models: Organisms/strains |
|
| Mouse: C57BL/6Ncr |
NCI Charles River |
N/A |
| Mouse: pet store |
Minneapolis/St. Paul area Petco stores |
N/A |
|
| Software and algorithms |
|
| Prism 10 |
GraphPad |
https://www.graphpad.com/scientific-software/prism/
|
| FlowJo |
BD Biosciences |
www.flowjo.com
|
| FacsDiva |
BD Biosciences |
N/A |
| Bio-plex Manager Software 5.0 |
Bio Rad |
www.bio-rad.com
|
| bowtie2 version 2.3.4.1 |
John Hopkins Univ |
https://bowtie-bio.sourceforge.net/bowtie2/index.shtml
|
| Subread version 1.5.1 |
R package |
https://subread.sourceforge.net
|
| edgeR version 3.24.3 |
R package |
https://bioconductor.org/packages/release/bioc/html/edgeR.html
|
| Complexheatmap |
R package |
https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html
|
| clusterProfile |
R package |
https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html
|
