(A) Mammary glands from 10-week-old mice (n = 4) were assessed for CD45+ and CD45– Lyve-1+ cells by flow cytometry. (B) Mammary glands from 10-week-old mice (n = 4) were assessed for CD45+CD11b+F4/80…
Source data for graphs in panels A and B.
(A) Gating of flow cytometry for CD45+ and CD45– Lyve-1+ cells. (B) Gating of flow cytometry for CD45+CD11b+F4/80+Lyve-1– and CD45+CD11b+F4/80+Lyve-1+ cells.
Image of a mammary gland from a 6-week-old female mouse (n = 3) stained for F4/80 (red), Lyve-1 (green) and DAPI (blue). Insets show examples of the mammary gland capsule (a–d) and lymph nodes (e–h).
(A) Heat map of RNA-seq analysis of CD45+CD11b+F4/80+Lyve-1– and CD45+CD11b+F4/80+Lyve-1+ cells isolated from 6-week-old (lane 1) and 10-week-old (lanes 2–3) mice. Genes shown have an adjusted …
(A) Post-sort analysis of CD45+CD11b+F4/80+Lyve-1– and CD45+CD11b+F4/80+Lyve-1+ cells that were submitted for bulk RNA-seq analysis. (B) scRNA-seq data showing genes associated with macrophages …
(A) Violin plot of Mrc1 expression in the single-cell RNA-seq dataset shown in Figure 2. (B) Mammary glands from 10-week-old mice (n = 4) were assessed for CD206 expression in CD45+CD11b+F4/80+Lyve-1…
Source data for graphs in panels B, F, and G.
(A) Gating of flow cytometry for Lyve-1 expression in CD45+CD11b+F4/80+CD206– and CD45+CD11b+F4/80+CD206+ cells. (B) Gating of flow cytometry for CD206 expression in CD45+CD11b+F4/80+Lyve-1– and …
(A) Schematic of shielded bone marrow chimera experiment. (B) Representative flow cytometry plots showing the gating and identification of host (CD45.2) and donor (CD45.1) cells in the blood and …
Source data for graphs in panels B and C.
(A) Mammary glands from 6-week-old mice were immunostained for HA using HA binding protein (HABP, green) and smooth muscle actin (SMA, red) (n = 3, three images/sample). (B) Mammary glands from …
Source data for graph in panel C.
Mammary glands were stained for F4/80, Lyve-1 and HABP to confirm that Lyve-1+ cells associated with HA are also F4/80+. Insets show higher magnification.
(A) 5-week-old female mice were treated with pexidartinib for 2 weeks and mammary glands were harvested for analysis of macrophages for CD45+CD11b+F4/80+ by flow cytometry. Flow cytometry …
Source data for graphs in panels A, C, and D.
Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
---|---|---|---|---|
Strain, strain background (Mus musculus, female) | FVB/N | Envigo | FVB/NHsd | |
Strain, strain background (Mus musculus, female) | Balb/c CD45.2 Mice | Jackson Laboratories | Stock No.: 000651 | Balb/cJ Mouse Strain |
Strain, strain background (Mus musculus) | Balb/c CD45.1 Mice | Jackson Laboratories | Stock No.: 006584 | CByJ.SJL(B6)-Ptprca/J Mouse Strain |
Antibody | violetFluor 450-Conjugated anti-CD45.1 (mouse monoclonal) | Tonbo Biosciences | Cat #: 75–0453 U025 RRID:AB_2621949 | Flow cytometry: 1:200 |
Antibody | Alexa Fluor 700-Conjugated anti-CD45.2 (mouse monoclonal) | BioLegend | Cat #: 109822 RRID:AB_493731 | Flow cytometry: 1:200 |
Antibody | BUV395-conjugated anti-Ly6G (rat monoclonal) | BioLegend | Cat #: 563978 RRID:AB_2716852 | Flow cytometry: 1:400 |
Antibody | Brilliant Violet 421-Conjugated Anti-CD64 (mouse monoclonal) | BioLegend | Cat #: 139309 RRID:AB_2562694 | Flow cytometry: 1:100 |
Antibody | Brilliant violet 711-conjugated anti-CD11c (Armenian hamster monoclonal) | BioLegend | Cat #: 117349 RRID:AB_2563905 | Flow cytometry: 1:200 |
Antibody | PE/Cy7-conjugated anti-CD11b (rat monoclonal) | BioLegend | Cat #: 101216 RRID:AB_312799 | Flow cytometry: 1:200 |
Antibody | PE-conjugated anti-F4/80 (rat monoclonal) | BioLegend | Cat #: 123109 RRID:AB_893498 | Flow cytometry: 1:200 |
Antibody | Biotinylated anti-Lyve-1 (goat polyclonal) | R and D Systems | Cat #: BAF2125 RRID:AB_2138529 | Flow cytometry:4 μg/mL |
Antibody | Anti-CD16/CD32 (rat monoclonal) | eBioscience | Cat #: 14-0161-82 RRID:AB_467133 | Flow cytometry: 1:200 |
Antibody | Rat anti-mouse monoclonal F4/80 (clone: CI: A3-1) | Bio-Rad laboratories | Cat# MCA497GA RRID:AB_323806 | IF 1:100 |
Antibody | Goat polyclonal anti-mouse LYVE-1 (Ala24-Thr234) | R and D Systems | Cat# AF2125 RRID:AB_2297188 | IF 1:60 |
Antibody | Anti-mannose receptor (rabbit polyclonal) | Abcam | Cat# ab64693 RRID:AB_1523910 | IF 1:1000 |
Antibody | Anti-BrdU antibody [BU1/75 (ICR1)] | Abcam | Cat# ab6326 RRID:AB_305426 | IF 1:200 |
Antibody | Hyaluronic acid bindingprotein, biotinylated | Millipore Sigma | Cat# 385911–50 UG | IF 1:100 |
Antibody | Actin-smooth muscle (rabbit polyclonal) | Spring Bioscience | Cat# E2464 RRID:AB_95752 | IF 1:50 |
Antibody | CD68 monoclonal antibody (514H12) | Thermo- Fisher Scientific | Cat# MA1-80133 RRID:AB_929283 | IF 1:100 |
Antibody | Human LYVE-1 antibody (goat polyclonal) | R and D Systems | Cat# AF2089 RRID:AB_355144 | IF 1:60 |
Antibody | Alexa 594 secondary antibody (donkey anti-mouse) | Thermo- Fisher Scientific | Cat# A-32744 RRID:AB_2762826 | IF 1:400 |
Antibody | Alexa 594 secondary antibody (donkey anti-rat) | Thermo- Fisher Scientific | Cat# A-21209 RRID:AB_2535795 | IF 1:400 |
Antibody | Alexa Fluor 488 conjugated streptavidin secondary antibody | Thermo- Fisher Scientific | Cat# S11223 | IF 1:400 |
Antibody | Alexa 488 secondary antibody (donkey anti-goat) | Thermo- Fisher Scientific | Cat# A-11055 RRID:AB_2534102 | IF 1:400 |
Antibody | Alexa 488 secondary antibody (goat anti-rabbit) | Thermo- Fisher Scientific | Cat# A-11008 RRID:AB_143165 | IF 1:400 |
Antibody | Alexa 594 secondary antibody (goat anti-rat) | Thermo- Fisher Scientific | Cat # A-11007 RRID:AB_10561522 | IF 1:400 |
Antibody | Alexa 594 secondary antibody (goat anti-rabbit) | Thermo- Fisher Scientific | Cat# A-11012 RRID:AB_2534079 | IF 1:400 |
Antibody | Alexa Fluor 647 conjugated streptavidin secondary antibody | Thermo- Fisher Scientific | Cat# S-32357 | IF 1:400 |
Commercial assay or kit | Hyaluronan enzyme-linked immunosorbent assay | Echelon Biosciences | Cat #: K-1200 | |
Chemical compound, drug | Busulfan | Sigma-Aldrich | Cat #: B2635-10G | |
Chemical compound, drug | Pexidartinib | Selleck Chem | Cat #: S7818 | |
Chemical compound, drug | Heparin | Sigma-Aldrich | Cat #: H3149-10KU | |
Chemical compound, drug | Collagenase A | Sigma-Aldrich | Cat #: 10103586001 | |
Chemical compound, drug | DNase I | Sigma-Aldrich | Cat #: DN25-100MG | |
Software, algorithm | GraphPad Prism 8.0 | GraphPad Prism 8.0 | RRID:SCR_002798 | http://www.graphpad.com/scientific-software/prism/ |
Software, algorithm | ImageJ 2.0.0 | ImageJ 2.0.0 | RRID:SCR_003070 | https://imagej.nih.gov/ij/download.html |
Software, algorithm | Hisat2 | Kim et al., 2015 | RRID:SCR_015530 | version 2.0.2 |
Software, algorithm | DESeq2 software | Love et al., 2014 | RRID:SCR_015687 | version 1.20.0 |
Software, algorithm | ggplot2 | R | RRID:SCR_014601 | v3.0.0 |
Software, algorithm | pheatmap | R | RRID:SCR_016418 | 1.0.12 |
Other | Flow Cytometry Perm Buffer (10X) | Tonbo Biosciences | Cat #: TNB-1213-L150 | |
Other | Fixable Viability Dye eFluor 780 | eBioscience | Cat #: 65-0865-14 | Flow cytometry: 1:1000 dilution |
Other | APC-conjugated streptavidin | eBioscience | Cat #: 17-4317-82 | Flow cytometry: 1:100 dilution |
Other | ProLong Gold Antifade Mountant (DAPI) | Thermo- Fisher Scientific | Cat# P36931 | |
Other | Trichrome stain kit | Abcam | Cat# ab150686 | |
Other | Antigen Retrieval Buffer (100X EDTA Buffer, pH 8.0) | Abcam | Cat# ab93680 | 1x |
Other | Antigen unmasking solution, PH 6.0 | Thermo- Fisher Scientific | Cat# NC9401067 | 1x |
List of 155 differentially expressed genes in CD45+CD11b+F4/80+Lyve-1– and CD45+CD11b+F4/80+Lyve-1+ bulk RNA-seq analysis.
List of the top 100 differentially regulated genes in each cluster from the scRNA-seq analysis.
GSEA analysis using gene sets created from a differentially expressed ranked list from the bulk RNA-seq data (adjusted p-value <0.1 and a fold-change >0.25) to determine enrichment of cluster 4.
List of top gene sets identified by GSEA analysis including core enriched genes.