| Antibodies |
| anti-mouse CD16/32 (clone 2.4G2) |
Tonbo Biosciences |
70-0161-U500 |
| anti-mouse CD45 Alexa Fluor 647 (clone 30-F11) |
Biolegend |
103124 |
| anti-mouse GPNMB eFluor™ 660 (clone CTSREVL) |
eBioscience |
50-5708-80 |
| anti-h/mPeriostin (clone 345613) |
R&D Systems |
MAB3548 |
| anti-alpha smooth muscle actin antibody (polyclonal) |
Abcam |
AB5694 |
| anti-mouse P-selectin (polyclonal) |
R&D Systems |
AF737 |
| anti-CD31 AlexaFluor647 (clone 390) |
BioLegend |
102416 |
| anti-CD11b AlexaFluor594 (clone M1/70) |
BioLegend |
101254 |
| anti-CD206-AlexaFluor647 (clone C068C2) |
BioLegend |
141712 |
| anti-I-A/I-E AlexaFluor594 (clone M5/114.15.2) |
BioLegend |
107650 |
| anti-I-A/I-E AlexaFluor488 (clone M5/114.15.2) |
BioLegend |
107616 |
| goat anti-rat IgG (H+L) AlexaFluor488 |
Thermo Fisher Scientific |
A11006 |
| donkey anti-goat IgG (H+L) AlexaFluor488 |
Thermo Fisher Scientific |
A11055 |
| F(ab')2-Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor™ Plus 555 |
Thermo Fisher Scientific |
A48283 |
| Alexa Fluor® 488 AffiniPure Fab Fragment Goat Anti-Rat IgG (H+L) |
Jackson ImmunoResearch |
112-547-003 |
| Alexa Fluor® 647 AffiniPure Fab Fragment Goat Anti-Rat IgG (H+L) |
Jackson ImmunoResearch |
112-607-003 |
| anti-mouse B220 (clone RA3–6B2) |
Biolegend |
103202 |
| anti-mouse CCR7 (clone 4B12) |
Biolegend |
120101 |
| anti-mouse CD103 (clone 2e7) |
Biolegend |
121402 |
| anti-mouse CD11b (clone M1/70) |
Biolegend |
101202 |
| anti-mouse CD11c (clone N418) |
Biolegend |
117302 |
| anti-mouse CD16/32 (clone 2.4G2) |
BD |
553142 |
| anti-mouse CD19 (clone 6D5) |
Biolegend |
115501 |
| anti-mouse CD206 (clone C068C2) |
Biolegend |
141702 |
| anti-mouse CD207 (clone 4C7) |
Biolegend |
144202 |
| anti-mouse CD24 (M1/69) |
Biolegend |
101802 |
| anti-mouse CD3e (clone 17A2) |
Biolegend |
100202 |
| anti-mouse CD38 (clone 90) |
Biolegend |
102702 |
| anti-mouse CD4 (clone RM4-5) |
Biolegend |
100506 |
| anti-mouse CD44 (clone IM7) |
Biolegend |
103002 |
| anti-mouse CD45 (clone 30-F11) |
Biolegend |
103102 |
| anti-mouse CD49b (clone HMa2) |
Biolegend |
103513 |
| anti-mouse CD62L (clone MAB5671) |
R&D |
MAB5761 |
| anti-mouse CD64 (clone (X54-5/7.1) |
Biolegend |
139302 |
| anti-mouse CD69 (polyclonal) |
R&D |
AF2386 |
| anti-mouse CD8a (clone 53-6.7) |
Biolegend |
100702 |
| anti-mouse CD86 (clone GL-1) |
Biolegend |
105002 |
| anti-mouse CD90 (clone G7) |
Biolegend |
105202 |
| anti-mouse c-Kit (clone 2B8) |
Biolegend |
105802 |
| anti-mouse CTLA-4 (clone UC10-4B9) |
Biolegend |
106302 |
| anti-mouse F4/80 (clone BM8) |
Biolegend |
123102 |
| anti-mouse FceR1a (clone MAR-1) |
Biolegend |
134302 |
| anti-mouse Foxp3 (clone NRRF-30) |
eBiosciences |
14-4771-80 |
| anti-mouse GATA3 (clone 16E10A23) |
Biolegend |
653802 |
| anti-mouse Ki67 (clone SolA15) |
eBiosciences |
14-5698-82 |
| anti-mouse Ly6C (clone HK1.4) |
Biolegend |
128002 |
| anti-mouse Ly6G (clone 1A8) |
Biolegend |
127602 |
| anti-mouse MHC-II (clone M5/114.15.2) |
Biolegend |
107602 |
| anti-mouse PD-1 (clone 29F.1A12) |
Biolegend |
135202 |
| anti-mouse PD-L1 (clone 10F.9G2) |
Biolegend |
124302 |
| anti-mouse PDCA1 (clone 927) |
Biolegend |
127002 |
| anti-mouse RORgt (clone B2D) |
eBiosciences |
14-6981-82 |
| anti-mouse Siglec F (clone E50-2440) |
BD Biosciences |
552125 |
| anti-mouse SIRPa (clone P84) |
Biolegend |
144002 |
| anti-mouse T-bet (clone 4B10) |
Biolegend |
644802 |
| anti-mouse TCRgd (clone GL3) |
Biolegend |
118101 |
| anti-mouse Ter119 (clone Ter119) |
Biolegend |
116202 |
| anti-mouse TIM-3 (clone B8.2C12) |
Biolegend |
134002 |
| anti-human CD45 APC/e780 (clone HI30) |
Thermo Fisher |
47-0459-42 |
| anti-human CD3e PerCP/e710 (clone OKT3) |
Thermo Fisher |
46-0037-42 |
| anti-human HLA-DR BUV395 (clone G46-6) |
BD Biosciences |
564040 |
| Biological samples |
|
|
| Fetal Bovine Serum, Benchmark |
GeminiBio |
100-106 |
| Chemicals, peptides, and recombinant proteins |
|
|
| Methanol |
Fisher Scientific |
A412-4 |
| recombinant human Tenascin |
Merck Millipore |
CC-065 |
| recombinant mouse Periostin |
R&D Systems |
2955-F2-050 |
| recombinant mouse Oncostatin M |
BioLegend |
762802 |
| Albumin, Bovine (BSA), nuclease free |
VWR |
332 |
| Albumin, Bovine (BSA) |
Sigma |
A7906 |
| EDTA |
Teknova |
E0306 |
| Maxpar PBS |
Fluidigm |
201058 |
| Maxpar Cell Staining Buffer |
Fluidigm |
201068 |
| Maxpar Water |
Fluidigm |
201069 |
| EQ Four Element Calibration Beads |
Fluidigm |
201078 |
| Saponin |
Sigma |
S-7900 |
| Cisplatin |
Enzo Life Sciences |
ALX-400-040 |
| NaN3 |
Sigma |
S-8032 |
| Cell-ID 20-Plex Pd Barcoding Kit |
Fluidigm |
201060 |
| Cell-ID 125 μm Iridium Intercalator |
Fluidigm |
201192A |
| 16% paraformaldehyde |
Electron Microscopy Sciences |
15710 |
| DNase I |
Millipore Sigma |
10104159001 |
| Collagenase IX |
Millipore Sigma |
C7657 |
| Hyaluronidase |
Worthington Biochemical Corp |
LS005477 |
| buprenorphine hydrochloride |
Hospira |
0409-2012-32 |
| bupivicaine |
AuroMedica Pharma LLC |
55150-167-10 |
| OCT |
Sakura |
4583 |
| Triton X-100 |
Sigma |
T8787 |
| Mouse serum |
Jackson ImmunoResearch |
015-000-120 |
| Normal rat serum |
Stem Cell Technologies |
13551 |
| Goat serum |
Sigma |
G9023 |
| Histodenz |
Sigma |
D-2158 |
| N-methylacetamide |
Sigma |
M26305-100G |
| 1-Thioglycerol |
Sigma |
M1753-100ML |
| 5X iScript RT Supermix |
Bio-Rad |
L001404B |
| SsoFast EvaGreen Supermix |
Bio-Rad |
L000915B |
| Critical commercial assays |
|
|
| Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1, 16 rxns |
10X Genomics |
PN1000121 |
| Chromium Next GEM Chip G Single Cell Kit, 48 rxns |
10X Genomics |
PN-1000120 |
| Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit v1.1, 16 rxns |
10x Genomics |
PN-1000165 |
| 10X Chromium Controller |
10x Genomics |
N/A |
| Deposited data |
|
|
| Mouse spatiotemporal scRNAseq wound data set |
This paper |
GEO: GSE204777
|
| Human tumor scRNAseq data set |
This paper |
10.17632/nnmb6m5p5j.1
|
| Mouse melanoma fibroblast data set |
Davidson et al. (PMID: 32433953)73
|
ArrayExpress: E-MTAB-7427 |
| Mouse pan-tissue fibroblast scRNAseq atlas |
Buechler et al. (PMID: 33981032)22
|
ArrayExpress:E-MTAB-10315 |
| Mouse pancreatic cancer fibroblast scRNAseq data set |
Dominguez et al. (PMID: 31699795)54
|
ArrayExpress: E-MTAB-8483 |
| Mouse wound scRNAseq data set |
Guerrero-Juarez et al. (PMID: 31699795)26
|
GEO: GSE113854
|
|
Supplementary Mendeley Figures & Tables
|
Mendeley Data |
10.17632/kmmw43j2z6.2 |
| Experimental models: Cell lines |
|
|
| B16-F10 (mouse melanoma cell line) |
ATCC |
CRL-6475 |
| MC38 (mouse colorectal tumor cell line) |
Kerafast |
ENH204-FP |
| Experimental models: Organisms/strains |
|
|
| Mouse: wild-type C57BL/6 |
The Jackson Laboratory |
Stock# 000664 |
| Mouse: Arg1-tdTomato-CreERT2 × R26R-EYFP |
H.-E. Liang & R. Locksley (UCSF)49
|
https://www.sciencedirect.com/science/article/pii/S1074761319301992
|
| Mouse: Pdgfra-H2B-EGFP |
A. Molofsky (UCSF)58
|
Stock# 007669, |
| Oligonucleotides |
|
|
| See Supplementary Table S2 for qPCR primers |
IDT |
N/A |
| Software and algorithms |
| Normalizer |
Finck et al, 20131103; https://onlinelibrary.wiley.com/doi/10.1002/cyto.a.22271
|
https://rdrr.io/bioc/CATALYST/man/normCytof.html
|
| Rphenograph |
Levine et al, 2015104; https://www.sciencedirect.com/science/article/pii/S0092867415006376
|
https://github.com/JinmiaoChenLab/Rphenograph
|
| R environment |
R Development Core Team |
https://cran.r-project.org/bin/windows/base/
|
| Premessa |
Parker ICI |
https://github.com/ParkerICI/premessa
|
| Flow Jo v10.8.1 |
Tree Star |
https://www.flowjo.com/
|
| Imaris 9.2.1 |
Bitplane |
https://imaris.oxinst.com/products/imaris-for-cell-biologists?gad=1&gclid=Cj0KCQjw3a2iBhCFARIsAD4jQB2RkztA4vyhmDUQ3_eo2WwjysDt-NhFrH-evt8PxW5s5oKpw_WYJhcaAuhZEALw_wcB
|
| MATLAB |
The MathWorks, Inc. |
https://www.mathworks.com/products/matlab.html
|
| LASX |
Leica Microsystems |
https://www.leica-microsystems.com/products/microscope-software/p/leica-las-x-ls/
|
| CellChat (R package) |
Jin et al. 202110; https://www.nature.com/articles/s41467-021-21246-9
|
https://github.com/sqjin/CellChat
|
| Seurat v3 (R package) |
Stuart and Butler et al.105; Comprehensive Integration of Single-Cell Data. Cell (2019) [Seurat V3] |
https://satijalab.org/seurat/
|
| NMF (R package) |
Gaujoux R, Seoighe C (2010)110. “A flexible R package for nonnegative matrix factorization.” BMC Bioinformatics, 11(1), 367. ISSN 1471-2105, doi: 10.1186/1471-2105-11-367, http://www.biomedcentral.com/1471-2105/11/367. |
https://cran.r-project.org/web/packages/NMF/index.html
|
| Corrplot (R package) |
https://cran.r-project.org/web/packages/corrplot/vignettes/corrplot-intro.html
|
https://cran.r-project.org/web/packages/corrplot/vignettes/corrplot-intro.html
|
| Ggpubr (R package) |
https://cran.r-project.org/web/packages/ggpubr/index.html
|
https://cran.r-project.org/web/packages/ggpubr/index.html
|
| PhEMD |
Chen et al., 2020106; https://www.nature.com/articles/s41592-019-0689-z
|
https://www.bioconductor.org/packages/release/bioc/html/phemd.html
|
| Monocle 3 |
Trapnell et al., 201443; http://dx.doi.org/10.1038/nbt.2859
|
https://github.com/cole-trapnell-lab/monocle3
|
| CellRanger v 4.0.0 |
10X Genomics |
https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest
|
| Biorender |
https://www.biorender.com
|
https://www.biorender.com/
|
| Other |
|
|
| lipid-modified oligonucleotides (LMO) |
McGinnis et al., 201937; https://www.nature.com/articles/s41592-019-0433-8
|
N/A |
| MaxPAR antibody conjugation kit |
Fluidigm |
201146B |
| Dermal biopsy punch, 2 mm |
Acuderm inc. |
69038-02 |
| Dermal biopsy punch, 4 mm |
Integra |
33-34 |
| Dermal biopsy punch, 6 mm |
Integra |
33-36 |
| Dermal biopsy punch, 8 mm |
Integra |
33-37 |
| RNeasy Mini Kit |
Qiagen |
74104 |
