|
Antibodies
|
| mAb to alpha Smooth Muscle Actin |
Abcam |
Cat# 32575 |
| mAb to FAK |
Abcam |
Cat# 40794 |
| pAb to Collagen I |
Abcam |
Cat# Ab34710 |
| pAb to Collagen III |
Abcam |
Cat# Ab7778 |
| mAb to FAP |
Cell Signaling |
Cat# 66562S |
| mAb to MGP |
ThermoFisher |
Cat# 60055-1 |
| Ab to Phospho-FAK (pTyr397) |
Invitrogen |
Cat# 700255 |
| Ab to DPP4 (CD26) |
Abcam |
Cat# Ab28340 |
| Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 |
Invitrogen |
Cat# A-11008 |
| Goat anti-Mouse IgG2a heavy chain, PE/Cy7 ®preadsorbed |
Abcam |
Cat# Ab130787
|
| Donkey anti-Rat IgG H&L, Alexa Fluor 647 preadsorbed |
Abcam |
Cat# Ab150155
|
| Anti-mouse CD45, Alexa Fluor 647 |
Biolegend |
Cat# 103124 |
| Anti-mouse CD31, Alexa Fluor 647 |
Biolegend |
Cat# 102516 |
| Anti-mouse TER-119, Alexa Fluor 647 |
Biolegend |
Cat# 116218 |
| Anti-mouse/human CD324, Alexa Fluor 647 |
Biolegend |
Cat# 147308 |
| Anti-mouse CD326, Alexa Fluor 647 |
Biolegend |
Cat# 118212 |
| Anti-mouse CD202b (TIE2), Biotin |
Invitrogen |
Cat# 124006 |
| Streptavidin, Alexa Flour 647 conjugate |
Invitrogen |
Cat# S32357
|
|
Chemicals, Peptides, and Recombinant Proteins
|
| (Z)-4-Hydroxyta moxifen |
Millipore Sigma |
Cat# H7904 |
| Tamoxifen |
Sigma |
|
| Corn oil |
Sigma |
|
| Hematoxylin |
Sigma |
Cat# H3136 |
| Acetic Acid EMD |
Millipore |
Cat# AX0073 |
| Phosphotungstic Acid |
Sigma |
Cat# P4006 |
| Eosin Y solution, alcoholic |
Sigma |
Cat# HT1101128 |
| Ethanol Gold Shield |
Sigma |
Cat# 64-17-5 |
| BABB (Benzoic acid:benzyl Benzoate) |
Sigma |
Cat# B6630 |
|
tert-butanol |
Sigma |
Cat# 360538 |
| Triethylamine |
FisherSci |
Cat# 04885 |
| Permount |
Fisher Chemicals |
Cat# SP15 |
| Triton X-100 |
Sigma |
Cat# X100 |
| Fluoromount-G |
SouthernBiotech |
Cat# 0100-01 |
| Prolong Gold Antifade Mountant with DAPI |
ThermoFisher |
Cat# P36935
|
| DAPI (4’, 6-Diamido-2-Phenylindole, Dihydrochloride) |
ThermoFisher |
Cat# D1306 |
| Collagenase (Collagenase Type IV) |
ThermoFisher |
Cat# 17104019 |
| Liberase |
Sigma Aldrich |
Cat# 05401020001 |
| Medium 199 |
Sigma Aldrich |
Cat# M2520 |
| Fetal Bovine Serum |
Thermo Fisher |
Cat# 10438026 |
| DNase I |
Worthington |
Cat# LS006330
|
| Poloxamer 188 |
Sigma |
Cat# P5556 |
| HEPES |
Sigma Aldrich |
Cat# H3375 |
| Calcium Chloride |
Sigma Aldrich |
Cat# 499609 |
| Dulbecco’s Modified Eagle Medium |
ThermoFisher |
Cat# 11320082 |
| SYTOX ADvanced Ready Flow Reagent |
ThermoFisher |
Cat# R37173
|
| Digitonin |
Promega |
Cat# G9441 |
| Tween-20 |
Sigma/Roche |
Cat# 11332465001 |
| 1X Power Block |
BioGeneX |
Cat# HK085-5K |
| NP40 |
Sigma/Roche |
Cat# 11332473001 |
| RNAse Inhibitor |
Protector |
Cat# 3335402001 |
|
Critical Commercial Assays
|
| Trichrome Stain Kit |
Abcam |
Cat# Ab150686
|
| Picro Sirius Red Stain Kit |
Abcam |
Cat# Ab150681
|
| Chromium Single Cell Chip B Kit |
10X Genomics |
Cat# 1000154 |
| Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 |
10X Genomics |
Cat# 1000092 |
| Chromium Next GEM Chip H Single Cell Kit |
10X Genomics |
Cat# 1000161 |
| Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 |
10X Genomics |
Cat#1000175 |
| Single Index Kit N Set A |
10X Genomics |
Cat# 100021289 |
| Visium Spatial Gene Expression Solution v1 |
10X Genomics |
Cat#PN-1000184 |
| Visium Spatial Tissue Optimization Slide & Reagent Kit |
10X Genomics |
Cat#PN-1000193 |
| Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle |
10X Genomics |
Cat#PN-1000285 |
|
Deposited Data
|
| The gene expression and chromatin accessibility datasets generated during this study are publicly available and can be found through the GEO web portal using the accession listing at right. |
Gene Expression Omnibus (GEO) |
GSE212482 and its subseries (GSE212461, GSE212481, GSE212706, GSE212707, GSE212708) |
|
Experimental Models: Organisms/Strains
|
| Black6 (C57BL/6J) mice |
The Jackson Laboratory |
Stock#000664 |
| Actin-Cre-ERT2 (Tg(CAG-cre/Esr1)5Amc/J) mice |
The Jackson Laboratory |
Stock#004682 |
| Col1-CreERT2 (Tg(Col1a2-cre/ERT,-ALPP)7Cpd/J) mice |
The Jackson Laboratory |
Stock#029235 |
| MMTV-PyMT (FVB/N-Tg(MMTV-PyVT)634Mul/J) mice |
The Jackson Laboratory |
Stock#002374 |
| FAKfl/fl (B6.129P2(FVB)-Ptk2tm1.1Guan/J) mice |
The Jackson Laboratory |
Stock#031956 |
| αSMA-CreERT2 mice |
Courtesy of Dr. Ivo Kalajzic, University of Connecticut |
|
| Rainbow (ROSA26VT2/GK3) mice |
Courtesy of the Weissman Laboratory, Stanford University School of Medicine |
|
|
Software and Algorithms
|
| Adobe Photoshop CC |
Adobe |
RRID:SCR 014199 |
| Adobe Illustrator CC |
Adobe |
RRID:SCR 010279 |
| Prism 5 |
GraphPad |
RRID:SC R 002798 |
| FIJI/ImageJ |
National Institutes of Health |
RRID:SCR 002285 |
| Imaris |
Oxford Instruments |
RRID:SCR 007370 |
