| Antibodies |
| AlexaFluor 594 donkey anti-goat IgG |
Invitrogen |
A11058 |
| AlexaFluor Goat 546 anti-rat IgG |
Invitrogen |
A11081 |
| AlexaFluor Goat 633 anti-rabbit IgG |
Invitrogen |
A21071 |
| Alpha-smooth muscle actin |
Abcam |
5694; RRID: AB_2223021 |
| Armenian Hamster IgG Isotype Control |
eBioscience |
eBio299Arm |
| Beta-Actin |
Sigma |
A5441 |
| CD31 |
BD |
557355; RRID: AB_396660 |
| CD34 |
BioLegend |
119310 |
| CD45-APC |
invitrogen |
17045182 |
| CD55 clone RIKO-3 |
BioLegend |
131803 |
| CD81-biotin Clone EAT2 |
eBioscience |
13-0811-81 |
| EpCAM-PE clone G8.8 |
eBioscience |
12-5791-83 |
| GFP |
Abcam |
6556/6662RRIDs: AB_305564 and AB_305635 |
| Goat anti-mouse IgG HRP conjugate |
Invitrogen |
62-6520 |
| Goat anti-rabbit IgG HRP-conjugate |
Invitrogen |
656120 |
| Laminin |
Sigma |
L9393; RRID: AB_477163 |
| Lysozyme |
Dako |
A0099; RRID: AB_2341230 |
| MKi67 |
Invitrogen |
MA5-14520 |
| Pdgfra (IHC) |
R&D Systems |
AF1062; RRID: AB_2236897 |
| Pdgfra (CD140a-Ab) for FACS |
BioLegend |
135905 |
| PE Armenian Hamster IgG Isotype Ctrl |
BioLegend |
400907 |
| Phospho-Smad 1/5(ser463/465) (41D10) Rabbit mAb |
Cell Signaling Technology |
9516 RRID: AB_491015 |
| Streptavidin-APC |
eBioscience |
17431782 |
| anti-rabbit biotinylated 2nd antibody |
Jackson Immuno Research |
111-065-003 |
| Streptavidin-HRP |
Jackson Immuno Research |
016-030-084 |
| Tyramide-C3 |
Perkin Elmer |
NEL744E001KT |
| Chemicals, peptides, and recombinant proteins |
| Agarose |
A1705Z |
Azura Genomics |
| Alexa Fluor 647 Phalloidin |
Life Technologies |
A22287 |
| AMPure beads |
Beckman Coulter |
A63880 |
| B-27 Supplement (50X) |
Life Technologies |
17504001 |
| Blocking Reagent |
Perkin Elmer |
FP1020 |
| Bovine Serum Albumin |
Sigma |
A9647 |
| CHIR99021 (Chir) |
Sigma-Aldrich |
SML1046-5MG |
| Chlorophorm |
Sigma-Aldrich |
C2432 |
| Collagenase II |
Worthington |
LS004176 |
| Collagenase XI |
Sigma |
C7657 |
| Complete (Protease Inhibitor Cocktail Tablets) |
Sigma Aldrich |
11697498001 |
| DAPI |
BD PharMingen |
5649097 |
| DAPI solution |
BD Bioscience |
564907 |
| Dispase II |
Sigma |
D4693 |
| Dulbecco’s Modified Eagle Medium (DMEM) |
Corning |
17-205-CV |
| DMEM/F12 Media |
GIBCO |
12634-010 |
| EDTA |
Gibco |
AM9260G |
| Fetal Bovine Serum |
Corning |
35-010-CV |
| FocusClear |
CelExplorer |
FC-101 |
| Glutamax |
GIBCO |
35050-661 |
| Hanks’ Balanced Salt Solution (HBSS, 10X) |
GIBCO |
14065-056 |
| HEPES |
Sigma |
H3375 |
| 30% H2O2 |
Electron Microscopy Science |
2621-02 |
| Matrigel |
Corning |
356231 |
| Mini-Protean TGX Gels |
BioRad |
4561084 |
| N-2 Supplement (100X) |
Life Technologies |
17502001 |
| N-Acetylcysteine |
Sigma |
A9165 |
| Normal Goat Serum |
Cell Signaling |
5425S |
| Paraformaldehyde |
EMS |
15714-S |
| PBS (10X) |
Corning |
46-013-CM |
| Penicillin/Streptomycin |
Life Technologies |
15140163 |
| Pierce Bovine Serum Albumin Standard Ampules |
Life Technologies |
23209 |
| Recombinant EGF |
ThermoFisher |
PHG0311 |
| Recombinant Gremlin-1 |
ThermoFisher |
956GR050 |
| Recombinant Human/Murine/Rat BMP-2 |
Peprotech |
120-02C-10UG |
| Recombinant Murine BMP-4 |
Peprotech |
315-27-10UG |
| Recombinant Murine BMP-7 |
R&D |
5666-BP/CF |
| Recombinant Noggin |
Peprotech |
120-10C |
| Sodium azide |
Sigma |
S2002 |
| T ransfer Buffer (10x) |
Boston BioProducts |
BP-190 |
| Tris-Glycine-SDS Running buffer (10x) |
Boston BioProducts |
BP-150 |
| Triton X-100 |
Sigma |
T8787 |
| Trizol reagent |
ThermoFisher |
15596026 |
| T rypLE Express |
Thermo Fisher Scientific |
12604-021 |
| Trypsin 0.25% EDTA |
Life Technologies |
25200114 |
| VectaShield mounting medium |
Vector Laboratories |
H-1000 |
| Wnt-C59 |
ThermoFisher |
NC0186427 |
| Critical commercial assays |
| BCA PROTEIN ASSAY KIT |
Thermo Fisher |
PI23227 |
| Agilent High Sensitivity DNA Kit |
Agilent |
5067-4626 |
| Agilent RNA 6000 Pico Kit |
Agilent |
NoImage 5067-1513 |
| Alcian Blue Counterstain |
Thermo Fisher |
NC1318236 |
| Chromium Next GEM Chip G Single Cell Kit |
10X Genomics |
PN-1000120 |
| Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1, 4 rxns PN-1000128 |
10X Genomics |
PN-1000128 |
| DNA-purification kit |
Qiagen |
28004 |
| ECL Prime Western Blotting Detection Reagents |
GE Healthcare |
RPN2232 |
| High-Fidelity 2X PCR master mix |
New England Biolabs |
M0541S |
| Nextera Tn5 Transposase |
Illumina |
FC-121-1030 |
| Power SYBR Green PCR MasterMix |
Life Technologies |
4367659 |
| PureLink RNA mini kit |
Life Technologies |
12183018A |
| Qubit dsDNA high-sensitivity assay |
Life Technologies |
Q32851 |
| RNAscope Hydrogen Peroxide |
ACD |
322335 |
| RNAscope Multiplex Fluorescent Reagent Kit v2 |
ACD |
323100 |
| RNAscope Protease III |
ACD |
322337 |
| RNeasy Plus micro kit |
Qiagen |
74034 |
| SapphireAmp Fast PCR Mastermix |
Takara |
RR350 |
| Single Index Kit T Set A |
10X Genomics |
PN-100021 |
| SMART-Seq v4 Ultra Low Input RNA kit |
Clontech |
634890 |
| SUPERSCRIPT III 1ST STRAND |
Life Technologies |
18080051 |
| Deposited data |
| Bulk RNA-seq mesenchymal cells |
This study |
GEO accession: GSE211275
|
| ATAC-seq mesenchymal cells |
This study |
GEO accession: GSE211275
|
| scRNA-seq whole mesenchyme colon |
This study |
GEO accession: GSE211275
|
| scRNA-seq PdgfraLow cells colon |
This study |
GEO accession: GSE211275
|
| scRNA-seq Pdgfra+ cells small intestine |
This study |
GEO accession: GSE212601
|
| scRNA-seq whole mesenchyme small Intestine |
McCarthy et al |
GEO: GSE130681 GSM4196131, GSM4196131
|
| scRNA-seq whole mesenchyme colon |
Kinchen et al |
GEO: GSE114374
|
| scRNA-seq whole mesenchyme small Intestine |
Kim et al |
GEO: GSE116514
|
| Mouse reference genome Mm10, GRCm38 |
Genome Reference Consortium |
https://www.ncbi.nlm.nih.gov/grc/mouse
|
| Experimental models: Organisms/strains |
|
Atoh1fl/fl (B6.129S7-Atoh1tm3Hzo/J)
|
The Jackson Laboratory |
008681 RRID:IMSR_JAX:008681 |
|
FoxL1-CreERT2-2A-tdTomato (B6.Cg-Foxl1tm2(cre/ERT2)Khk)
|
The Jackson Laboratory |
RRID: MMRRC_068163-JAX |
|
Grem1tdTom (Grem1-P2A-DTR-P2A-TdTomato)
|
This study |
|
|
Wnt4-CreERT2 (B6.Cg-Wnt4tm2(EGFP/cre/ERT2)Amc/J)
|
The Jackson Laboratory |
032489 RRID: IMSRJAX:032489 |
|
Myh11-CreERT2 (B6.FVB-Tg(Myh11-icre/ERT2)1Soff/J)
|
The Jackson Laboratory |
19079 RRID:IMSR_JAX:019079 |
|
PdgfraCreERT2 B6.129S-Pdgfratm1.1(cre/ERT2)Blh/J
|
The Jackson Laboratory |
032770 RRID:IMSR_JAX:032770 |
|
PdgfraH2BeGFP (B6.129S4-Pdgfratm11(EGFP)Sor/J)
|
The Jackson Laboratory |
007669 RRID:IMSR_JAX:007669 |
|
PorcnFl
|
L. Charles Murtaugh, University of Utah, United States |
|
|
Rosa26-TdTomato B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J
|
The Jackson Laboratory |
007909 RRID:IMSR_JAX:007909 |
|
Rosa mT/mG (B6.129(Cg)-Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo/J)
|
The Jackson Laboratory |
007676 RRID:IMSR_JAX:007676 |
|
Rosa26-EYFP (B6.129X1-Gt(ROSA)26Sortm1(EYFP)Cos/J)
|
The Jackson Laboratory |
006148 RRID:IMSR_JAX:006148 |
|
Vil1-Cre(ER-T2)
|
Sylvie Robine, Institut Pasteur, Paris, France |
|
| Oligonucleotides |
| RNAscope® Ackr4 probes |
ACD |
1081831 |
| RNAscope® Bmp4 probes |
ACD |
454301 |
| RNAscope® Bmp5 probes |
ACD |
401241 |
| RNAscope® Grem1 probes |
ACD |
314741 |
| RNAscope® Olfm4 probes |
ACD |
311831 |
| RNAscope® Rspo3 probes |
ACD |
483781 |
| RNAscope® Sfrp1 probes |
ACD |
404981 |
| RNAscope® Wnt2b probes |
ACD |
405031 |
| RNAscope® Wnt4 probes |
ACD |
401101 |
| Software and algorithms |
| Cell Ranger v2.1.1 |
10X Genomics |
https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation
|
| BioRender |
|
BioRender.com
|
| cnmf v1.3.2 |
Kotliar et al., 2019
|
https://github.com/dylkot/cNMF
|
| Corrplot |
Wei et al., 2017 |
https://github.com/taiyun/corrplot
|
| DeepTools |
Ramírez et al., 2016
|
https://github.com/deeptools/deepTools
|
| DESeq2_1.26.0 |
Love et al., 2014
|
https://bioconductor.org/packages/release/bioc/html/DESeq2.html
|
| Diffusion Pseudotime (dpt) |
Haghverdi et al., 2016
|
https://www.nature.com/articles/nmeth.3971
|
| Fiji (ImageJ 1.52p) |
Schindelin et al., 2012 |
https://imagej.net/Fiji/
|
| FlowJo v10.6 |
BD Biosciene |
|
| ggplot2_3.3.2 |
Wickham H., 2016 |
ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. ISBN 978-3-319-24277-4, https://ggplot2.tidyverse.org
|
| GraphPad Prism |
GraphPad, Inc |
|
| Integrated Genomics Viewer, ver 2.9.4 |
Robinson et al., 2011 |
http://software.broadinstitute.org/software/igv/
|
| LAS X Version 3.5.7.23225 |
Leica Microsystems CMS GmbH |
|
| MAST algorithm |
Finak et al., 2015 |
https://github.com/RGLab/MAST
|
| Morpheus |
Broad Institute |
https://software.broadinstitute.org/morpheus/
|
| Python functions for scRNA-seq |
Wager Lab, UCSF |
DOI: 10.5281/zenodo.7686568
|
| R software for statistical computing |
R Development Core Team, 2013 |
https://cran.r-project.org/bin/windows/
|
| RSeQC |
Wang et al., 2012
|
http://rseqc.sourceforge.net/
|
| RStudio |
RStudio Team (2020). |
RStudio: Integrated Development for R. RStudio, PBC, Boston, MA URL http://www.rstudio.com
|
| Seurat_3.2.2 |
Butler et al., 2018
|
https://github.com/satijalab/seurat
|
| slingshot_1.4.0 |
Street et al., 2018
|
https://bioconductor.org/packages/release/bioc/html/slingshot.html
|
| STAR |
Dobin et al., 2013 |
https://github.com/alexdobin/STAR/releases
|
| t-SNE algorithm |
van der Maaten, 2014 |
https://lvdmaaten.github.io/tsne/
|
| VIPER |
Cornwell et al., 2018
|
https://bitbucket.org/cfce/viper/
|
| Zen blue 3.5 (Zen lite) Version 3.5.093 |
Carl Zeiss Microscopy GmbH |
|
| Other |
| ACD HybEZ II Hybridization System |
ACD |
321710 |
| 10X Genomics Controller |
10X Genomics |
1000204 |
| Leica cryostat |
Leica Microsystems |
CM-1510-3 |
| Slide Spacers |
Grace Bio-Labs |
654002 |
