Antibodies |
|
BD Pharm Lyse |
BD Biosciences |
Cat#555899; RRID: AB_2869057
|
Biotin anti-mouse CD45 Antibody |
Biolegend |
Cat#103104; RRID: AB_312969
|
Biotin anti-mouse CD71 Antibody |
Biolegend |
Cat#113803; RRID: AB_313564
|
CD41-Biotin |
Biolegend |
Cat#133930; RRID: AB_2572133
|
Lineage Cell Depletion Kit, mouse |
Miltenyi Biotec |
Cat#130-090-858 |
APC/Cyanine7 anti-mouse CD41 Antibody |
Biolegend |
Cat#133928; RRID: AB_2572131
|
APC/Cyanine7 anti-mouse CD3 Antibody |
Biolegend |
Cat#100222; RRID: AB_2242784
|
APC/Cyanine7 anti-mouse/human CD11b Antibody |
Biolegend |
Cat#101226; RRID: AB_830642
|
APC/Cyanine7 anti-mouse Ly-6G/Ly-6C (Gr-1) Antibody |
Biolegend |
Cat#108424; RRID: AB_2137485
|
APC/Cyanine7 anti-mouse TER-119/Erythroid Cells Antibody |
Biolegend |
Cat#116223; RRID: AB_2137788
|
APC/Cyanine7 anti-mouse/human CD45R/B220 Antibody |
Biolegend |
Cat#103224; RRID: AB_313007
|
APC/Cyanine7 anti-mouse CD45.1 Antibody |
Biolegend |
Cat#110716; RRID: AB_313505
|
APC/Cyanine7 anti-mouse CD45.2 Antibody |
Biolegend |
Cat#109824; RRID: AB_830789
|
PerCP/Cy5.5 anti-mouse Ly-6A/E (Sca-1) |
Sony Biotechnologies |
Cat#1212615; RRID: AB_2877117
|
APC anti-mouse CD31 Antibody |
Biolegend |
Cat#102410; RRID: AB_312905
|
PE anti-mouse CD51 Antibody |
Biolegend |
Cat#104106; RRID: AB_2129493
|
Hoechst Solution 33342 |
BD Biosciences |
Cat#561908 |
Pacific Blue anti-mouse CD45 Antibody |
Biolegend |
Cat#103125; RRID: AB_493536
|
CD11b Monoclonal Antibody (M1/70), eFluor 450 |
ThermoFisher |
Cat#48-0112-80; RRID: AB_1582237
|
PE/Cy7 anti-mouse CD140a Antibody |
Biolegend |
Cat#135911; RRID: AB_2715973
|
APC CD140b (PDGFRB) Monoclonal Antibody (APB5) |
ThermoFisher |
Cat#14-1402-82; RRID: AB_467493
|
PE anti-mouse CD106 Antibody |
Biolegend |
Cat#105713; RRID: AB_1134166
|
FITC CD107a antibody |
BD Biosciences |
Cat#553793; RRID: AB_395057
|
Recombinant Anti-MRP8 antibody [EPR3554] |
abcam |
Cat#ab92331; RRID: AB_2050283
|
Rabbit anti-CD56 (clone RCD56, Isotype IgG) |
Zytomed Systems |
Cat#RBK050; RRID: AB_2864528
|
APC anti-human CD105 Antibody |
Biolegend |
Cat#323208; RRID: AB_755960
|
PE anti-human CD271 (NGFR) Antibody |
Biolegend |
Cat#345106; RRID: AB_2152647
|
APC/Cyanine7 anti-human CD31 Antibody |
Biolegend |
Cat#303120; RRID: AB_10640734
|
FITC anti-human CD45 Antibody |
Biolegend |
Cat#368508; RRID: AB_2566368
|
FITC anti-human CD235ab Antibody |
Biolegend |
Cat#306610; RRID: AB_756046
|
FITC anti-human CD71 Antibody |
Biolegend |
Cat#334104; RRID: AB_2201482
|
FITC anti-human CD41 Antibody |
Biolegend |
Cat#303704; RRID: AB_314374
|
FITC anti-human CD61 Antibody |
Biolegend |
Cat#336404; RRID: AB_1227580
|
7-AAD Viability Staining Solution |
Biolegend |
Cat#420404 |
goat anti-IL-33 Antibody |
R&D Systems |
Cat#AF3626; RRID: AB_884269
|
Rabbit anti goat Antibody |
DAKO |
Cat#E0466 |
rabbit-anti-S100-Antibody |
DAKO |
Cat#Z0311 |
goat anti-rabbit-Antibody |
Vector |
Cat#BP-9100 |
Anti-Actin, α-Smooth Muscle - FITC Antibody |
Sigma Aldrich |
Cat#F3777; RRID: AB_476977
|
|
Bacterial and Virus Strains |
|
pRRL.PPT.SFFV.IRES2.EGFP.WPRE |
Axels Schambach, Dirk Heckl |
N/A |
MSCV-IRES-EGFP |
Tannishtha Reya |
Addgene Plasmid #20672; RRID:Addgene_20672 |
pMIG-JAK2WT-IRES-EGFP |
Melanie Curie |
N/A |
pMIG-JAK2V617F-IRES-EGFP |
Melanie Curie |
N/A |
Biological Samples |
|
|
|
Chemicals, Peptides, and Recombinant Proteins |
|
Murine thrombopoietin |
Peprotech |
Cat#351-14 |
Murine stem cell factor |
Peprotech |
Cat#250-03 |
Retronectin |
Takara Bio |
Cat#T100A/B |
Polybrene |
Merck Millipore |
Cat#TR-1003-G |
Fugene |
Promega |
Cat#E2691 |
StemSpan SFEM |
Stem Cell Technologies |
Cat#09600 |
Collagenase II |
Invitrogen |
Cat#17101015 |
Murine bFGF |
Peprotech |
Cat#450-33 |
Murine EGF |
Peprotech |
Cat#315-09 |
Recombinant murine IL-33 |
Peprotech |
Cat#210-33 |
Recombinant human TGF-β1 |
InvivoGen |
Cat#rcyc-htgfb1 |
Poly(ethylene glycol) BioUltra 300 |
Sigma |
Cat#90878-250ML-F |
Tasquinimod (ABR-215050) |
Biorbyt |
Cat#ORB251345 |
B-27 Supplement (50X), serum free |
ThermoFisher |
Cat#17504044 |
Forskolin |
Sigma-Aldrich |
Cat#F6886 |
Recombinant Human PDGF-AA |
Peprotech |
Cat#100-13A |
Heregulin-β3, Epidermal growth factor (EGF) domain |
Sigma-Aldrich |
Cat#01-201 |
Liberase |
Roche |
Cat#5401020001 |
DNaseI |
Sigma |
Cat#DN25 |
Antigen unmasking solution |
Vector |
Cat#H-3300 |
Hematoxylin Solution, Gill No. 1 |
Sigma |
Cat#GHS1128 |
|
Critical Commercial Assays |
|
Chromium Single Cell 3′ Reagent Kits (v2) |
10x Genomics |
Cat#PN-120237 |
Chromium Single Cell A Chip Kit (v2) |
10x Genomics |
Cat#PN-120236 |
i7 Multiplex Kit, 96 rxns |
10x Genomics |
Cat#PN-120262 |
Single Cell 3′Reagent Kits (v2) User Guide |
10x Genomics |
Cat#CG00052, Rev D |
High-Capacity cDNA Reverse Transcription Kits |
Thermo Fisher |
Cat#4368814 |
Fast SYBR Green Master Mix |
Applied Biosystems |
Cat#4385616 |
MesenCult Expansion Kit (Mouse) |
STEMCELL |
Cat#05513 |
Reticulin silver plating kit acc. to Gordon & Sweets |
Sigma |
Cat#1002510001 |
Human S100A8 DuoSet ELISA |
R&D Systems |
Cat#DY4570-05 |
Chromium Single Cell 3′ Reagent Kits (v2) |
10x Genomics |
Cat#PN-120237 |
Chromium Single Cell A Chip Kit (v2) |
10x Genomics |
Cat#PN-120236 |
i7 Multiplex Kit, 96 rxns |
10x Genomics |
Cat#PN-120262 |
Single Cell 3′Reagent Kits (v2) User Guide |
10x Genomics |
Cat#CG00052, Rev D |
AVIDIN/BIOTIN blocking Kit |
Vector |
Cat#SP-2001 |
Peroxidase substrate Kit |
Vector |
Cat#SK-4100 |
ABC-Kit |
Vector |
Cat#PK-6100 |
|
Deposited Data |
|
Genome Reference Consortium Mouse Build 38 patch release 6, mm10 |
Genome Reference Consortium |
https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.26 |
Raw Data |
This paper |
GEO: GSE156644
|
Analyzed Data |
This paper |
10.5281/zenodo.3979087 |
|
Experimental Models: Cell Lines |
|
Hek293T |
ATCC |
CRL-3216; RRID:CVCL_0063 |
|
Experimental Models: Organisms/Strains |
|
B6.SJL-Ptprca Pepcb/BoyJ Mus musculus
|
The Jackson Laboratory |
Cat#JAX:002014; RRID:IMSR_JAX:002014 |
C57BL/6J Mus musculus
|
The Jackson Laboratory |
Cat# JAX:000664; RRID:IMSR_JAX:000664 |
Gli1tm3(re/ERT2)Alj/J |
The Jackson Laboratory |
Cat#007913 |
Rosa26tdTomato (i.e., B6-Cg-Gt(ROSA)26Sorttm(CAG-tdTomato)Hze/J) |
The Jackson Laboratory |
Cat#007909 |
|
Oligonucleotides |
|
See Table S6
|
See Table S6
|
See Table S6
|
|
Recombinant DNA |
|
psPAX2 (lentivral packaging) |
Didier Trono |
Addgene Plasmid #12259; RRID:Addgene_12259 |
pCMV-VSV-G (lentiviral envelope) |
Didier Trono |
Addgene Plasmid #8454; RRID:Addgene_8454 |
pCL-Eco (retroviral packaging) |
Novus Biologicals |
Cat# NBP2-29540 |
|
Software and Algorithms |
|
GraphPadPrism v8 |
GraphPad Software Inc. |
RRID:SCR_002798
|
FlowJo v10 |
Tree Star Inc. |
RRID:SCR_008520
|
Adobe Phostoshop CC 2018 |
Adobe Systems Inc. |
RRID:SCR_014199
|
Adobe Illustrator CC 2018 |
Adobe Systems Inc. |
RRID:SCR_010279
|
Cellranger v 2.1.1 |
10x Genomics |
https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/2-1 |
Seurat (v2.3.4; v3.1.0) |
Butler et al., 2018 |
https://satijalab.org/seurat |
clusterProfiler v3.12.0 |
(Yu et al., 2012) |
https://git.bioconductor.org/packages/clusterProfiler |
edgeR v3.26.7 |
McCarthy et al., 2012 |
https://git.bioconductor.org/packages/edgeR |
Monocle v2.12.0 |
Trapnell et al., 2014 |
https://git.bioconductor.org/packages/monocle |
Qiu et al., 2017 |
R v3.6.1 |
CRAN |
https://www.R-project.org |
Progeny v1.11.0 |
Schubert et al., 2018 |
https://github.com/saezlab/progeny |
Viper v1.20.0 |
(Alvarez et al., 2016) |
https://git.bioconductor.org/packages/viper |
CellPhoneDB v2.0.5 |
Efremova et. al, 2020 |
https://github.com/Teichlab/cellphonedb |
biomaRt v1.2.0 |
(Durinck et al., 2009) |
https://git.bioconductor.org/packages/biomaRt |