REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse monoclonal αSMA antibody	Sigma	Cat# a5228; RRID:AB_262054
Rabbit polyclonal Axin2 antibody	Abcam	Cat# ab32197; RRID:AB_2290204
Rabbit polyclonal β-catenin antibody	Sigma	Cat# SAB4500541; RRID:AB_10743932
Rabbit monoclonal E-cadherin antibody	Cell Signaling	Cat# 3195; RRID:AB_2291471
Rat monoclonal E-cadherin antibody	Invitrogen	Cat # 13-1900; RRID:AB_86571
Rabbit polyclonal Foxp1 antibody	Cell Signaling	Cat# 2005; RRID:AB_2106979
Rabbit polyclonal GFP antibody	Invitrogen	Cat# A-11122; RRID:AB_221569
Rabbit monoclonal Lef1 antibody	Cell Signaling	Cat# 2230; RRID:AB_823558
Rabbit polyclonal CD31 (PECAM) antibody	Abcam	Cat# ab28364; RRID:AB_726362
Rabbit polyclonal Pitx2 antibody	L’Honoré et al., 2007, gift of Jacques Drouin	N/A
Rabbit polyclonal RFP antibody	Abcam	Cat# ab62341; RRID:AB_945213
Rabbit polyclonal Tbx3 antibody	Invitrogen	Cat# 42-4800; RRID:AB_2533526
Goat anti-Mouse IgG1 Cross-Adsorbed Secondary Antibody, Alexa Fluor 647	Invitrogen	Cat# A-21240; RRID:AB_141658
Goat anti-Rat IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488	Invitrogen	Cat# A-11006; RRID:AB_141373
Goat anti-Rat IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 594	Invitrogen	Cat# A-11007; RRID:AB_141374
Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 594	Invitrogen	Cat# A-11012; RRID:AB_141359
Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 647	Invitrogen	Cat# A-21244; RRID:AB_2535812
Alexa Fluor 568 Phalloidin	Thermo Fisher Scientific	Cat# A12380
Alexa Fluor 488 Phalloidin	Thermo Fisher Scientific	Cat# A12379
Chemicals, peptides, and recombinant proteins
LiCl	Sigma	L9650
IWR1	Sigma	I0161
Cyclopamine	Tocris	1623
Critical commercial assays
RNAScope Multiplex Fluorescent V2 Assay	ACD	Cat No. 323100
RNAScope Probe Mm-Hoxb6	ACD	Cat No. 564171
RNAScope Probe Mm-Ptn-C3	ACD	Cat No. 486381-C3
Deposited data
Raw and analyzed scRNA-seq data of E11.5 lungs	This paper	GEO: GSE153069
Raw and analyzed bulk RNA-seq data of E13.5 Myocd mutant lungs	Young et al., 2020	GEO: GSE143394
ENCODE E14 lung DNase-hypersensitivity dataset	Yue et al., 2014	http://www.mouseencode.org/
Experimental models: Organisms/strains
Mouse: CD1
Mouse: B6.129-Ctnnb1tm2Kem/KnwJ	The Jackson Laboratory	JAX: 004152
Mouse: B6.129X1-Twist2tm1.1(cre)Dor/J	The Jackson Laboratory	JAX: 008712
Mouse: B6.129P2-Gt(ROSA)26Sortm1(CAG-Brainbow2.1)Cle/J	The Jackson Laboratory	JAX: 017492
Mouse: B6.129(Cg)-Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo/J	The Jackson Laboratory	JAX: 007676
Mouse: B6.FVB-Tg(Acta2-DsRed)1Rkl/J	The Jackson Laboratory	JAX: 031159
Mouse: Tbx4-rtTA	Gift from Wei Shi	N/A
Mouse: tet-O-Cre	The Jackson Laboratory	JAX: 006234
Mouse: VinTS	Laboratory of Sevan Hopyan, Tao et al., 2019	N/A
Mouse: Yap1tm1.1Dupa/J	The Jackson Laboratory	JAX: 027929
Oligonucleotides
Primer: Cre, Forward: GCATTACCGGTCGATGCAACGAGTGATGAG	Devenport Lab	N/A
Primer: Cre, Reverse: GAGTGAACGAACCTGGTCGAAATCAGTGCG	Devenport Lab	N/A
Primer: Tbx4, Forward: CGGCCCCGAATTCACCATGTCTAGA	Zhang et al., 2013	N/A
Primer: Tbx4, Reverse: ACGCGTCGACACTTAGTTACCCGGGGAGCATG	Zhang et al., 2013	N/A
Primer: Ctnnb1-flox, Forward: AAGGTAGAGTGATGAAAGTTGTT	The Jackson Laboratory	Primer no. oIMR1512
Primer: Ctnnb1-flox, Reverse: CACCATGTCCTCTGTCTATTC	The Jackson Laboratory	Primer no. oIMR1513
Primer: Yap1-flox, Forward: AGGACAGCCAGGACTACACAG	The Jackson Laboratory	Primer no. 29878
Primer: Yap1-flox, Reverse: CACCAGCCTTTAAATTGAGAAC	The Jackson Laboratory	Primer no. 29879
Primer: mTmG, Wildtype Forward: AGGGAGCTGCAGTGGAGTAG	The Jackson Laboratory	Primer no. 30298
Primer: mTmG, Mutant Forward: TAGAGCTTGCGGAACCCTTC	The Jackson Laboratory	Primer no. 30297
Primer: mTmG, Common Reverse: CTTTAAGCCTGCCCAGAAGA	The Jackson Laboratory	Primer no. 12177
Software and algorithms
ImageJ	Schneider et al., 2012	https://imagej.nih.gov/ij/
MATLAB	MathWorks	N/A
CellRanger	10× Genomics	Version 2.0.1
R	R Foundation for Statistical Computing	N/A
Python	N/A	N/A
HOMER	Heinz et al., 2010	http://homer.ucsd.edu/homer/
Regulatory Sequence Analysis Tools	Nguyen et al., 2018	http://rsat.sb-roscoff.fr/
DESeq2	Love et al., 2014	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
Seurat	Butler et al., 2018	https://satijalab.org/seurat/
Destiny	Haghverdi et al., 2015	https://www.bioconductor.org/packages/release/bioc/html/destiny.html
Edge	Storey et al., 2019	https://www.bioconductor.org/packages/release/bioc/html/edge.html
clusterProfiler	Yu et al., 2012	https://www.bioconductor.org/packages//2.10/bioc/html/clusterProfiler.html
Other
Opal 520 Reagent Pack	Akoya Biosciences	FP1487001KT
Opal 620 Reagent Pack	Akoya Biosciences	FP1495001KT