Reagent/Resource	Reference or Source	Identifier or Catalog Number
Experimental models
WT (Mus musculus)	Charles River Laboratory	C57BL/6JCrl
mTmG (M. musculus)	Jackson Laboratory	B6.129 (Cg)‐Gt (ROSA)26Sor tm4 (ACTB‐tdTomato‐EGFP)Luo /J
PDGFRαEGFP (M. musculus)	Jackson Laboratory	B6.129S4‐Pdgfra tm11(EGFP)Sor /J
PDPNEGFP (M. musculus)	Jackson Laboratory	B6;D2‐Tg (Pdpn,‐EGFP)16Dobb /J
UBI‐GFP (M. musculus)	Jackson Laboratory	(C57BL/6‐Tg(UBC‐GFP)30Scha/J
Scgb1a1 mCherry Sftpc YFP double transgenic mice (M. musculus)	Salwig et al (2019)	SPC‐2A-YFP‐2A-tTA‐N, CCSP‐2A-mCherry‐2A-tTA‐C
BASC viewer (M. musculus)	Salwig et al (2019)	SPC‐2A-YFP‐2A-tTA‐N, CCSP‐2A-mCherry‐2A-tTA‐C, tetObi lacZ/huGFP
BASC v‐race (M. musculus)	Salwig et al (2019)	SPC‐2A-YFP‐2A-tTA‐N, CCSP‐2A-mCherry‐2A-tTA‐C, tetObiluc/Cre, Rosa26stopflox‐lacZ
Antibodies
Anti‐goat Alexa Fluor® 488	Thermo Scientific	Cat #A‐21467
Anti‐goat Alexa Fluor® 647	Thermo Scientific	Cat #A‐21469
Anti‐mouse Alexa Fluor® 488	Thermo Scientific	Cat #A‐21206
Anti‐rabbit Alexa Fluor® 555	Thermo Scientific	Cat #A‐31572
Biotinylated rat anti‐mouse CD16/32	BD Bioscience	Clone 2.4G2
Biotinylated rat anti‐mouse CD31	BD Bioscience	Clone MEC 13.3
Biotinylated rat anti‐mouse CD45	BD Bioscience	Clone 30‐F11
Goat influenza A virus HA	Abcam	Cat# ab20841
Goat SCGB1A1	Santa Cruz Biotechnology	Clone T‐18
Mouse Connexin 43	Thermo Scientific	Clone CX‐1B1
Mouse IgG1 Ctl	Abcam	Clone CT6
Mouse influenza A virus NP FITC	Abcam	Cat #ab128193
Mouse β‐IV tubulin	Abcam	Clone ONS.1A6
Rabbit Mature SPB	Seven Hills	Cat #WRAB‐48604
Rabbit pro‐SPB	Seven Hills	Cat #WRAB‐55522
Rabbit purified pro‐SPC	Millipore	Cat #AB3786
Rabbit SPA	Abcam	Cat #ab115791
Rabbit β‐actin	Abcam	Cat #ab8227
Rat CD11c FITC	BioLegend	Clone N4189
Rat CD206 Alexa Fluor® 488	BioLegend	Clone MMR
Rat CD24 PE‐Cy7	BioLegend	Clone M1/69
Rat CD31 Alexa Fluor® 488, PE or Pacific Blue	BioLegend	Clone 390
Rat CD326 (EpCAM) APC‐Cy7 or APC‐eF780	BioLegend	Clone G8.8
Rat CD45 FITC, APC‐C7 or Horizon™ V450	BD Biosciences	Clone 30‐F11
Rat CD45 V500	BioLegend	Clone 30‐F11
Rat GR1 PE‐Cy7	BioLegend	Clone RB6‐8C5
Rat IgG2a Ctl	BioLegend	Clone RTK2758
Rat Ly6A/E (SCA‐1) APC or Pacific Blue	BioLegend	Clone D7
Rat Ly6G APC	BioLegend	Clone 1A8
Rat Siglec‐F APC‐Cy7	BD Biosciences	Clone E50‐2440
Siglec‐F eFluor 660 and	Thermo Scientific	Clone 1RNM44N
Swine anti‐rabbit IgG	Agilent	Cat #F0054
Syrian hamster IgG Ctl	BioLegend	Clone SHG‐1
Syrian hamster PDPN APC	BioLegend	Clone 8.1.1
Oligonucleotides and other sequence‐based reagents
5S rRNA	This study	FP 5′‐TCTCGGAAGCTAAGCAGGGTC‐3′; RP 5′‐AGCCTACAGCACCCGGTATTC‐3′
Apc	This study	FP 5′‐CATGGACCAGGACAAAAACC‐3′ RP5′‐GAACACACACAGCAGGACAGA‐3′
Foxj1	This study	FP 5′‐GAGCCAGGCCTCACATTCG‐3′ RP 5′‐CGCTGGTAACCCAGACTCC‐3′
Hopx	This study	FP 5′‐CAACAAGGTCAACAAGCACCC‐3′ RP 5′‐GCGCTGCTTAAACCATTTCTGC 3′
Ifnb	This study	FP 5′‐GTTACACTGCCTTTGCCATCC‐3′ RP 5′‐GTGGAGTTCATCCAGGAGACG‐3′
miR‐142-3p	This study	FP 5′‐ACTCCAGCTGGGTGTAGTGTTTC CTACTT‐3′; stem loop reverse 5′‐CTCAAC TGGTGTCGTGGAGTCGGCAATTCAGTTGAGTCCATAAA‐3′
miRNA	This study	Universal reverse 5′ TCAACTGGTG TCGTGGAGTCG‐3′
Muc5ac	This study	FP 5′‐AGGACCACTGTATTGCTGGC‐3′ RP 5′‐TCCAGAACATGTGTTGGTGC‐3′
NP	This study	FP 5′‐ACGAAGGTGGTCCCAAGAGG‐3′ RP 5′‐GATTTGGCCCGCAGATGCC‐3′
Rps‐18	This study	FP 5′‐CCGCCATGTCTCTAGTGATCC‐3′ RP 5′‐TTGGTGAGGT CGATGTCTGC‐3′
Sftpc	This study	FP 5′‐GGAGGAAGGGCATGATACTGG‐3′ RP 5′‐TTCTACCGACCCTGTGGATGC‐3′
miR‐142-3p‐specific morpholino	Gene Tools, LLC	5′TCCATAAAGTAG GAAACACTACACC‐3′
Scramble morpholino	Gene Tools, LLC	5′‐CCTCTTACCTCAGT TACAATTTATA‐3′
Chemicals, enzymes, and other reagents
Biotin‐binder magnetic beads	Life Technologies	Cat #11947
Insulin‐Transferrin‐Selenium	Biozym	Cat #41400‐045
l‐Glutamine	Gibco	Cat #11539876
Matrigel matrix	Corning	Cat #356231
Paraformaldehyde	Merck	Cat #104005
αMEM	Gibco	Cat #41061029
DMEM	Gibco	Cat #12491023
Dispase	Corning	Cat #354235
DNase I	Serva	Cat #18535.01
Heparin	Stem cell Technologies	Cat #07980
Software
DIVA software (v8.02)	https://www.bdbiosciences.com
FlowJo (v6.10.1)	https://www.flowjo.com
GraphPad PRISM 5 (v5.01)	https://www.graphpad.com
ImageJ (v1.53c)	https://imagej.nih.gov/ij
R (v3.3.3)	https://cran.r-project.org/web/packages/Seurat/index.html