| Antibodies |
| Mouse monoclonal to acetylated alpha-tubulin (clone 6–11B-1) |
Millipore Sigma |
T6793 |
| Mouse monoclonal to MUC5AC (clone 45M1) |
ThermoFisher |
MS-145-P0 |
| Purified anti-keratin 5 polyclonal chicken antibody |
BioLegend |
905903 |
| Mouse monoclonal to MUC5B (clone 5B19–2E) |
ThermoFisher |
37–7400 |
| Mouse monoclonal to FOXJ1 (IgG1) |
ThermoFisher |
14–9965-82 |
| Rabbit polyclonal to FOXJ1 |
Millipore Sigma |
HPA005714 |
| Goat anti-Mouse IgG2b Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 |
ThermoFisher |
A-21242 |
| Goat anti-Mouse IgG1 Cross-Adsorbed Secondary Antibody, Alexa Fluor 546 |
ThermoFisher |
A-21123 |
| Goat anti-Mouse IgG2b Cross-Adsorbed Secondary Antibody, Alexa Fluor 546 |
ThermoFisher |
A-21144 |
| Goat anti-Mouse IgG1 Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 |
ThermoFisher |
A-21121 |
| Goat anti-Chicken IgY, |
ThermoFisher |
A-21449 |
| Alexa Fluor 647 Phalloidin |
ThermoFisher |
A22287 |
| Bacterial and virus strains |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| Biological samples |
|
|
| Human bronchial epithelial cells; see Methods Table 1 for detailed donor information) |
Lonza |
CC-2540 |
|
|
|
|
|
|
|
|
|
|
|
|
| Chemicals, peptides, and recombinant proteins |
| Hoechst |
ThermoFisher |
H3570 |
| Recombinant human Activin A |
R&D Systems |
338-AC-010 |
| Recombinant human BMP4 |
Peprotech |
120–05 |
| Recombinant human EGF |
ThermoFisher |
PHG0311 |
| Recombinant human FGF10 |
Sino Biological |
10573-HNAE |
| Recombinant human FGF2 |
ThermoFisher |
PHC9534 |
| CHIR99021 |
Stem Cell Technologies |
72052 |
| Recombinant human HGF |
ThermoFisher |
PHG0254 |
| Human IFN-Alpha (alpha 2A) |
PBL Assay Science |
11100 |
| Recombinant human IFN-Gamma |
Peprotech |
300–02 |
| Recombinant human IL-13 |
Peprotech |
200–13 |
| Recombinant human IL-17A |
ThermoFisher |
PHC9714 |
| Recombinant human Oncostatin M |
Peprotech |
300–10 |
| Recombinant human TNF-alpha |
Peprotech |
300–01A |
| Recombinant human Adiponectin |
Peprotech |
450–24 |
| Recombinant human Leptin |
R&D Systems |
398-LP |
| Trypan Blue Solution |
ThermoFisher |
15250061 |
| Triton X-100 |
Millipore Sigma |
X-100 |
| Tween-20 |
Millipore Sigma |
P2287 |
| 16% Paraformaldehyde |
Fisher Scientific |
50–980-487 |
| Lucifer Yellow CH dipotassium salt |
Millipore Sigma |
L0144 |
| Aphidicolin from Nigrospora sphaerica |
Millipore Sigma |
A0781 |
| Palbociclib (PD0332991) |
Millipore Sigma |
PZ0383 |
| ProLong Diamond AntiFade Mountant |
ThermoFisher |
P36965 |
| OptiPrep Density Gradient Medium |
Millipore Sigma |
D1556 |
| Formalin solution, neutral buffered |
Millipore Sigma |
HT501128 |
| Thymidine |
Millipore Sigma |
T9250 |
| Normal goat serum |
ThermoFisher |
38172 |
| Critical commercial assays |
| Click-iT EdU Pacific Blue Flow Cytometry Assay Kit |
ThermoFisher |
C10418 |
| High-Capacity RNA-to-cDNA Kit |
ThermoFisher |
4388950 |
| Taqman assay: FOXJ1
|
ThermoFisher |
Cat. # 4331182, assay ID Hs00230964_m1 |
| Taqman assay: MUC5B
|
ThermoFisher |
Cat. # 4331182, assay ID Hs00861595_m1 |
| Taqman assay: MUC5AC
|
ThermoFisher |
Cat. # 4331182, assay ID Hs01365616_m1 |
| Taqman assay: SCGB1A1
|
ThermoFisher |
Cat. # 4331182, assay ID Hs00171092_m1 |
| Taqman assay: SPRR1A
|
ThermoFisher |
Cat. # 4331182, assay ID Hs00954595_s1 |
| Taqman assay: SPRR3
|
ThermoFisher |
Cat. # 4331182, assay ID Hs01878180_s1 |
| Taqman assay: KRT6B
|
ThermoFisher |
Cat. # 4331182, assay ID Hs00749101_s1 |
| Taqman assay: EGR1
|
ThermoFisher |
Cat. # 4331182, assay ID Hs00152928_m1 |
| Taqman assay: FOS
|
ThermoFisher |
Cat. # 4331182, assay ID Hs04194186_s1 |
| Taqman assay: SOCS3
|
ThermoFisher |
Cat. # 4331182, assay ID Hs02330328_s1 |
| Taqman assay: FST
|
ThermoFisher |
Cat. # 4331182, assay ID Hs01121165_g1 |
| Taqman assay: HES1
|
ThermoFisher |
Cat. # 4331182, assay ID Hs00172878_m1 |
| Taqman assay: MET
|
ThermoFisher |
Cat. # 4331182, assay ID Hs01565584_m1 |
| Taqman assay: SOX2
|
ThermoFisher |
Cat. # 4331182, assay ID Hs04234836_s1 |
| Taqman assay: PPARG
|
ThermoFisher |
Cat. # 4331182, assay ID Hs01115513_m1 |
| TaqMan assay: 18S ribosomal RNA
|
ThermoFisher |
Cat. # 4448481, assay ID Hs03928985_g1 |
| TaqMan Fast Universal PCR Master Mix (2X), no AmpErase UNG |
ThermFisher |
4366072 |
| RNEasy Plus Mini Kit |
Qiagen |
74134 |
| Deposited data |
| Single cell RNA sequencing: ALI with 17 signaling conditions |
This paper |
GSE246368 |
| Single cell RNA sequencing: Additional ALI data with control, OSM and IFNG |
This paper |
GSE246441 |
| Single cell RNA sequencing: Timecourse of calcium depletion assay |
This paper |
GSE247613 |
|
|
|
| Experimental models: Cell lines |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| Experimental models: Organisms/strains |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| Oligonucleotides |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| Recombinant DNA |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| Software and algorithms |
| ImageJ |
National Institutes of Health |
https://Imagej.nih.gov/ij/
|
| Indrop.py pipeline |
Zilionis et al. (2017) |
https://github.com/swolock/indrops
|
| ImageStudio (version 5.2) |
LI-COR |
https://www.licor.com/bio/image-studio/
|
| Zen Blue |
Carl Zeiss |
https://www.zeiss.com/microscopy/en/products/software/zeiss-zen.html
|
| scSplit |
Xu et al. (2019)58
|
https://github.com/jon-xu/scSplit
|
| Scanpy |
Wolf et al. (2018)59
|
https://scanpy.readthedocs.io/en/stable/index.html
|
| cNMF |
Kotliar et al. (2019)38
|
https://github.com/dylkot/cNMF
|
| Python 3.7 or above |
Anaconda |
https://www.python.org/
|
| Custom code to generate analyses for this paper |
This paper |
http://github.com/AllonKleinLab/paper-data
|
| Other |
| BEGM Bronchial Epithelial Cell Growth Medium BulletKit |
Lonza |
CC-3171 |
| Bronchial Epithelial SingleQuots Kit |
Lonza |
CC-4175 |
| 96-well F-bottom black assay plate |
Greiner |
655076 |
| 12 mm Transwell with 0.4 μm Pore Polyester Membrane Insert, Sterile |
Corning |
3460 |
| 75cm2 U-Shaped Canted Neck Cell Culture Flask with Vent Cap |
Corning |
430641U |
| Micro Cover Glasses, Rectangular, no. 1 |
VWR International |
48393–026 |
| Frosted Micro Slides |
VWR International |
48312–004 |
| Trypsin-EDTA (0.25%) |
ThermoFisher |
25200056 |
| Phosphate buffered saline, pH 7.4 |
ThermoFisher |
10010072 |
| Fetal bovine serum |
ThermoFisher |
16000044 |
| Hank’s Balanced Salt Solution |
ThermoFisher |
14025092 |
| Bovine serum albumin |
ThermoFisher |
B14 |
| Trypsin Neutralizer Solution |
ThermoFisher |
R002100 |
| MEM |
ThermoFisher |
10370088 |
| DMEM, high glucose |
ThermoFisher |
11965175 |
