Growth Protocol:	Human lung organoids (HLO) were derived from hPSCs as previously described (Carvalho et al., 2019; Jacob et al., 2017; Miller et al., 2019), with minor modifications. Briefly, H9 hPSCs were maintained in mTeSR Plus media and were seeded on Day 0 onto matrigel (Corning) coated surface. On Days 1-4 cells were treated with 100 ng/mL Activin A and increasing concentration of defined FBS (dFBS, HyClone) in RPMI 1640 medium (Thermo), to induce definitive endoderm formation (Day 1: 3 µM CHIR99021 and no dFBS; Day 2: 0.2% dFBS; Days 3-4: 2% dFBS). On Day 4, cells were >95% double positive for CXCR4/CD184 and c-Kit/CD117 as determined by flow cytometry. On Days 5-9 cells were treated with anterior foregut induction medium, containing 10 µM SB431542, 100 nM LDN193189, 2 µM CHIR99021, 1 µM SAG, 500 ng/mL FGF4 in Foregut Basal Medium (Advanced DMEM, 1x B27, 1x N2, 10 mM HEPES, 1x Glutagro (all Thermo), 50 µg/mL ascorbic acid (Sigma), 0.4 µM monothioglycerol (Sigma)). On Day 9, anterior foregut spheroids were harvested by gentle pipetting and transferred into an ultra-low attachment plate, in Lung Organoid Medium I (3 µM CHIR99021, 10 ng/mL BMP4, 10 ng/mL FGF7, 10 ng/mL FGF10, 50 nM all-trans retinoic acid, in Foregut Basal Medium). The medium was changed every two days until Day 15. On Day 15, the medium was changed to Lung Organoid Medium II (3 µM CHIR99021, 10 ng/mL FGF7, 10 ng/mL FGF10, in Foregut Basal Medium). On Day 25 the organoids were embedded in matrigel, in transwell inserts, and grown in Lung Organoid Medium III (3 µM CHIR99021, 10 ng/mL FGF7, 10 ng/mL FGF10, 50 nM dexamethasone (Sigma), 100 µM 8-bromo-cAMP (Sigma), 100 µM IBMX (Sigma), in Foregut Basal Medium). The medium was changed every 3 days. The CHIR99021 was withdrawn on Days 35-42. All media components were from Stem Cell Technologies unless noted otherwise.
Treatment Protocol:	-
Extract Protocol:	RNA was extracted using Quick-RNA 96 Kit (Zymo) with on-column DNaseI treatment.
Library Construction Protocol:	QuantSeq FWD Kit (with UMI module, Lexogen) was used for RNAseq library preparation.

Molecule Type:	Total RNA
Library Source:
Library Layout:	SINGLE
Library Strand:	Reverse
Platform:	ILLUMINA
Instrument Model:	Illumina HiSeq 4000
Strand-Specific:	Specific

Data Resource	GEN Sample ID	GEN Dataset ID	Project ID	BioProject ID	Sample ID	Sample Name	BioSample ID	Sample Accession	Experiment Accession	Release Date	Submission Date	Update Date	Species	Race	Ethnicity	Age	Age Unit	Gender	Source Name	Tissue	Cell Type	Cell Subtype	Cell Line	Disease	Disease State	Development Stage	Mutation	Phenotype	Case Detail	Control Detail	Growth Protocol	Treatment Protocol	Extract Protocol	Library Construction Protocol	Molecule Type	Library Layout	Strand-Specific	Library Strand	Spike-In	Strategy	Platform	Instrument Model	Cell Number	Reads Number	Gbases	AvgSpotLen1	AvgSpotLen2	Uniq Mapping Rate	Multiple Mapping Rate	Coverage Rate