REAGENT or SOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit anti TTF-1	Abcam	Cat# ab133638;RRID: AB_2734144
Rabbit anti Napsin A	Abcam	Cat# ab129189; RRID:AB_11143020
Rabbit anti CK-7	Abcam	Cat# ab181598;RRID: AB_2783822
Rabbit anti P63	Abcam	Cat# ab124762; RRID: AB_10971840
Rabbit anti P40	Abcam	Cat# ab273135; RRID: AB_2927663
Rattbit anti CK5/6	Abcam	Cat# ab52635;RRID: AB_869890
Rattbit anti CD56	Abcam	Cat# ab220360; RRID: AB_2927664
Rattbit anti Synaptophysin	Abcam	Cat# ab32127; RRID: AB_2286949
Rabbit anti Chromogranin	Abcam	Cat# ab254322; RRID: AB_2910555
Rabbit anti EGF Receptor (L858R Mutant Specific) (43B2)	ewEast	Cat# 26082; RRID: AB_2629297
Goat Anti-Rabbit IgG H&L (HRP)	Abcam	Cat# ab205718;RRID: AB_2819160
Goat Anti-Mouse IgG H&L (HRP)	Abcam	Cat# ab205719;RRID: AB_2755049
Goat Anti-Rabbit IgG H&L (Alexa Fluor® 488)	Abcam	Cat# ab150077;RRID: AB_2630356
Biological samples
Human tumor tissue samples	This study	N/A
Human effusion samples	This study	N/A
Chemicals, peptides, and recombinant proteins
B27 supplement (-Vit A)	GIBCO	Cat# 17504044
N2 supplement	GIBCO	Cat# 17502048
GlutaMax	GIBCO (ThermoFisher)	Cat# 35050061
Wnt3A	Novoprotein	Cat# C06D
R-Spondin1	Novoprotein	Cat# CX83
Noggin	Novoprotein	Cat# CB89
EGF	Peprotech	Cat# AF-100-15
FGF-basic	Peprotech	Cat# 100-18C
Y27632	MCE	Cat# HY-10071
A83-01	Sigma-Aldrich	Cat# SML0788
DMEM/F12	GIBCO	Cat# 12634028
Green Chromogen	Leica	Cat# DC9913
BOND IHC polymer detection kit	Leica	Cat# DS9800
FBS	GIBCO	Cat# 10099141
PBS	Sangon	Cat# E607008-0500
HEPES	Sigma-Aldrich	Cat# H6147
HBSS	GIBCO	Cat# 14175095
Penicillin-Streptomycin	Sigma-Aldrich	Cat# V900929
Amphotericin B	GIBCO	Cat# 15290026
Cell recovery solution	Corning	Cat# 354253
Matrigel	Corning	Cat# 356231
DNase	Sigma-Aldrich	Cat# 11284932001
Collagenase/dispase	Roche	Cat# 10269638001
BOND IHC polymer detection kit	Leica	Cat# DS9800
Afatinib	MCE	Cat# HY-10261
Osimertinib	MCE	Cat# HY-15772
Erlotinib	MCE	Cat# HY-50896
Gefitinib	MCE	Cat# HY-50895
Dacomitinib	MCE	Cat# HY-13272
Almonertinib	MCE	Cat# HY-112823
Icotinib	MCE	Cat# HY-15164A
SAF-189s	Fochon Pharmaceuticals	N/A
Crizotinib	MCE	Cat# HY-50878
Alectinib	MCE	Cat# HY-13011
Ceritinib	MCE	Cat# HY-15656
Brigatinib	MCE	Cat# HY-12857
Lorlatinib	MCE	Cat# HY-12215
Entrectinib	MCE	Cat# HY-12678
Dabrafenib	MCE	Cat# HY-14660
Pyrotinib	MCE	Cat# HY-104065
Larotrectinib	MCE	Cat# HY-12866
Savolitinib	MCE	Cat# HY-15959
Bozitinib	MCE	Cat# HY-125017
BLU667	MCE	Cat# HY-112301
Docetaxel	MCE	Cat# HY-B0011
Paclitaxel	MCE	Cat# HY-B0015
Gemcitabine	MCE	Cat# HY-17026
Etoposide	MCE	Cat# HY-13629
Pemetrexed	MCE	Cat# HY-10820
Cisplatin	MCE	Cat# HY-17394
Carboplatin	MCE	Cat# HY-17393
Irinotecan	MCE	Cat# HY-16562
Experimental models:Organisms/Strains
Human lung cancer organoid samples	This study	N/A
Software and algorithms
R	R Development Core Team, 2008	https://www.r-project.org/
Critical commercial assays
CellTiter-Glo® 3D Cell Viability Assay	Promega	Cat# G9681
Deposited data
DNA sequencing	This paper	National Genomics Data Center (HRA003231)
LC-MS/MS	This paper	ProteomeXchange Consortium (PXD037076)
Others
Cytation 5 Cell Imaging Multimode Reader	Agilent	Cat# BTCYT5M
Fluorescence microscope	Olympus	Cat# 29560
BOND-III automated stainer	Leica	Cat# 22.2201