REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
DAPI	BioLegend	Cat # 422801
PI	BioLegend	Cat # 421301
anti-human CD45 FITC	BioLegend	Cat # 304054; RRID:AB_2564154
anti-human CD4 BV605	BioLegend	Cat # 344710; RRID:AB_2044010
anti-human CD19 Pacific blue	BioLegend	Cat # 302224; RRID:AB_493653
anti-human CD11b APC	BioLegend	Cat # 301310; RRID:AB_314162
anti-human CD8 PE-CY7	BioLegend	Cat # 344712; RRID:AB_2044008
anti-mouse CD45.2 APC	eBioscience	Cat # 17-0454-82; RRID: AB_469400
anti-mouse CD20 PE	Biolegend	Cat # 150410; RRID:AB_2566779
anti-human CD19	ZSGB-Bio	Cat # ZM-0038
Anti-human CD20	abcam	Cat #ab9475; RRID: AB_307267
anti-human CD4	ZSGB-Bio	Cat # ZA-0418; RRID: AB_2890106
anti-human CD8	ZSGB-Bio	Cat # ZA-0508; RRID:AB_2890107
anti-human CXCL13	Novus	Cat # NBP2-16041; RRID: AB_2892564
Anti-human KI67	Gene Tech	Cat # GT209402
Anti-human CD138	Gene Tech	Cat # GT245102
Anti-human COL1	Proteintech	Cat # 67288-1; RRID: AB_2882554
Anti-human CD21	abcam	Cat # ab75985; RRID: AB_1523292
Anti-human PNAD	abcam	Cat # ab111710; RRID: AB_10861722
Anti-mouse IL-21R	bioxcell	Cat # BE0258; RRID: AB_2687737
Anti-mouse CD3	abcam	Cat # ab16669; RRID: 443425
Anti-mouse CD19	abcam	Cat # ab245235; RRID: 2895109
Anti-mouse CD20	bioxcell	Cat # BE0356; RRID: 2894775
Chemicals, peptides, and recombinant proteins
RiboLock RNase inhibitor	invitrogen	Cat # EO0384
SuperScript™ III Reverse Transcriptase	Invitrogen	Cat # 18080-085
Exonuclease I	NEB	Cat #M0293
Exonuclease I 10x Buffer	NEB	Cat #B0293S
NEBNext® mRNA Second Strand Synthesis Module	NEB	Cat #E6111L
HiScribe™ T7 High Yield RNA Synthesis Kit	NEB	Cat #E2040S
RNA Fragmentation Reagents	Ambion	Cat # AM8740
AffinityScript Multi-Temp RT	Agilent	Cat # 600107
Kapa HiFi HotStart PCR ReadyMix	Kapa Biosystems	Cat # KK2602
ATP solution	thermo	Cat #R0441
T4 RNA Ligase 1 (ssRNA Ligase)	NEB	Cat #M0204L
dNTPs	Solarbio	Cat # PC2300
VAHTS ® DNA Clean Beads	Vazyme	Cat #N411-02
Fast SYBR Green master mix	accurate biology (AG)	Cat # AG11719
Absolute ethanol	Sigma	Cat #E7023-1L
nuclease-free water	thermo	Cat # AM9932
Equalbit 1 × dsDNA HS Assay Kit	Vazyme	Cat # EQ121-01
TapeStation High Sensitivity D1000 Reagent	Agilent	Cat # 5067-5583
PANO6-plexIHCkit	Panovue	Cat # 102C4100100
Tissue enzymatic reagent
DNase I	Roche	Cat #10104159001
Collagenase IV	Worthington	Cat # LS004188
Experimental models: Organisms
KPC (KrasG12D, p53-CKO, Sftpc-creER) mice	Prof. Shun Li	N/A
CD4CRE; Bcl6fl/fl mice	Prof. Nengming Xiao	N/A
Experimental models: Cell lines
LLC (Lewis Lung Carcinoma)	ATCC	Cat # CRL-1642; RRID: CVCL_4358
Critical commercial assays
10X Chromium Next GEM Single Cell 5′Kit v2	10X Genomics	Cat # PN-1000287
10X Library Construction Kit	10X Genomics	Cat # PN-1000190
10X Chromium Next GEM chip K Single Cell Kit	10X Genomics	Cat # PN-1000287
10X Dual Index Kit TT Set A	10X Genomics	Cat # PN-1000215
10X Chromium Single Cell Human TCR Amplification Kit	10X Genomics	Cat # PN-1000252
Deposited data
TCGA LUAD dataset	XENA data portal	http://xena.ucsc.edu/
Invasive and pre-invasive RNA-seq dataset	(Haiquan et al., 2019)	EGAD00001005479
This Paper	NGDC GSA for human	HRA002961
Jermaine_Goveia_2020 (fastq)	ArrayExpress	E-MTAB-6308
He_Fan_2021 (fastq)	NGDC GSA	CRA001963
Kim_Lee_2020 (processed)	GEO	GSE131907
Leader_Merad_2021 (processed)	GEO	GSE154826
Maynard_Bivona_2020 (fastq)	SRA	PRJNA591860
Lambrechts_Thienpont_2018 (fastq)	ArrayExpress	E-MTAB-6653
Stefan_Salcher_2023 (processed)	Zenodo	https://doi.org/10.5281/zenodo.6411867
Software and algorithms
R (v4.1.3)	(R Core Team, 2013)54	https://cran.r-project.org/bin/
HISAT2 (v2.1.0)	(Daehwan et al., 2015)55	http://daehwankimlab.github.io/hisat2
CellRanger (v7.0.0)	10X Genomics	http://10xgenomics.com
Python (v3.8.1)	(Guido et al., 2009)56	https://www.python.org/downloads/release/python-379/
MetaCell (v0.3.41)	(Baran et al., 2019)57	https://github.com/tanaylab/metacell/
Scanpy (v1.9.1)	(F. Alexander et al., 2018)58	https://github.com/scverse/scanpy
scvi-tools (v1.1.0)	(Adam Gayoso et al., 2022)59	https://scvi-tools.org/
Monocle 2 (v2.4.0)	(Xiaojie Qiu et al., 2017)60	https://github.com/cole-trapnell-lab/monocle-release
AUCell (1.4.1)	(Aibar et al., 2017)61	https://github.com/aertslab/AUCell
Immunarch (v0.7.0)	(Vadim et al.,2022)62	https://immunarch.com/
scRepertoire (v1.0.2)	(Borcherding N et al.,2022)63	https://github.com/ncborcherding/scRepertoire
Toomanycells (v2.2.0.0)	(Gregory et al.,2020)64	https://github.com/GregorySchwartz/too-many-cells
clusterProfiler (v4.4.4)	(Guangchuang et al.,2012)65	https://github.com/YuLab-SMU/clusterProfiler
ssGSEA (GSVA package) (v3.12)	(Hänzelmann et al.,2013)66	https://www.bioconductor.org/packages/release/bioc/html/GSVA.html
QuPath (v0.3.0)	(Humphries et al.,2021)67	https://qupath.github.io/
Halo (v3.3)	Indica labs	https://www.indicalab.com/halo
FACSDiva (v8.0.3)	BD Biosciences	NA
FlowJo (v10)	BD Biosciences	NA