| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit polyclonal anti-SFTPC | Millipore | Cat# AB3786; RRID: AB_91588 |
| Rabbit monoclonal anti-FABP4 | Abcam | Cat# ab92501; RRID: AB_10562486 |
| Mouse monoclonal anti-CD68 | BioLegend | Cat# 916104; RRID: AB_2616797 |
| Rat monoclonal anti-FOXP3 | Thermo Fisher Scientific | Cat# 14-4776-80; RRID: AB_467553 |
| Mouse monoclonal anti-PanCK | Abcam | Cat# ab7753; RRID: AB_306047 |
| Rabbit monoclonal anti-CD47 | Abcam | Cat# ab226837 |
| Rabbit recombinant anti-PD-L1 | Abcam | Cat# ab213524; RRID: AB_2857903 |
| Rabbit polyclonal anti-CTSH | Proteintech | Cat# 10315-1-AP; RRID: AB_2087534 |
| Rabbit polyclonal anti-GPR116 | ImmunoWay Biotechnology Company | Cat# YT1960 |
| Rabbit monoclonal anti-LPCAT1 | Abcam | Cat# ab214034 |
| Rabbit polyclonal anti-PABPC1 | Cell Signaling Technology | Cat# 4992; RRID: AB_10693595 |
| Rabbit polyclonal anti-MIF | Atlas Antibodies | Cat# HPA041219; RRID: AB_10794268 |
| Rabbit polyclonal anti-CD4 | Abcam | Cat# ab133616; RRID: AB_2750883 |
| Mouse monoclonal anti-MHC Class II | Abcam | Cat# ab55152; RRID: AB_944199 |
| Biological samples | ||
| Lung cancer tissue and normal lung tissue collection (n = 22) | West China Hospital, Sichuan University | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| Bovine Serum Albumin (BSA) | Roche | Cat# 10711454001 |
| Collagenase I | Biosharp | BS163 |
| Collagenase IV | Biosharp | BS165 |
| DAPI (4′,6-diamidino-2-phenylindole) | Thermo Fisher Scientific | R37606 |
| Dimethyl Sulfoxide (DMSO) | MP Biomedicals | Cat# 196055 |
| Fetal Bovine Serum (FBS) | Gibco | Cat# 10099-141C |
| Formalin | Fisher Scientific | Cat# SF98-4 |
| Hank’s Balanced Salt Solution (HBSS) | Gibco | Cat# 14175095 |
| Phosphate Buffered Saline (PBS) | Bio-Channel | BC-BPBS-01 |
| Parafin | Sigma Aldrich | P3683-1KG |
| Red blood lysis buffer | Biosharp | BL503A |
| Critical commercial assays | ||
| Chromium™ Single Cell 3′ Library & Gel Bead Kit v2 | 10X Genomics | PN-120237 |
| Chromium™ Single Cell A Chip Kit | 10X Genomics | PN-120236 |
| Chromium™ Single Cell 3′ Library & Gel Bead Kit v3 | 10X Genomics | PN-1000075 |
| Chromium™ Single Cell B Chip Kit | 10X Genomics | PN-1000073 |
| Chromium™ i7 Multiplex Kit | 10X Genomics | PN-120262 |
| Dead Cell Removal Kit | Miltenyi Biotec | Cat# 130-090-101 |
| DAB substrate kit | Abcam | Cat# ab64238 |
| GeneReadTM DNA FFPE Kit | QIAGEN | Cat# 180134 |
| NEBNext Ultra DNA Library Prep kit | NEB | E7370S |
| KAPA library quantification universal kit | Roche | Cat# 07960140001 |
| OncoScreen™ Plus Cancer Mutation Profiling Tissue Kit | Guangzhou Burning Rock Biotech | LK103 (C) |
| Oncology Multi-Gene Variant Assay | Geneplus Medical Laboratory | BE201911001 |
| Qubit® dsDNA BR Assay Kit | Invitrogen | Q32850 |
| Qubit® dsDNA HS Assay Kit | Invitrogen | Q32854 |
| The Opal Polaris 7-Color Manual IHC Kit | Perkin Elmer | NEL861001KT |
| Deposited data | ||
| TCGA LUAD bulk RNA-seq | The Cancer Genome Atlas (TCGA) | https://portal.gdc.cancer.gov/projects/TCGA-LUAD |
| GSVA Hallmark gene sets | The Molecular Signatures Database (MsigDB) | https://www.gsea-msigdb.org/gsea/msigdb/collections.jsp#H |
| scRNA-seq data from Kim N et al.15 | Gene Expression Omnibus (GEO) | GSE131907 |
| Software and algorithms | ||
| Burrows-Wheeler Aligner (BWA) | Li and Durbin, 200956 | http://bio-bwa.sourceforge.net/ |
| MuTect2 1.1.4 | Benjamin et al., 201957 | https://gatk.broadinstitute.org/hc/en-us/articles/4414594392347-Mutect2 |
| GATK 4.1.2.0 | Benjamin et al., 201957 | https://github.com/broadinstitute/gatk/releases |
| Cellranger 3.0 | 10x Genomics | https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest |
| Seurat 4.0.0 | Hao et al., 202158 | https://satijalab.org/seurat/ |
| SingleR | Bioconductor | https://www.bioconductor.org/packages/release/bioc/html/SingleR.html |
| inferCNV | Bioconductor | http://www.bioconductor.org/packages/release/bioc/html/infercnv.html |
| Monocle 2.0 | Qiu et al., 201759 | https://github.com/cole-trapnell-lab/monocle-release |
| GSVA 1.38.2 | Bioconductor | https://www.bioconductor.org/packages/release/bioc/html/GSVA.html |
| survival package | R | https://cran.r-project.org/web/packages/survival/ |
| survminer package | R | https://cran.r-project.org/web/packages/survminer/ |
| CellphoneDB2 | Efremova et al., 202060 | https://www.cellphonedb.org/ |
| GraphPad Prism 8.0.2 | GraphPad Software lnc. | http://www.graphpad.com/scientific-software/prism/ |
| IBM SPSS statistics 25 | IBM | https://www-01.ibm.com/software/analytics/spss |
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