KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| TotalSeq™-A0062 anti-human CD10 Antibody | Biolegend | Cat #312231; RRID: AB_2734286 |
| TotalSeq™-A0145 anti-human CD103 (Integrin aE) Antibody | Biolegend | Cat #350231; RRID: AB_2800933 |
| TotalSeq™-A0068 anti-human CD105 Antibody | Biolegend | Cat #323221; RRID: AB_2750350 |
| TotalSeq™-A0398 anti-human CD115 (CSF-1R) Antibody | Biolegend | Cat #347325; RRID: AB_2783237 |
| TotalSeq™-A0061 anti-human CD117 (c-kit) Antibody | Biolegend | Cat #313241; RRID: AB_2734287 |
| TotalSeq™-A0161 anti-human CD11b Antibody | Biolegend | Cat #301353; RRID: AB_2734249 |
| TotalSeq™-A0053 anti-human CD11c Antibody | Biolegend | Cat #371519; RRID: AB_2749971 |
| TotalSeq™-A0064 anti-human CD123 Antibody | Biolegend | Cat #306037; RRID: AB_2749977 |
| TotalSeq™-A0390 anti-human CD127 (IL-7Rα) Antibody | Biolegend | Cat #351352; RRID: AB_2734366 |
| TotalSeq™-A0158 anti-human CD134 (OX40) Antibody | Biolegend | Cat #350033; RRID: AB_2783245 |
| TotalSeq™-A0055 anti-human CD138 (Syndecan-1) Antibody | Biolegend | Cat #356533; RRID: AB_2749973 |
| TotalSeq™-A0051 anti-human CD14 Antibody | Biolegend | Cat #367131; RRID: AB_2734412 |
| TotalSeq™-A0128 anti-human CD140a (PDGFRα) Antibody | Biolegend | Cat #323509; RRID: AB_2750354 |
| TotalSeq™-A0129 anti-human CD140b (PDGFRβ) Antibody | Biolegend | Cat #323609; RRID: AB_2783192 |
| TotalSeq™-A0163 anti-human CD141 (Thrombomodulin) Antibody | Biolegend | Cat #344121; RRID: AB_2783229 |
| TotalSeq™-A0134 anti-human CD146 Antibody | Biolegend | Cat #361017; RRID: AB_2750355 |
| TotalSeq™-A0151 anti-human CD152 (CTLA-4) Antibody | Biolegend | Cat #369619; RRID: AB_2734423 |
| TotalSeq™-A0083 anti-human CD16 Antibody | Biolegend | Cat #302061; RRID: AB_2734255 |
| TotalSeq™-A0149 anti-human CD161 Antibody | Biolegend | Cat #339945; RRID: AB_2749998 |
| TotalSeq™-A0358 anti-human CD163 Antibody | Biolegend | Cat #333635; RRID: AB_2750343 |
| TotalSeq™-A0206 anti-human CD169 (Sialoadhesin, Siglec-1) Antibody | Biolegend | Cat #346011; RRID: AB_2750011 |
| TotalSeq™-A0140 anti-human CD183 (CXCR3) Antibody | Biolegend | Cat #353745; RRID: AB_2749993 |
| TotalSeq™-A0144 anti-human CD185 (CXCR5) Antibody | Biolegend | Cat #356937; RRID: AB_2750356 |
| TotalSeq™-A0050 anti-human CD19 Antibody | Biolegend | Cat #302259; RRID: AB_2734256 |
| TotalSeq™-A0071 anti-human CD194 (CCR4) Antibody | Biolegend | Cat #359423; RRID: AB_2749979 |
| TotalSeq™-A0141 anti-human CD195 (CCR5) Antibody | Biolegend | Cat #359135; RRID: AB_2749994 |
| TotalSeq™-A0143 anti-human CD196 (CCR6) Antibody | Biolegend | Cat #353437; RRID: AB_2750534 |
| TotalSeq™-A0148 anti-human CD197 (CCR7) Antibody | Biolegend | Cat #353247; RRID: AB_2750357 |
| TotalSeq™-A0160 anti-human CD1c Antibody | Biolegend | Cat #331539; RRID: AB_2734326 |
| TotalSeq™-A0100 anti-human CD20 Antibody | Biolegend | Cat #302359; RRID: AB_2749984 |
| TotalSeq™-A0205 anti-human CD206 (MMR) Antibody | Biolegend | Cat #321143; RRID: AB_2750010 |
| TotalSeq™-A0152 anti-human CD223 (LAG-3) Antibody | Biolegend | Cat #369333; RRID: AB_2749999 |
| TotalSeq™-A0368 anti-human CD226 (DNAM-1) Antibody | Biolegend | Cat #338335; RRID: AB_2783220 |
| TotalSeq™-A0180 anti-human CD24 Antibody | Biolegend | Cat #311137; RRID: AB_2750374 |
| TotalSeq™-A0189 anti-human CD244 (2B4) Antibody | Biolegend | Cat #329527; RRID: AB_2750007 |
| TotalSeq™-A0085 anti-human CD25 Antibody | Biolegend | Cat #302643; RRID: AB_2734258 |
| TotalSeq™-A0356 anti-human CD254 (TRANCE, RANKL) Antibody | Biolegend | Cat #347509; RRID: AB_2750377 |
| TotalSeq™-A0396 anti-human CD26 Antibody | Biolegend | Cat #302720; RRID: AB_2734261 |
| TotalSeq™-A0154 anti-human CD27 Antibody | Biolegend | Cat #302847; RRID: AB_2750000 |
| TotalSeq™-C0170 anti-human CD272 (BTLA) Antibody | Biolegend | Cat #344527; RRID: AB_2800919 |
| TotalSeq™-A0008 anti-human CD273 (B7-DC, PD-L2) Antibody | Biolegend | Cat #329619; RRID: AB_2734321 |
| TotalSeq™-A0007 anti-human CD274 (B7-H1, PD-L1) Antibody | Biolegend | Cat #329743; RRID: AB_2749959 |
| TotalSeq™-A0171 anti-human/mouse/rat CD278 (ICOS) Antibody | Biolegend | Cat #313555; RRID: AB_2800824 |
| TotalSeq™-A0088 anti-human CD279 (PD-1) Antibody | Biolegend | Cat #329955; RRID: AB_2734322 |
| TotalSeq™-A0386 anti-human CD28 Antibody | Biolegend | Cat #302955; RRID: AB_2783159 |
| TotalSeq™-A0369 anti-human CD29 Antibody | Biolegend | Cat #303027; RRID: AB_2783160 |
| TotalSeq™-A0034 anti-human CD3 Antibody | Biolegend | Cat #300475; RRID: AB_2734246 |
| TotalSeq™-A0124 anti-human CD31 Antibody | Biolegend | Cat #303137; RRID: AB_2750360 |
| Purified anti-human CD298 Antibody | Biolegend | Cat # 341711; RRID: AB_2876646 |
| Purified anti-human β2-microglobulin Antibody | Biolegend | Cat #316302; RRID: AB_492835 |
| Anti-human CD10 (clone 200103) | R&D systems | Cat#: MAB1126; RRID: AB_2250882 |
| Anti-Human DC-LAMP (clone 1010E1.01) | Novus Biologicals | Cat#: DDX0191P; RRID: AB_2827532 |
| Pan-cytokeratin (clone AE1/AE3) | Dako | Cat#: M3515; RRID: AB_2132885 |
| PD-L1 (clone E1L3N) | Cell Signaling Tech | Cat#: 13684S; RRID: AB_2687655 |
| PD1 (clone EPR4877(2)) | Abcam | Cat#: ab137132 |
| Anti-Human CD20 (clone L26) | Dako | Cat#: 0755; RRID: AB_2282030 |
| CD138 (clone MI15) | Dako | Cat#: M7228; RRID: AB_2254116 |
| Anti-Human CD68 (clone KP1) | Dako | Cat#: M081401–2; RRID: AB_2750584 |
| CD1C (clone 2F4) | Abcam | Cat#: ab156708; RRID: AB_2889187 |
| FABP4 polyclonal | R&D | Cat#: AF3150; RRID: AB_2278261 |
| Anti-human CD326 (clone 9C4) | Biolegend | Cat#:324202; RRID: AB_756076 |
| Anti-human CD45 (clone HI30) | Fluidigm | Cat#:3089003B; RRID: AB_2661851 |
| Anti-human CD19 (clone HIB19) | Biolegend | Cat#:302202; RRID: AB_314232 |
| Anti-human CD38 (clone HB-7) | Biolegend | Cat#:356602; RRID: AB_2561794 |
| Anti-human CD45RA (clone HI100) | Biolegend | Cat#:304102; RRID: AB_314406 |
| Anti-human CD123 (clone 6H6) | Biolegend | Cat#:306002; RRID: AB_314576 |
| Anti-human CD16 (clone 3G8) | Biolegend | Cat#:302014; RRID: AB_314202 |
| Anti-human CD56 (clone B159) | BD Biosciences | Cat#:555513; RRID: AB_395903 |
| Anti-human CD3 (clone UCHT1) | Biolegend | Cat#:300402; RRID: AB_314056 |
| Anti-human CD4 (clone RPA-T4) | Biolegend | Cat#:300502; RRID: AB_314070 |
| Anti-human CD8 (clone RPA-T8) – 146Nd | Biolegend | Cat#:301002; RRID: AB_314120 |
| CD39 anti-human purified (clone A1) | Biolegend | Cat#: 328202; RRID: AB_940438 |
| CD279 (PD-1) anti-human purified (clone EH12.2H7) | Biolegend | Cat#: 329902; RRID: AB_940488 |
| Anti-human CD127 (clone A019D5) | Biolegend | Cat#:351302; RRID: AB_10718513 |
| Anti-human CD64 (clone 10.1) | Biolegend | Cat#:305016; RRID: AB_2103461 |
| Anti-human CD11c (clone Bu15) | Biolegend | Cat#:337202; RRID: AB_1236381 |
| Anti-human CD11b (clone ICRF44) | Fluidigm | Cat#:3209003B; RRID: AB_2687654 |
| Anti-human CD66b (clone G10F5) | Biolegend | Cat#:305102; RRID: AB_314494 |
| Anti-human CD206 (clone 15–2) | Biolegend | Cat#:321102; RRID: AB_571923 |
| CD10 anti-human purified (clone HI10a) | Biolegend | Cat#: 312202; RRID: AB_314913 |
| Anti-human CD14 (clone M5E2) | Biolegend | Cat#:301810; RRID: AB_314192 |
| Anti-human HLA-DR (clone L243) | Biolegend | Cat#:307602; RRID: AB_314680 |
| Anti-human CD1c (clone L161) | Biolegend | Cat#:331502; RRID: AB_1088995 |
| Biological Samples | ||
| Tumor and non-involved lung tissue from NSCLC patients | Fresh resections from patients with informed consent for an IRB-approved study. Surgeries were performed by the Department of Thoracic Surgery at Mount Sinai Hospital. | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| Collagenase, Type IV, Clostridium histolyticum | Sigma-Aldrich | Cat# C5138 |
| Collagenase D | Sigma-Aldrich | Cat#: 11088858001 |
| DNAse I | Sigma-Aldrich | Cat# 10104159001 |
| Rh103 intercalator | Fluidigm | Cat#: 201103A |
| 0.125uM Ir intercalator | Fluidigm | Cat#: 201192A |
| Osmium tetroxide, 99.9+%, (trace metal basis) | ACROS Organics | Cat # AC191181000 |
| Critical commercial assays | ||
| Chromium Single Cell A Chip Kit, 48 rxns | 10X Genomics | Cat#: PN-120236 |
| Chromium Single Cell 3′ Library & Gel Bead Kit v2, 16 rxns | 10X Genomics | Cat#: PN-120237 |
| Chromium i7 Multiplex Kit, 96 rxns | 10X Genomics | Cat#: PN-120262 |
| Chromium Single Cell 5’ Library & Gel Bead Kit, 16 rxns | 10X Genomics | Cat#: PN-1000006 |
| Chromium Single Cell 5’ Library Construction Kit, 16 rxns | 10X Genomics | Cat#: PN-1000020 |
| Chromium Single Cell V(D)J Enrichment Kit, Human T Cell, 96 rxns | 10X Genomics | Cat# PN-1000005 |
| Dead Cell Removal Kit | Miltenyi Biotec | Cat# 130-090-101 |
| CD45 Microbeads, human | Miltenyi Biotec | Cat# 130-045-801 |
| Oligonucleotide Conjugation Kit | Abcam | Cat # ab218260 |
| SPRIselect beads | Beckman Coulter | Cat # B23317 |
| Protein Block, Serum-Free | Dako | X0909 |
| High Pure FFPET RNA Isolation Kit | Roche | Cat # 06650775001 |
| TruSeq RNA Access Library Prep Kit | Illumina | Cat # 20020189 |
| Deposited data | ||
| Single cell RNaseq, CITEseq, and TCRseq data | GEO | GSE154826 |
| Human reference genome NCBI build 38, GRCh38/84 | Genome Reference Consortium | http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/ |
| scRNAseq data from Lambrechts, et al. | ArrayExpress | E-MTAB-6149 and E-MTAB-6653 and https://gbiomed.kuleuven.be/english/research/50000622/laboratories/54213024/scRNAseq-NSCLC. |
| scRNAseq data from Zilionis, et al. | GEO | GSE127465 |
| TCGA RNAseq and mutation data | GDC | N/A |
| CPTAC LUAD RNAseq and mutation data | CPTAC Data Portal | https://cptac-data-portal.georgetown.edu/cptacPublic/ |
| ESTIMATE scores | Yoshihara, et al., 2013 | https://bioinformatics.mdanderson.org/public-software/estimate/ |
| Mutational signature scores | Alexandrov et al. (2016) and Huang et al. (2017) | http://tardis.cgu.edu.tw/msignaturedb/ |
| Software and algorithms | ||
| QuPath 0.1.3 | Bankhead et al. (2017) | https://qupath.github.io/ |
| Fiji - ImageJ 1.52 h | Schindelin et al. (2012) | https://imagej.net/Fiji/Downloads |
| Cytobank | Mountain View | https://cytobank.org/ |
| Cellranger version 3.1.0 | 10x Genomics | https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest |
| R | R Development Core Team, 2008 | http://www.R-project.org |
| scDissector (R-package) 1.0 | Ephraim Kenigsberg Lab | https://github.com/effiken/scDissector |
| R code for clustering and analyses | This study | https://github.com/effiken/Leader_et_al |
| Seurat v4.0 | Stuart et al. (2019). | https://satijalab.org/seurat/ |
| CellPhoneDB | Efremova et al. (2020) | https://www.cellphonedb.org/ |
| TCGAbiolinks (R package) | Bioconductor | https://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html |
| Skmeans (R-package) | CRAN Repository | http://R-Forge.R-project.org/ |