| Antibodies |
|
InVivoMAb PD1 |
BioXCell |
Clone 29F.1A12; Cat# BE0273; RRID: AB_2687796 |
|
InVivoMAb CTLA4 |
BioXCell |
Clone 9H10; Cat# BE0131; RRID: AB_10950184 |
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InVivoMAb rat IgG2a |
BioXCell |
Clone 2A3; Cat# BE0089; RRID: AB1107769 |
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InVivoMAb polyclonal Syrian Hamster IgG |
BioXCell |
Cat# BE0087; RRID: AB_1107782 |
| t-CyCIF: anti-human and mouse TTF1 |
Abcam |
Clone EPR5955(2); Cat# ab206726; RRID: AB_2857980 |
| t-CyCIF: anti-mouse B220 (CD45R) |
ThermoFisher Scientific |
Clone RA3–6B2; Cat# 41–0452-80; RRID: AB_2573598 |
| t-CyCIF: anti-mouse CD45 |
BioLegend |
Clone 30-F11; Cat# 103123; RRID: AB_493534 |
| t-CyCIF: anti-mouse FOXP3 |
ThermoFisher Scientific |
Clone FJK-16s; Cat# 11–5773-82; RRID: AB_465243 |
| t-CyCIF: anti-mouse CD4 |
ThermoFisher Scientific |
Clone 4SM95; Cat# 41-9766–82; RRID: AB_2573637 |
| t-CyCIF: anti-mouse CD8α |
Cell Signaling Technology |
Clone D4W2Z; Cat# 98941; RRID: AB_2756376 |
| t-CyCIF: anti-mouse CD103 |
R&D Systems |
Clone Polyclonal; Cat# AF1990; RRID: AB_2128618 |
| t-CyCIF: anti-mouse CD11c |
Cell Signaling Technology |
Clone D1V9Y; Cat# 97585; RRID: AB_2800282 |
| t-CyCIF: anti-human and mouse CD11b |
Abcam |
Clone EPR1344; Cat# ab204471; RRID: AB_2650514 |
| t-CyCIF: anti-mouse Nkp46 |
R&D Systems |
Clone Polyclonal; Cat# FAB2225F-025; RRID: AB_2149149 |
| t-CyCIF: anti-mouse CD3e |
Cell Signaling Technology |
Clone D4V8L; Cat# 99940; RRID: AB_2755035 |
| t-CyCIF: anti-human and mouse Ki-67 |
Cell Signaling Technology |
Clone D3B5; Cat# 12075; RRID: AB_2728830 |
| t-CyCIF: anti-mouse PD-L1 |
Cell Signaling Technology |
Clone D5V3B; Cat# 64988s; RRID: AB_2799672 |
| t-CyCIF: anti-mouse PD-1 |
Cell Signaling Technology |
Clone D7D5W; Cat# 61237; RRID: AB_2799604 |
| t-CyCIF: anti-mouse Granzyme B |
Cell Signaling Technology |
Clone E5V2L; Cat# 44153; RRID: AB_2857976 |
| t-CyCIF: anti-mouse Perforin |
Cell Signaling Technology |
Clone E3W4I; Cat# 31647; RRID: AB_2857978 |
| t-CyCIF: anti-mouse TIM3 |
Cell Signaling Technology |
Clone D3M9R; Cat# 83882; RRID: AB_2800033 |
| t-CyCIF: anti-mouse Ly6G |
eBioscience |
Clone 1A8-Ly6G; Cat#: 12–9668-82; RRID: AB_2572720 |
| t-CyCIF: anti-human and mouse TCF1 |
Cell Signaling Technology |
Clone C63D9; Cat# 6709; RRID: AB_2797631 |
| t-CyCIF: anti-human and mouse Vimentin |
Cell Signaling Technology |
Clone D21H3; Cat# 9854; RRID: AB_10829352 |
| t-CyCIF: anti-human and mouse αSMA |
Cell Signaling Technology |
Clone D4K9N; Cat# 76113; RRID: |
| t-CyCIF: anti-mouse F4/80 |
Cell Signaling Technology |
Clone D2S9R; Cat# 70076; RRID: AB_2799771 |
| t-CyCIF: anti-human and mouse Pan-Keratin |
ThermoFisher Scientific |
Clone AE1/AE3; Cat# 53–9003-82; RRID: AB_1834350 |
| t-CyCIF: anti-human and mouse PCNA |
Abcam |
Clone PC10; Cat# ab201674; RRID: AB_2857977 |
| t-CyCIF: anti-human CD4 |
R&D |
Clone Polyclonal; Cat# FAB8165G; RRID: AB_2728839 |
| t-CyCIF: anti-human CCR6 |
Abcam |
Clone EPR22259; Cat# ab243852; RRID: AB_2860033 |
| t-CyCIF: anti-human Granzyme B |
Agilent Dako |
Clone GrB-7; Cat# M7235; RRID: AB_2114697 |
| t-CyCIF: anti-human and mouse TCF1 |
Cell Signaling Technology |
Clone C63D9; Cat# 6444; RRID: AB_2797627 |
| t-CyCIF: anti-human FOXP3 |
eBioscience |
Clone 236A/E7; Cat# 41–4777-82; RRID: AB_2573609 |
| t-CyCIF: anti-human CD8α |
eBioscience |
Clone AMC908; Cat# 50–0008-82; RRID: AB_2574149 |
| t-CyCIF: anti-human and mouse TTF1 |
Abcam |
Clone EPR5955(2); Cat# ab206726; RRID: AB_2857980 |
| t-CyCIF: anti-human PD-L1 |
Cell Signaling Technology |
Clone E1L3N; Cat# 14123; RRID: AB_2798397 |
| t-CyCIF: anti-human CD20 |
eBioscience |
Clone L26; Cat# 50– 0202-82; RRID: AB_11150959 |
| t-CyCIF: anti-human TIM-3 |
Cell Signaling Technology |
Clone D5D5R; Cat# 54669; RRID: AB_2799468 |
| t-CyCIF: anti-human CD45 |
BioLegend |
Clone HI30; Cat# 304008; RRID: AB_314396 |
| t-CyCIF: anti-human PD-1 |
Abcam |
Clone EPR4877(2); Cat# ab201825; RRID: AB_2728811 |
| t-CyCIF: anti-human CD163 |
Abcam |
Clone EPR14643–36; Cat# ab218293; RRID: AB_2889155 |
| t-CyCIF: anti-human CD68 |
Cell Signaling Technology |
Clone D4B9C; Cat# 79594; RRID: AB_2799935 |
| t-CyCIF: anti-human and mouse Ki-67 |
Cell Signaling Technology |
Clone D3B5; Cat# 12075; RRID: AB_2728830 |
| t-CyCIF: anti-human HLA-DPB1 |
Abcam |
Clone EPR11226; Cat# ab201527; RRID: AB_2890211 |
| t-CyCIF: anti-human CD3D |
Abcam |
Clone EP4426; Cat# ab208514; RRID: AB_2728789 |
| t-CyCIF: anti-human HLA A |
Abcam |
Clone EP1395Y; Cat# ab199837; RRID: AB_2728798 |
| t-CyCIF: anti-human and mouse PCNA |
Cell Signaling Technology |
Clone PC10; Cat# 8580; RRID: AB_11178664 |
| t-CyCIF: anti-human αSMA |
Abcam |
Clone EPR5368; Cat# ab202509; RRID: AB_2868435 |
| t-CyCIF: anti-human and mouse Vimentin |
Cell Signaling Technology |
Clone D21H3; Cat# 9856; RRID: AB_10834530 |
| t-CyCIF: anti-human CD16 |
Santa Cruz |
Clone DJ130c; Cat# sc-20052 AF488; RRID: AB_2890161 |
| t-CyCIF: anti-human and mouse Pan-Keratin |
eBioscience |
Clone AE1/AE3; Cat# 41–9003-82; RRID: AB_11218704 |
| t-CyCIF: anti-human CD14 |
Abcam |
Clone EPR3653; Cat# ab196169; RRID: AB_2890135 |
| t-CyCIF: anti-human CD19 |
Abcam |
Clone EPR5906; Cat# ab196468; RRID: AB_2889156 |
| t-CyCIF: anti-human CD103 |
Abcam |
Clone EPR4166(2); Cat# ab225153; RRID: AB_2884945 |
| FC: anti-mouse CD3e |
BD Biosciences |
Clone 145–2C11; Cat# 565922; RRID: AB_2738278 |
| FC: anti-mouse CD8ɑ |
BD Biosciences |
Clone 53–6.7; Cat# 563786, 612759; RRID: AB_2732919, AB_2870090 |
| FC: anti-mouse CD4 |
ThermoFisher |
Clone: RM4–5; Cat# 46–0042-82; RRID: AB_1834431 |
| FC: anti-mouse Foxp3 |
ThermoFisher |
Clone FJK-16s; Cat# 48–5773-82; RRID AB_1518812 |
| FC: anti-mouse CD44 |
BD Biosciences |
Clone IM7; Cat# 563736; RRID: AB_2738395 |
| FC: anti-mouse CD45 |
ThermoFisher |
Clone 30-F11; Cat# 47– 0451-80; RRID: AB_1548790 |
| FC: anti-human Granzyme B |
BD Biosciences |
Clone GB11; Cat# 515408, 562462; RRID: AB_2562196, AB_2737618 |
| FC: anti-human Ki67 |
BD Biosciences |
Clone B56; Cat# 561277; RRID: AB_10611571 |
| FC: anti-mouse PD1 (CD279) |
BioLegend |
Clone RMP1–30; Cat# 109120; RRID: AB_2566641 |
| FC: TCF1/TCF7 |
Cell Signaling Technology |
Clone C63D9; Cat# 6444; RRID: AB_2797627 |
| FC: TIM3 |
BioLegend |
Clone RMT3–23; Cat# 119721; RRID: AB_2616907 |
| FC: H-2Kb SIINFEKL monomer |
NIH Tetramer Core Facility |
Custom |
| FC: H-2Kb SIYRYYGL monomer |
NIH Tetramer Core Facility |
Custom |
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| Bacterial and virus strains |
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| Biological samples |
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| Human formalin fixed paraffin embedded tissue samples from lung adenocarcinoma cases |
Partners Healthcare Institutional Review Board at Brigham Health, Boston, MA, USA |
Excess tissue, discarded tissue protocol number 2018P001627 |
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| Chemicals, peptides, and recombinant proteins |
| SMLVLLPDEVSGLEQLESIINYEKLTEWTS |
New England Peptide |
Custom |
| SMLVLLPDEVSGLEQLESIINFEKLTEWTS peptide |
New England Peptide |
Custom |
| Cyclic-di-GMP |
Invitrogen |
Cat# tlrl-nacdg |
| Mirus TransIT LT1 |
Mirus Bio |
Cat# MIR 2300 |
| Polybrene Infection Reagent |
Millipore |
Cat# TR-1003-G |
| Collagenase IV |
Worthington Biochemical |
Cat# LS004189
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| DNase I |
Sigma-Aldrich |
Cat# 10104159001 |
| Streptavidin, allophycocyanin conjugate |
Invitrogen |
Cat# S32362
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| Mirus TransIT LT1 |
Mirus Bio |
Cat# MIR 2300 |
| Zombie Fixable Viability Kit |
BioLegend |
Cat# 423102 |
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| Critical commercial assays |
| Mouse CXCL10/IP-10/CRG-2 DuoSet ELISA |
R&D Systems |
Cat# DY466–05 |
| Fisherbrand Superfrost Plus Microscope Slides |
ThermoFisher Scientific |
Cat# 12–550-15 |
| Intracellular Fixation & Permeabilization Buffer Set Kit |
ThermoFisher Scientific |
Cat# 88–8824-00 |
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| Deposited data |
| Processed imaging data |
Synapse.org
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doi.org/10.7303/syn30715952
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| Experimental models: Cell lines |
| 293FS* viral packaging cell line |
This paper |
N/A |
| GreenGo 3TZ for lentiviral titering |
This paper |
N/A |
| 1233 KP lung adenocarcinoma |
This paper |
N/A |
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| Experimental models: Organisms/strains |
| Mouse: B6.129S4-Krastm4Tyj/J Jackson Laboratories |
Jackson Laboratories |
Stock No: 008179 |
| Mouse: B6.129P2-Trp53tm1Brn/J Jackson Laboratories |
Jackson Laboratories |
Stock No: 008462 |
| Mouse: Rosa26LSL-Cas9-GFP-Csy4
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Ng et al., 2020
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N/A |
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| Oligonucleotides |
| Cxcl10 dRNA Oligo 1: CACCGACAAGCAATGCCCT |
Sigma-Aldrich |
N/A |
| Cxcl10 dRNA Oligo 2: AAACAGGGCATTGCTTGTC |
Sigma-Aldrich |
N/A |
| Tomato dRNA Oligo 1: CACCCGAGTTCGAGATCGA |
Sigma-Aldrich |
N/A |
| Tomato dRNA Oligo 2: AAACTCGATCTCGAACTCG |
Sigma-Aldrich |
N/A |
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| Recombinant DNA |
| Plasmid: Lenti-Cre |
DuPage et al., 2011
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Addgene Cat# 198712 |
| Plasmid: Lenti-LucOS |
DuPage et al., 2011
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Addgene Cat# 22777 |
| Plasmid: Lenti-SAM-Puro |
This paper |
Addgene Cat# 198713 |
| Plasmid: Lenti-SAM-Cre |
This paper |
Addgene Cat# 198714 |
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| Software and algorithms |
| Aperio ImageScope |
Leica Biosystems |
Version 12 https://www.leicabiosystems.com
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| ImageJ |
NIH |
https://imagej.nih.gov/ij/
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| ImageJ BaSiC Plugin |
Peng et al., 2017
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https://www.helmholtz-muenchen.de/icb/research/groups/marr-lab/software/basic/index.html
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| ASHLAR |
The Python Package Index; Muhlich et al. 2021
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https://pypi.org/project/ashlar/
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| ilastik |
Berg et al., 2019
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https://www.ilastik.org/download.html
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| Visinity |
Warchol et al. 2022
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https://github.com/labsyspharm/visinity. |
| Code |
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doi.org/10.5281/zenodo.7670911
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| Other |
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