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. Author manuscript; available in PMC: 2023 May 26.
Published in final edited form as: Cell Rep. 2023 Mar 6;42(3):112219. doi: 10.1016/j.celrep.2023.112219

KEY RESOURCES TABLE

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
InVivoMAb anti-mouse IFNAR-1 BioXCell #BE0241; RRID:AB_2687723
InVivoMAb anti-mouse CD4 BioXCell #BE0003-1; RRID:AB_1107636
InVivoMAb anti-mouse CD8α BioXCell #BE0061; RRID:AB_1125541
InVivoMAb anti-mouse IFNγ BioXCell #BE0312; RRID:AB_2736992
InVivoMAb anti-mouse NK1.1 BioXCell #BE0036; RRID:AB_1107737
InVivoMAb rat IgG2b isotype control, anti-keyhole limpet hemocyanin BioXCell #BE0090; RRID:AB_1107780
InVivoMAb anti-mouse PD-1 (CD279) BioXCell #BE0146; RRID:AB_10949053
InVivoMAb anti-mouse CTLA-4 (CD152) BioXCell #BE0164; RRID:AB_10949609
Pacific Blue™ anti-mouse/human CD11b Antibody Biolegend 101,224; RRID:AB_755986
PE/Cyanine7 anti-mouse Ly-6G/Ly-6C (Gr-1) Antibody Biolegend 108,416; RRID:AB_313381
Brilliant Violet 570™ anti-mouse Ly-6C Antibody Biolegend 128,030; RRID:AB_2562617
Brilliant Violet 421™ anti-mouse CD4 Antibody Biolegend 100,438; RRID:AB_11203718
Brilliant Violet 785™ anti-mouse CD8a Antibody Biolegend 100,750; RRID:AB_2562610
APC anti-mouse CD11c Antibody Biolegend 117,310; RRID:AB_313779
Brilliant Violet 421™ anti-T-bet Antibody Biolegend 644,816; RRID:AB_10959653
APC anti-mouse CD366 (Tim-3) Antibody Biolegend 119,706; RRID:AB_2561656
PE anti-human CD111 (Nectin-1) Antibody Biolegend 340,404; RRID:AB_2174152
Brilliant Violet 711™ anti-mouse CD45 Antibody Biolegend 103,147; RRID:AB_2564383
APC anti-mouse CD274 (B7-H1, PD-L1) Antibody Biolegend 124,312; RRID:AB_10612741
Alexa Fluor ®488 anti-mouse I-A/I-E Antibody Biolegend 107,615; RRID:AB_493524
PE anti-mouse H-2Kb/H-2Db Antibody Biolegend 114,607; RRID:AB_313598
FITC anti-mouse NK-1.1 Antibody Biolegend 108,705; RRID:AB_313392
Anti-GAPDH antibody [6C5] Abcam ab8245; RRID:AB_2107448
Caspase-8 Antibody (Mouse Specific) Cell Signaling #4927; RRID:AB_2068301
Anti-Ki67 antibody Abcam ab15580; RRID:AB_443209
Goat anti-Rabbit IgG (H + L) Cross-Adsorbed Secondary Antibody, Alexa Fluor™ 488 ThermoFisher ThermoFisher A-11008; RRID:AB_143165
Bacterial and virus strains
NEB ® 5-alpha Competent E. coli (High Efficiency) NEB C2987H
HSV-1 d106S Liu et al.41 N/A
HSV-1 d106S-IL12 This paper N/A
Chemicals peptides and recombinant proteins
UltraPure™ BSA (50 mg/mL) ThermoFisher AM2618
Lipofectamine LTX with Plus Reagent ThermoFisher 15,338,100
Lipofectamine™ Stem Transfection Reagent ThermoFisher STEM00001
OptiMEM ThermoFisher 31,985,062
HBSS, calcium, magnesium, no phenol red ThermoFisher 14,025,126
HEPES (1 M) ThermoFisher 15,630,080
Penicillin-Streptomycin (10,000 U/mL) ThermoFisher 15,140,122
L-Glutamine (200 mM) ThermoFisher 25,030,081
Recombinant Murine GM-CSF Peprotech 315-03
Recombinant Murine IL-4 Peprotech 214-14
Recombinant Murine IFNγ Peprotech 315-05
Recombinant Human IL-2 Peprotech 200-02
XhoI NEB R0146S
NotI NEB R0189S
BbsI NEB R0539S
SwaI NEB R0604S
BsmBI-v2 NEB R0739S
T4 DNA ligase NEB M0202S
Puromycin Dihydrochloride ThermoFisher A1113803
Hygromycin B (50 mg/mL) ThermoFisher 10,687,010
Ambion™ DNase I (RNase-free) ThermoFisher AM2222
NP-40 Surfact-Amps™ Detergent Solution ThermoFisher 85,124
Sodium deoxycholate ThermoFisher 89,904
Halt™ Protease and Phosphatase Inhibitor Cocktail (100X) ThermoFisher 78,440
Critical commercial assays
Zombie NIR™ Fixable Viability Kit Biolegend 423,105
Dynabeads™ Mouse T-Activator CD3/CD28 for T cell Expansion and Activation ThermoFisher 11456D
EasySep™ Mouse CD8+ T cell Isolation Kit Stemcell Technologies 19,853
Quick Ligation™ Kit NEB M2200S
ELISA MAX™ Deluxe Set Mouse IL-12/IL-23 (p40) Biolegend 431,604
RNeasy Mini Kit Qiagen 74,106
High-Capacity cDNA Reverse Transcription Kit ThermoFisher 4,368,814
SYBR Green Master Mix ThermoFisher 4,309,155
Micro BCA™ Protein Assay Kit ThermoFisher 23,235
Tumor Dissociation Kit, mouse Miltenyi 130-096-730
10x Chromium Single Cell A Chip Kit 10x Genomics PN-1000152
10x Chromium Single Cell 5′ Library and Gel Bead Kit 10x Genomics PN-1000006
Deposited data
Bulk RNA-sequencing This paper NCBI GEO: GSE212829
Single-cell RNA-sequencing This paper NCBI GEO: GSE222795
Experimental models: Cell lines
B16F10 melanoma ATCC CRL-6475
B16F10-nectin1 This paper N/A
B16F10-nectin1 Stat1-knockout This paper N/A
B16F10-nectin1 Ifngr1-knockout This paper N/A
B16F10-nectin1 B2m-knockout This paper N/A
B16F10-nectin1 Casp8-knockout This paper N/A
KPC c6694c2 Li et al.54 N/A
KPC c6694c2 B2m-knockout Roehle et al.62 N/A
Vero E11 Samaniego et al.43 N/A
Vero E11 Cas9 Oh et al.76 N/A
K28; K29; UACC-257 Patient derived cell lines, Dana-Farber Cancer Institute N/A
A375 ATCC CRL-1619
SK-MEL-2 ATCC HTB-68
HEK293T ATCC CRL-3216
Experimental models: Organisms/strains
Mouse: C57BL/6J Jackson Laboratory RRID:IMSR_JAX:000,664
Mouse: B6.Cg-Rag2tm1.1Cgn/J Jackson Laboratory RRID:IMSR_JAX:008,449
Mouse: B6.129S2-Tcratm1Mom/J Jackson Laboratory RRID:IMSR_JAX:002,116
Mouse: B6.129S7-Ifngtm1Ts/J Jackson Laboratory RRID:IMSR_JAX:002,287
Mouse: B6.129S7-Ifngr1tm1Agt/J Jackson Laboratory RRID:IMSR_JAX:003,288
Mouse: B6.Cg-Rag2tm1.1Cgn TcrbLn5Sdou TcraLn3Sdou/J Dougan et al.57 RRID:IMSR_JAX:030,958
Oligonucleotides
GCGAGTCTCGAGATGTGTCCTCAGAAGCTAACC IDT XhoI_IL12_Fow
ATAGAAGCGGCCGCTCAGGCGGAGCTCAGATAG IDT NotI_IL12_Rev
CAGGCGCCCAATACGACCAAATC Merkl et al.77 GAPDH fow DNA
TTCGACAGTCAGCCGCATCTTCTT Merkl et al.77 GAPDH rev DNA
CAGGCGCCCAATACGACCAAATC Merkl et al.77 ICP8 fow DNA
GAGACCGGGGTTGGGGAATGAATC Merkl et al.77 ICP8 rev DNA
GTAACCCGTTGAACCCCATTCGT IDT m18S fow
CCATCCAATCGGTAGTAGCGAC IDT m18S rev
TGAAGCTTGACGCGGTACAT IDT mIfit2 fow
GCTGCCCTGAGGAGTGTATC IDT mIfit2 rev
ACCACAGCCCTCTCCATCAA IDT mIfnb1 fow
TTGAAGTCCGCCCTGTAGGT IDT mIfnb1 rev
AGCCGATGGGTTGTACCTTG IDT mTNF fow
ATAGCAAATCGGCTGACGGT IDT mTNF rev
CACTTCACAAGTCGGAGGCT IDT mIl6 fow
CTGCAAGTGCATCATCGTTGT IDT mIl6 rev
TGCAAGCTATGGCTCACTTCA IDT mIl1a fow
CTTCCCGTTGCTTGACGTTG IDT mIl1a rev
TCCTCCAAAACACTGCTGACA IDT mSting1 fow
GAGTCAAGCTCTGAAGGCCC IDT mSting1 rev
GGAAAGTCGTAAGGGGACCT IDT mCgas fow
TAGCTTGTCCGGTTCCTTCCT IDT mCgas rev
CGCTGCAACTGCATCCATATC IDT mCxcl10 fow
GATAGGCTCGCAGGGATGAT IDT mCxcl10 rev
GCAAACTTCCGTTGTGCCAT IDT mIrf1 fow
TCGGCTGGACTTGGACTTTC IDT mIrf1 rev
ACGCTGCCTATGATGTCTCG IDT mStat1 fow
AGAAAAGCGGCTGTACTGGT IDT mStat1 rev
GGTGTACGAACTTAGCCGGG IDT mIrf7 fow
AATGATCCTGGGGACACACC IDT mIrf7 rev
Recombinant DNA
Tandem p40p35 Addgene Addgene plasmid #108665
pSpCas9(BB)-2A-Puro (PX459) V2.0 Ran et al.78 Addgene plasmid #62988
lentiCRISPRv2 Sanjana et al.79 Addgene plasmid #52961
pVSV-G Stewart et al.80 Addgene plasmid #8454
psPAX2 Addgene Addgene plasmid #12260
hNectin-1 Nakashima et al.45 N/A
pd27B HSV-1 shuttle plasmid Oh et al.76 N/A
pd27-IL12 HSV-1 shuttle plasmid This paper N/A
Infectious d106S DNA Watanabe et al.42 N/A
Software and algorithms
Fiji/ImageJ2 Schindelin et al.81 RRID:SCR_002285
cellSens Imaging software Olympus RRID:SCR_014551
FlowJo v10.8 TreeStar RRID:SCR_008520
Prism v9 GraphPad RRID:SCR_002798
Cellranger v6.1.0 10x Genomics http://software.10xgenomics.com/; RRID:SCR_023221
R v4.2.2 R Project https://www.r-project.org/; RRID:SCR_001905
RStudio v2022.12.0 Posit https://posit.co/downloads/; RRID:SCR_000432
DropletUtils v1.10.3 Griffiths et al.82 Bioconductor
Seurat v4.0.2 Stuart et al.83 https://satijalab.org/seurat/
fgsea v.1.16.0 https://doi.org/10.1101/060012 Bioconductor
Molecular Signatures Database Liberzon et al.84 https://www.gsea-msigdb.org/gsea/msigdb/index.jsp; RRID:SCR_016863
Salmon v1.8.0 Patro et al.85 https://combine-lab.github.io/salmon/
tximport v1.18.0 Soneson et al.86 Bioconductor
DESeq2 v1.30.1 Love et al.87 Bioconductor
Gencode v27 http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/ http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/
ggplot2 v3.3.6 Hadley Wickham https://ggplot2.tidyverse.org/
cBioPortal Cerami et al.88; Gao et al.89 https://www.cbioportal.org/; RRID:SCR_014555
survival v3.2-13 Terry M Therneau https://CRAN.R-project.org/package=survival
survminer v0.4.9 Alboukadel Kassambara https://cran.r-project.org/web/packages/survminer/index.html
Gene Ontology Resource http://geneontology.org/ http://geneontology.org/; RRID:SCR_002811