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. Author manuscript; available in PMC: 2024 Aug 9.
Published in final edited form as: Cell Rep. 2024 Jun 2;43(6):114289. doi: 10.1016/j.celrep.2024.114289

KEY RESOURCES TABLE

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Anti-IRF1 Cell Signaling Cat# 8478S; RRID:AB_10949108
Anti-STAT1 (for mouse and human) Cell Signaling Cat# 9172; RRID:AB_2198300
p-STAT1 (Tyr701) (for human) Cell Signaling Cat# 9167; RRID:AB_561284
Rabbit a-CD4 (For immunofluorescence) Abcam cat# AB183685; RRID:AB_2686917
Rat a-CD8 (For Immunofluorescence) eBioscience Cat# 14–0808; RRID:AB_2572860
CD45_PerCPcy5.5 Biolegend Cat# 103236; RRID:AB_893354
CD3_APC eBioScience Cat# 17–0031-82; RRID:AB_469315
CD4_APC-PE780 eBioScience Cat# 47004280; RRID:AB_1272219
CD8_FITC eBioScience Cat# 11–0081-81; RRID:AB_464914
NK1.1_PE eBioScience Ca# 12–5941-82; RRID:AB_466050
PD1_BV421 Biolegend Ca# 135217; RRID:AB_2562568
Cd45_APC Biolegend Ca# 109813; RRID:AB_389210
Cd11b_APC-Alexafluor 750 (APC-Cy7) eBioscience Cat# 27–0112-81; RRID:AB_469343
Cd11c_PE Biolegend Cat# 117308; RRID:AB_313776
Ccr2_BV785 Biolegend Cat# 150621; RRID:AB_2721565
Ly6C_PE/Dazzle594 Biolegend Cat# 128043; RRID:AB_2566576
Ly6G_FITC Biolegend Cat# 127606; RRID:AB_1236488
Live/Dead Fixable Viable Stain 510 BD Horizon Cat# BDB564406; RRID:AB_2869572
anti-PD-L1-PE Biolegend Cat# 124308; RRID:AB_2073557
anti-MHC-I_AlexaFluor-647 Biolegend Cat# 114612; RRID:AB_492931
InVivoMAb anti-mouse PD-1 (CD279) BioXcell Cat# BE0146; RRID:AB_10949053
InVivoMAb anti-mouse CTLA-4 (CD152), clone 9H10 BioXcell Cat# BE0131; RRID:AB_10950184
InVivoMAb anti-mouse IFNAR-1, clone MAR1–5A3 BioXcell Cat# BE0241; RRID:AB_2687723
InVivoMAb rat IgG2a isotype control BioXcell Cat# BE0089; RRID: AB 1107769
inVivoMAb anti-mouse IFNγR (CD119), clone GR-20 BioXcell Cat# BE0029; RRID:AB 1107576
Chemicals, Peptides, and Recombinant Proteins
murine IFN-y Peprotech Cat# 315–05
Human IFN-y Invivogen Cat# rcyec-hifng
Collagenase-D Roche Cat# 11088866001
DNase I Roche Cat# 10104159001
SpCas9 2NLS Nuclease Synthego Cat# SpCas9 2NLS Nuclease
DSG Crosslinker Covachem Cat# 13301–1
Thermo Scientific™ Pierce™ Formaldehyde Ampules, Methanol-free Thermo Fisher Cat# 52622
Pierce Protease Inhibitor Mini Tablets, EDTA-Free Thermo Fisher Cat# A32955
Linear Acrylamide (5 mg/mL) Thermo Fisher Cat# AM9520
Proteinase K, recombinant, PCR grade Thermo Fisher Cat# EO0492
Linear Acrylamide Invitrogen Cat# AM9520
RNaseA Thermo Fisher Cat# EN0531
Critical Commercial Assays
TruSeq Stranded mRNA Sample Prep Kit B Illumina Cat# RS-122–2102
Kapa Hyper Prep Kit Ilumina Platform Kapa Biosystems Cat# KK8502
NEXTflex™ ChIP-Seq Barcodes - 12 BIOO Scientific Cat# 514121
AMPure XP purification beads for DNA purification Beckman Coulter Cat# A63881
RNeasy Mini Kit (250 rxn) Qiagen Cat# 74106
DNeasy Mini Kit Qiagen Cat# 69506
SuperScript™ III Reverse Transcriptase Invitrogen Cat# 18080044
Dynabeads Protein G Invitrogen Cat# 1004D
Tumor Dissociation Kit Miltenyi Biotec Cat# 130–096730
Dead Cell Removal Kit Miltenyi Biotec Cat# 130–090-101
gentleMACS™ C Tubes Miltenyi Biotec Cat# 130–093-237
MS Columns Miltenyi Biotec Cat# 130–042-201
CellTiter 96® AQueous One Solution
Cell Proliferation Assay (MTS)		 Promega Cat# G3580
BCA assay Thermo Fisher Scientific Cat# 23227
Supersignal West Pico chemiluminescence kit Thermo Fisher Scientific Cat# 34080
Neon™ Transfection System 10 μL Kit Thermo Fisher Cat# MPK1096
Deposited Data
All raw and analyzed bulk mRNA-seq, sc-RNA-seq and ChIP-seq datasets This Paper GEO Accession GSE246923
Experimental Models: Cell Lines
MC38, mouse colon adenocarcinoma C57BL/6 Kerafast #ENH204-FP, RRID:CVCL_B288
YUMM2.1 C57BL/6 Moreno et al.75
B16-F10 mouse melanoma C57BL/6 ATCC #CRL-6475, RRID:CVCL_0159
FSA (Fibrosarcoma) C3H strain derived McBride, UCLA Suit et al.76
M238 (human Melanoma cell line) Human melanoma derived, A. Ribas lab Grasso et al.62
HEK293T Cells ATCC CRL-11268, RRID:CVCL_1926
Experimental Models: Organisms/Strains
C57BL/6 Jackson Laboratory Cat# 000664, RRID:IMSR_JAX:000664
StingGt/Gt Jackson Laboratory Cat# 017537, RRID:IMSR_JAX:017537
Ifnar −/− G. Cheng, UCLA Müller et al.77
NOD Scid Jackson Laboratory Cat# 001303, RRID:IMSR_JAX:001303
Rag2−/− γC−/− Jackson Laboratory Cat# 014593, RRID:IMSR_JAX:014593
Rag1 −/− Jackson Laboratory Cat# 002216, RRID:IMSR_JAX:002216
Cd8 −/− Jackson Laboratory Cat# 002665, RRID:IMSR_JAX:002665
Irf1 −/− Jackson Laboratory Cat# 002762, RRID:IMSR_JAX:002762
Ifngr −/− Jackson Laboratory Cat# 003288, RRID:IMSR_JAX:003288
Irf3 −/− G. Cheng, UCLA Sato et al.78
Myd88 −/− G. Cheng, UCLA Cat# 009088, RRID:IMSR_JAX:009088
Trif −/− Hoebe et al., 2003 JAX stock #005037, RRID:IMSR_JAX:005037
Myd88 Trif DKO Geg Barton, UC Berkley Yamamoto et al.79
Oligonucleotides
mPD-L1_gateway cloning_forward (5′−3′)
GGGGACAAGTTTGTACAAAAAAGCAGGCT
tcgccaccATGAGGATATTTGCTGGCATTAT		 This paper NA
mPD-L1_gateway cloning_reverse (5′−3′)
GGGGACCACTTTGTACAAGAAAGCTGGGT cTCACGTCTCCTCGAATTGTG		 This paper NA
mIRF1 guide sequence g1_Forward for pX459
CACCGATGCCTGTCTGTTCCGGAGC		 This paper NA
mIRF1 guide sequence g1_Reverse for pX459
AAACGCTCCGGAACAGACAGGCATC		 This paper NA
mIRF1 guide sequence g2_Forward for pX459
CACCGGCTCTGCTGTGCGGGTGTAC		 This paper NA
mIRF1 guide sequence g2_Reverse for pX459
AAACGTACACCCGCACAGCAGAGCC		 This paper NA
mSTING guide sequence g1_Forward for pX459
CACCGCCCCACAGTCCAATGGAAAG		 This paper NA
mSTING guide sequence g1_Reverse for pX459
AAACCTTTCCATTGGACTGTGGGGC		 This paper NA
mSTING guide sequence g2_Forward for pX459
CACCGTCAGGCACCCCACAGTCCAA		 This paper NA
mSTING guide sequence g2_Reverse for pX459
AAACTTGGACTGTGGGGTGCCTGAC		 This paper NA
hIRF1 guide sequence g1 for RNP (Synthego)
CUCUAGGCCGAUACAAAGCA		 This paper NA
hIRF1 guide sequence g2 for RNP (Synthego)
GCCAGAUCCCAAGACGUGGA		 This paper NA
Recombinant DNA
pSpCas9(BB)-2A-puro(pX459)-V2.0 plasmid Addgene #62988 Cong and Zhang80
pX459V2_Irf1-gd1 This paper N/A
pX459V2_Irf1-gd2 This paper N/A
pX459V2_Sting-gd1 This paper N/A
pX459V2_Sting-gd2 This paper N/A
pLenti_puro_Pdl1 This paper N/A
Software and Algorithms
Seurat 4.1 https://github.com/satijalab/seurat Butler et al.81
FlowJo FlowJo Version 10.8.1
Cell Ranger v6.0.2 10X Genomics Version 6.0.2 https://www.10xgenomics.com/support/software/cell-ranger
Seurat 4.1 https://github.com/satijalab/seurat Butler et al.81
R/Rstudio CRAN Version 4.3.1
GGplot2 CRAN Version 3.4.3
https://ggplot2.tidyverse.org
DoubletFinder https://github.com/chris-mcginnis-ucsf/DoubletFinder McGinnis et al.82
cowplot https://wilkelab.org/cowplot/ Version 1.1.1
ProjecTILs https://github.com/carmonalab/ProjecTILs Andreatta et al.46
clusterProfiler https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html Wu et al.83
PMID: 34557778
Interferome database http://www.interferome.org Rusinova et al.84
EnhancedVolcano v1.20.0 package in Bioconductor https://bioconductor.org/packages/EnhancedVolcano Blighe et al.85
Hisat2 http://daehwankimlab.github.io/hisat2/ Kim et al.86
DEseq2 https://bioconductor.org/packages/release/bioc/html/DESeq2.html Anders and Huber87
BEDTools https://github.com/arq5x/bedtools2 Quinlan et al.88
Jasper TF motif database https://jaspar.genereg.net/ Castro-Mondragon et al.89
Homer http://homer.ucsd.edu/homer/ Heinz et al.90
Pscan http://159.149.160.88/pscan/ Zambelli et al.91
Jvenn http://jvenn.toulouse.inra.fr/app/index.html Bardou et al.92
R-Studio, https://www.rstudio.com RStudio Team (2015). RStudio:
Integrated Development for
R. RStudio, Inc., Boston, MA
Bioconductor DE-seq http://bioconductor.org/packages/release/bioc/html/DESeq.html Anders and Huber87
MS Office 2010 and 365 https://www.microsoft.com/ Microsoft Office
Samtools https://github.com/samtools/samtools Li et al.93
SeqMonk https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/ Simon Andrews (Head of Bioinformatics)
Email: simon.andrews@babraham.ac.uk