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. 2020 Oct 29;183(3):771–785.e12. doi: 10.1016/j.cell.2020.09.058
REAGENT or RESOURCE SOURCE IDENTIFIER
Cell Lines

Lewis lung carcinoma (LLC1) ATCC Cat#CRL-1642; RRID: CVCL_4358
B16-F10 ATCC Cat#CRL-6475; RRID: CVCL_0159
B16-F10-Luc Creative Biogene Cat#CSC-RR0234

Antibodies

Rat anti-mouse CD11b Biolegend Cat#101216; RRID: AB_312799
Rat anti-mouse Sca1 (Ly6-A/E) Biolegend Cat#122514; RRID: AB_756199
Mouse Lineage Antibody Cocktail BD Biosciences Cat#558074; RRID: AB_1645213
Biotin Mouse Lineage Panel BD Biosciences Cat#559971; RRID: AB_10053179
Rat anti-mouse cKit (CD117) BD Biosciences Cat#553355; RRID: AB_394806
Rat anti-mouse CD16/CD32 Biolegend Cat#101332; RRID: AB_2650889
Rat anti-mouse CD34 Thermo Fisher Scientific Cat#11-0341-82; RRID: AB_465021
Rat anti-mouse CD45 Biolegend Cat#103132; RRID: AB_893340
Rat anti-mouse CD4 Biolegend Cat#116006; RRID: 313691
Rat anti-mouse CD8 Biolegend Cat#100722; RRID: AB_312761
Rat anti-mouse Ly6g Biolegend Cat#127624; RRID: AB_10640819
Biotin anti-mouse Ly6g Biolegend Cat# 127604; RRID: AB_1186108
Rat anti-mouse anti-Ly6c Biolegend Cat#128032; RRID: AB_2562178
Biotin anti-mouse Ly6c Biolegend Cat#128004; RRID: AB_1236553
Rat anti-mouse F4/80 Biolegend Cat#123109 and 123116; RRID: AB_893498 and 893481
Rat anti-mouse Gr-1 Biolegend Cat#108445; RRID: AB_2562903
Rat anti-mouse CD115 Biolegend Cat#135523; RRID: AB_2566459
Rat anti-mouse CD169 Biolegend Cat#142417; RRID: AB_2565640
Rat anti-mouse B220 Biolegend Cat#103207; RRID: AB_312992
Armenian hamster anti-mouse CD11c Biolegend Cat#117310; RRID: AB_313779
Rat anti-mouse CD317 Biolegend Cat#127023; RRID: AB_2687109
Rat anti-mouse CD90.2 Biolegend Cat#105319; RRID: AB_493724
Rat anti-mouse CD19 Biolegend Cat#115527; RRID: AB_493734
Mouse anti-mouse NK1.1 Biolegend Cat#108729; RRID: AB_2074426
Rat anti-mouse anti-IFNα R&D Systems Cat#22100-3; RRID: AB_884210
Rat anti-mouse IFNγ Biolegend Cat#505808; RRID: AB_315402
Ultra-LEAF Purified anti-mouse IFNAR-1 Antibody Biolegend Cat#127321; RRID: AB_11150409
Ultra-LEAF™ Purified Mouse IgG1, κ Isotype Ctrl Antibody Biolegend Cat#400166; RRID:AB_11146992

Chemicals, Enzymes, and Buffers

Beta-glucan peptide (BGP) Invivogen Cat#tlrl-bgp
PMA Sigma Cat#P1585
Ionomycin Sigma Cat#I0634
Brefeldin A Biolegend Cat#420601
Deoxyribonuclease I from bovine pancreas Sigma-Aldrich Cat#D5025
Collagenase D Roche Cat#11088866001
10X RBC Lysis Buffer eBioscience Cat#00-4300-54
Puromycin Invivogen Cat#ant-pr1-1
N-Acetyl-L-cysteine Sigma Cat#A7250
Nonidet P40 Substrate Sigma Cat#74385
Nuclei Buffer 10x Genomics Cat#2000153
Dynabeads MyOne SILANE 10x Genomics Cat#2000048
SPRIselect Beckman Coulter Cat#B23318

Critical Commercial Assays

CellROX™ Green Flow Cytometry Assay Kit Thermo Fisher Cat#C10492
Foxp3/Transcription Factor Buffer Set eBioscience Cat#00-5523-00
Intracellular Fixation & Permeabilization Buffer eBioscience Cat#88-8824-00
iScript cDNA Synthesis Kit BioRad Cat#1708891
High-Capacity RNA-to-cDNA Kit Applied Biosystems Cat#4387406
SsoFast EvaGreen Supermix BioRad Cat#1725202
Fast SYBR Green Master Mix Applied Biosystems Cat#4385612
Anti-Biotin MicroBeads Miltenyi Biotec Cat#130-090-485
RNeasy Plus Micro Kit QIAGEN Cat#74034
MycoAlertTM Mycoplasma Detection Kit Lonza Cat#LT07-318
SMARTer Ultra Low Input RNA for Illumina Sequencing Takara Bio Cat#634828
NEBNext Ultra DNA Library Prep Kit for Illumina New England Biolabs Cat#E7370L
Luciferase assay system Promega Cat#E1500
Chromium Next GEM Chip H Single Cell Kit v1.1 10x Genomics Cat#1000162
Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 10x Genomics Cat#1000176
NGS High Sensitivity Fragment Analysis Kit Agilent Cat#DNF-474
NextSeq 500/550 High Output Kit v2.5;150 Cycles Illumina Cat#20024907

Deposited Data

RNA sequencing data This paper GEO: GSE139450, GSE139451, GSE139452, and GSE139456
Single cell ATAC sequencing data This paper GEO: GSE152353

Experimental models: Organisms/Strains

Mouse: C57BL/6 Janvier Labs C57BL/6JRj
Mouse: C57BL/6 The Jackson Laboratory Stock#000664
Mouse: C57BL/6-CD45.1 B6.SJL-PtprcaPepcb/BoyJ The Jackson Laboratory Stock#002014
Mouse: B6(Cg)-Ncf1m1J/J The Jackson Laboratory Stock#004742
Mouse: B6.129S7-Rag1tm1Mom/J The Jackson Laboratory Stock#002216
Mouse: B6(Cg)-Ifnar1tm1.2Ees/J The Jackson Laboratory Stock#028288

Oligonucleotides

qPCR primers This paper See Table S5

Software, Algorithms and Protocols

GraphPad Prism 6 Graphpad Software N/A
Ingenuity Pathway Analysis QIAGEN https://www.qiagenbioinformatics.com/products/ingenuity-pathway-analysis/
GSEA software Broad Institute http://software.broadinstitute.org/gsea/index.jsp
Morpheus Broad Institute https://software.broadinstitute.org/morpheus/
DESeq2 Love et al., 2014 https://bioconductor.org/packages/release/bioc/html/DESeq2.html
GSNAP Wu and Nacu, 2010 http://research-pub.gene.com/gmap/
Ensembl gene annotation version 81 EMBL-EBI https://www.ebi.ac.uk/
Ensembl Gene IDs using Ensembl Biomart (Release 96) EMBL-EBI https://www.ebi.ac.uk/
featureCounts Liao et al., 2014 http://bioinf.wehi.edu.au/featureCounts/
FlowJo version 10 Tree Star https://www.flowjo.com/solutions/flowjo
NovoExpress® software ACEA Biosciences https://www.aceabio.com
Cell Ranger ATAC version 1.2.0 10x Genomics https://support.10xgenomics.com/single-cell-atac/software/overview/welcome
R package ChIPseeker v1.22.1 Bioconductor https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html
R package clusterProfiler v3.14.3 Bioconductor https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html
Chromium Single Cell ATAC Reagent Kits protocol 10xGenomics Cat#CG000168