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
|