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. 2020 Dec 15;53(6):1215–1229.e8. doi: 10.1016/j.immuni.2020.10.020
REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies

Rabbit monoclonal anti-Cox1 (clone D2G6) Cell Signaling Technology Cat# 9896S; RRID: AB_10860249
Rabbit monoclonal anti- Cox2 (clone D5H5) Cell Signaling Technology Cat# 12282S; RRID: AB_2571729
Control rat IgG2a, κ Isotype Biolegend Cat# 400501; RRID: AB_326523
Control mouse IgG2b, κ Isotype Biolegend Cat# 401201; RRID: AB_2744505)
anti-Gr1 (clone RB6-8C5) Biolegend Cat# 108414; RRID: AB_313379
anti-NK1.1 (clone PK136) BioXCell Cat# BE0036; RRID: AB_1107737
Ultra-LEAF Purified anti-Asialo-GM1 Antibody Biolegend Cat# 146002; RRID: AB_2562206
anti-CD4 (clone GK1.5) BioXCell Cat# BE0003-1; RRID: AB_1107636
anti-CD8alpha (clone YTS169.4) BioXCell Cat# BE0117; RRID: AB_10950145
anti-CD49b-APC (clone DX5) BioLegend Cat# 103516; RRID: AB_2566101)
anti-Ly6G- PE/Dazzle 594 (clone 1A8) BioLegend Cat# 127648; RRID: AB_2566319
anti CD4-Alexa700 (RM4-5) BioLegend Cat# 100536; RRID: AB_493701
anti-CD8a-PE (clone 53-6.7) BioLegend Cat# 100708; RRID: AB_312747
CD45-BV605 (Clone 30-F11) eBioscience Cat# 103155; RRID: AB_2650656
CD11b-BV785 (Clone M1/70) BioLegend Cat# 101243; RRID: AB_2561373
Ly6C-FITC (Clone AL- 21) BD Bioscience Cat# 553104; RRID: AB_394628
F4/80-PE-Cy7 (Clone CI: A3-1) BioLegend Cat# 123114; RRID: AB_893478
anti-MHCII I-A/I-E-Alexa700 (Clone M5/114.15.2) BioLegend Cat# 107622; RRID: AB_493727
anti-MHCII I-A/I-E- APC- eFluor780 (Clone M5/114.15.2) Thermo Fisher Scientific Cat# 47-5321-82; RRID: AB_1548783
anti-CD11c-PerCP/Cy5.5 (Clone N418) BioLegend Cat# 117328; RRID: AB_2129641
anti- CD103-APC (Clone 2E7) BioLegend Cat# 121414; RRID: AB_1227502
anti- CD103-PE (Clone 2E7) BioLegend Cat# 121406; RRID: AB_1133989
NK1.1-APC (Clone PK136) BioLegend Cat# 108710; RRID: AB_313397
NK1.1- PE (Clone PK136) BioLegend Cat# 108708; RRID: AB_313395
CD49b-APC (Clone DX5) BioLegend Cat# 108910; RRID: AB_313417
XCR1- Alexa647 (Clone ZET) BioLegend Cat# 148214; RRID: AB_2564369
XCR1-BV421 (Clone ZET) BioLegend Cat# 148216; RRID: AB_2565230
Siglec-H-BV711 (Clone E50-2440) BD Bioscience Cat# 740764; RRID: AB_2740427
IFNγ-eFluor450 (Clone XMG1.2) Thermo Fisher Scientific Cat# 48-7311-82; RRID:
AB_1834366
CD44-APC-eFluor780 (Clone IM7) Thermo Fisher Scientific Cat# 47-0441-82; RRID: AB_1272244
CD3ε-Percp-Cy5.5 (Clone 145-2C11) BioLegend Cat# 100328; RRID: AB_893318
CD3ε-APC (Clone 145-2C11) BioLegend Cat# 100312; RRID: AB_312677
CD8a-PE (Clone 53-6.7) BioLegend Cat# 100708; RRID: AB_312747
CD8a-PE-Cy7 (Clone 53-6.7) BioLegend Cat# 100722; RRID: AB_312761
CD4-FITC (Clone RM4-5) BioLegend Cat# 100510; RRID: AB_312713
CD4-APC-eFluor780 (Clone GK1.5) Thermo Fisher Scientific Cat# 47-0041-82; RRID: AB_11218896
anti-CD16/32 (clone 2.4G2) BioLegend Cat# 101302; RRID: AB_312801
affinity purified anti-Ly6G (Clone 1A8) BD Bioscience Cat# 551459; RRID: AB_394206
affinity purified anti-NK1.1- biotynilated (Clone PK136) BioLegend Cat# 108704; RRID: AB_313391
CD19-eFluor450 (Clone eBio1D3) Thermo Fisher Scientific Cat# 48-0193-82; RRID: AB_2734905

Chemicals, Peptides, and Recombinant Proteins

Collagenase IV Worthington Biochemical Cat# LS004188
DNase I Roche Cat#11284932001
Aqua LIVE/Dead-405 nm staining Thermo Fisher Scientific Cat# L34957
Brefeldin A Solution (1,000X) Biolegend Cat# 420601
Monensin Solution (1,000X) Biolegend Cat# 420701
10 μm latex beads Beckman Coulter Cat# 6602796
OCT embedding medium Thermo Fisher Scientific Cat# 12678646
Recombinant FC IL-2 Thermo Fisher Scientific Cat# 34-8021-85
CellTrace Calcein Green Thermo Fisher Scientific Cat# C34852
Calcein Red- Orange Thermo Fisher Scientific Cat# C34851
RLT lysis buffer QIAGEN Cat# 79216
PureZOL RNA isolation Reagent BioRad Cat# 7326890

Critical Commercial Assays

RNeasy RNA isolation Kit QIAGEN Cat# 74106
Direct-zol RNA MiniPrep Kit Zymo Research Cat# R2052
High Capacity cDNA archive Kit Applied Biosystems Cat# 4368813
MojoSort Mouse NK Cell Isolation Kit Biolegned Cat# 480050
Lexogen QuantSeq 3′-mRNaseq Library Prep Kit FWD Lexogen Cat# 015
Chromium Single Cell 3′ Reagent Kit v3 10X Genomics PN- 1000075, PN-120262
Chromium Chip B 10X Genomics PN-1000073
Kapa Library Quantification Kit for Illumina sequencing platforms Kapa Biosystems Cat# KK4873
Prostaglandin E2 Express ELISA Kit Cyman Chemical Cat# 500141

Deposited Data

Raw and processed data (bulk tumor RNaseq) This paper GEO: GSE139044
Raw and processed data (sorted TAM RNaseq) This paper GEO: GSE139045
Raw and processed data (single cell RNaseq) This paper GEO: GSE139046
Table of cluster biomarkers (scRNaseq) This paper Table S1
DEG analysis in Myeloid population (scRNaseq) This paper Table S2
Single sample GSEA (scRNaseq) This paper Table S3
Ingenuity Pathway Analysis (sorted TAM RNaseq) This paper Table S4
Signature gene list (human dataset analysis) This paper Table S5
Immune infiltrate in neutrophil-depleted tumor bearing mice (FACS analysis) This paper https://doi.org/10.17632/gngxk9mjkm.1

Experimental Models: Cell Lines

Melanoma C57BL/6 Braf +/LSL-V600E;Tyr::CreERT2 +/o;p16 INK4a−/− cell line Dhomen et al., 2009 Ptgs+/+
Melanoma C57BL/6 Braf +/LSL-V600E;Tyr::CreERT2 +/o;p16 INK4a−/− cell line COX1/2-deficient Zelenay et al., 2015 Ptgs−/−
CT26 Cancer Research UK Manchester Institute N/A
MC38 Cancer Research UK Manchester Institute N/A
4T1 Cancer Research UK Manchester Institute N/A
CT26 COX2-deficient Zelenay et al., 2015 N/A
MC38 COX2-deficient This paper N/A
4T1 COX1/2-deficient Zelenay et al., 2015 N/A

Experimental Models: Organisms/Strains

Mouse: C57BL/6JOlaHsd ENVIGO Stock No: 057
Mouse: BALB/cOlaHsd ENVIGO Stock No: 162
Mouse: Rag1−/− Cancer Research UK Manchester Institute N/A
Mouse: Ifng−/− Cancer Research UK Manchester Institute N/A
Mouse: Tmem173−/− Cancer Research UK Manchester Institute N/A
Mouse: Cgas−/− Cancer Research UK Manchester Institute N/A
Mouse: Trif−/− Cancer Research UK Manchester Institute N/A
Mouse: Mavs−/− Cancer Research UK Manchester Institute N/A
Mouse: Myd88−/− Cancer Research UK Manchester Institute N/A
Mouse: Gzmb-Cre Ptger4floxed/floxed /Ptger2−/− Cancer Research UK Manchester Institute N/A
Mouse: Gzmb-Cre Ptger4floxed/floxed Cancer Research UK Manchester Institute N/A
Mouse: Ptger2−/− Cancer Research UK Manchester Institute N/A
Mouse: Tcrd−/− Instituto de Medicina Molecular, Lisbon N/A

Oligonucleotides

Ccl2-Taqman probe Thermo Fisher Scientific Mm00441242_m1
Ccl5-Taqman probe Thermo Fisher Scientific Mm01302427_m1
Cd8a-Taqman probe Thermo Fisher Scientific Mm01182107_g1
Ptgs2-Taqman probe Thermo Fisher Scientific Mm00478374_m1
Cxcl1 -Taqman probe Thermo Fisher Scientific Mm04207460_m1
Cxcl10-Taqman probe Thermo Fisher Scientific Mm00445235_m1
Cxcl2-Taqman probe Thermo Fisher Scientific Mm00436450_m1
Cxcl9-Taqman probe Thermo Fisher Scientific Mm00434946_m1
Eomes-Taqman probe Thermo Fisher Scientific Mm01351984_m1
Csf3-Taqman probe Thermo Fisher Scientific Mm00438334_m1
Gapdh-Taqman probe Thermo Fisher Scientific Mm99999915_g1
Gzmb -Taqman probe Thermo Fisher Scientific Mm00442837_m1
Hprt-Taqman probe Thermo Fisher Scientific Mm03024075_m1
Ifng-Taqman probe Thermo Fisher Scientific Mm01168134_m1
Il12a-Taqman probe Thermo Fisher Scientific Mm00434169_m1
Il12b-Taqman probe Thermo Fisher Scientific Mm01288989_m1
Il1a-Taqman probe Thermo Fisher Scientific Mm00439620_m1
Il1b-Taqman probe Thermo Fisher Scientific Mm00434228_m1
Il6-Taqman probe Thermo Fisher Scientific Mm00446190_m1
Prf1-Taqman probe Thermo Fisher Scientific Mm00812512_m1
Stat1-Taqman probe Thermo Fisher Scientific Mm01257286_m1
Tbx21-Taqman probe Thermo Fisher Scientific Mm00450960_m1
Vegfa-Taqman probe Thermo Fisher Scientific Mm00437306_m1

Software and Algorithms

ImageJ/Fiji software https://imagej.nih.gov/ij/ version 2.0.0-rc14/1.49
Ingenuity Pathways Analysis software (IPA) QIAGEN 2018 update
Cell Ranger Pipeline 10X Genomics version 3.1
GraphPad Prism GraphPad Software version 8.2.0
FlowJo Software TreeStar FlowJo LLC. version 10.4.2
Cytobank Software CytoBank, Inc. N/A
Partek Flow software (Single cell Toolkit) Partek build version 8.0.19.0610
R software R project N/A

Other

Mouse Diet: RM3 expanded and irradiated SDS Code: 801185