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 |