Control:Article Title: Tumor-educated T regs drive organ-specific metastasis in breast cancer by impairing NK cells in the lymph node niche.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Armenian Hamster anti-CD3e, APC (clone 145-2C11) Invitrogen #Cat 17-0031-82 Armenian Hamster anti-CD3e, FITC (clone 145-2C11) Biolegend #Cat 100306 Armenian Hamster anti-CD3e, PE-Cy7 (clone 145-2C11) eBioscience #Cat 25-0031-82 Armenian Hamster anti-CD3e, PE (clone 145-2C11) Biolegend #Cat 100307 Rat anti-CD4, BV421 (clone GK1.5) BD #Cat 562891 Rat anti-CD4, BUV805 (clone GK1.5) BD #Cat 612900 Rat anti-CD4, PE (clone GK1.5) Invitrogen #Cat 12-0041-82 Rat anti-CD8, AF700 (clone 56-6.7) BioLegend #Cat 100730 Rat anti-CD8, BUV395 (clone 56-6.7) BD #Cat 563786 Rat anti-CD8, FITC (clone 56-6.7) eBioscience #Cat 11-0081-85 Rat anti-CD11b, APC (clone M1/70) eBioscience #Cat 17-01120-82 Rat anti-CD11b, BV786 (clone M1/70) BD #Cat 740861 Rat anti-CD25, PE (clone PC61) Biolegend #Cat 102008 Rat anti-CD25, APC (clone PC61) Biolegend #Cat 102011 Armenian Hamster anti-CD27, PerCP-eFluor 710 (clone LG.7F9) ThermoFisher #Cat 46-0271-82 Rat anti-CD44, BV605 (clone IM7) Biolegend #Cat 103047 Rat anti-CD45, BUV395 (clone 30F11) BD #Cat 564279 Rat anti-CD45, BUV563 (clone 30F11) BD #Cat 612924 Rat anti-CD45, APC-eF780 (clone 30F11) eBioscience #Cat 47-0451-82 Rat anti-CD49b, eF450 (clone DX5) ThermoFisher #Cat 48-5971-82 Rat anti-CD62L, AF700 (clone MEL-14) ThermoFisher #Cat 56-0621-82 Hamster anti-CD69, BUV737 (clone H1.2F3) BD #Cat 612793 Rat anti-CD103, BV711 (clone M290) BD #Cat 564320 Rat anti-mouse CD107a, PE (clone 1D4B) Biolegend #Cat 121611 Armenian hamster anti-CD152, PE-Cy7 (clone UC10-4B9) Biolegend #Cat 106313 Armenian hamster anti-CD278, PerCP-Cy5.5 (clone C398.4A) Biolegend #Cat 313517 Mouse anti-FOXP3, AF647 (clone 150D) Biolegend #Cat 320014 Mouse anti-Granzyme B, PE (clone QA16A02) Biolegend #Cat 372208 Rat anti-IFNy, eF450 (clone XMG1.2) ThermoFisher #Cat 48-7311-82 Rat anti-Ki67, PE (clone SOL-A15) ThermoFisher #Cat 12-5698-80 Mouse anti Ki-67, BV786 (clone B56) BD #Cat 563756 Mouse anti-NK1.1, APC-eFluor 780 (clone PK136) ThermoFisher #Cat 47-5941-82 Rat anti-NKp46, FITC (clone 29A1.4) ThermoFisher #Cat 11-3351-82 Rat anti-ST2, PE (clone RMST2-2) ThermoFisher #Cat 12-9335-82 Rat anti-TNFa, AF700 (clone MP6-XT22) Biolegend #Cat 506338 anti-CD25, mIgG2a (clone M2A) Gift from S. Quezada (under MTA), produced by Evitria N/A (Continued on next page) e1 Cell Reports 38, 110447, March 1, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER Mouse IgG2a isotype control (clone C1.18.4) BioXcell #Cat BE0085 InVivoPlus anti-mouse CD8a (clone 2.43) BioXcell #Cat BP0061 InVivoPlus anti-mouse NK1.1 (clone PK136) BioXcell #Cat BP0036 Purified Hamster Anti-Mouse CD3e BD #Cat 553058 Goat anti-IL-33 (polyclonal) R&D Systems #Cat AF3626 Goat IgG control (polyclonal) R&D Systems #Cat AB-108-C Rat anti-Keratine-8 (TROMA I) DSHB University of Iowa #Cat Troma I Rabbit anti-E-Cadherin (24E10) Cell Signaling #Cat 3195 Rat Anti-Mouse CD16/CD32, purified (clone 2.4G2) BD #Cat 553141 Armenian Hamster anti-CD3e, purified (clone 145-2C11) Biolegend #Cat 100302 Mouse anti-human CD3, APC (clone SK7) BD #Cat 340661 Mouse anti-human CD3, PerCP-cy5.5 (clone SK7) BD #Cat 340949 Mouse anti-human CD56, PE (clone B159) BD #Cat 561903 Mouse anti-human CD16, FITC (clone 3G8) BD #Cat 555406 Mouse anti-human IgG1, FITC (clone X40) BD #Cat 345815 Mouse anti-human CD25, APC (2A3) BD #Cat 340939 Mouse anti-human FoxP3, PE (PCH101) ThermoFisher #Cat 12-4776-42 Bacterial and virus strains pLenti#737-P2A-Cre Gift from Jos Jonkers (NKI) N/A Biological samples KEP tumor fragments This paper N/A Chemicals, peptides, and recombinant proteins Dynabeads mouse T-activator CD3/CD28 Thermofisher #Cat 11452D Recombinant murine IL-2 Peprotech #Cat 212-12 7-AAD Viability Staining Solution Thermofisher #Cat 00-6993-50 Ionomycin (calcium salt from Streptomyces conglobatus) Sigma #Cat I0634-1mg Phorbol 12-myristate 13-acetate (PMA) Sigma #Cat P1585-1MG UltraComp eBeads eBioscience #Cat 01-2222-42 DNAse I Invitrogen #Cat 18068-015 Collagenase A Roche #Cat 11088793001 BD Brilliant stain buffer BD #Cat 563794 Liberase TL Research Grade Roche #Cat 5401020001 Diphtheria Toxin from Corynebacterium diphtheriae Sigma-Aldrich #Cat D0564-1MG RLT Buffer Qiagen #Cat 79216 5-Ethynyl-2’-deoxyuridine Sigma #Cat 900584-50MG GolgiStop BD #Cat 554724 GolgiPlug BD #Cat 555029 IL-33 Trap Gift from Rudi Beyaert, VIB (under MTA) N/A Critical commercial assays LEGENDplexTM Mouse IL-33 Capture Bead B5, 13X Biolegend #Cat 740144 LEGENDplexTM Mouse Cytokine Panel 2 Standard Biolegend #Cat 740372 LEGENDplexTM Mouse Cytokine Panel 2 Detection Antibodies Biolegend #Cat 740149 LEGENDplexTM Buffer Set B Biolegend #Cat 740373 (Continued on next page) Cell Reports 38, 110447, March 1, 2022 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER LIVE/DEADTM Fixable Near-IR Dead Cell Stain Kit ThermoFisher #Cat L34975 LIVE/DEADTM Fixable Aqua Dead Cell Stain Kit ThermoFisher #Cat L34957 Zombie RedTM Fixable Viability Kit Biolegend #Cat 423109 Zombie NIRTM Fixable Viability Kit Biolegend #Cat 423105 CellTraceTM Violet Cell Proliferation Kit ThermoFisher #Cat C34557 Click-iTTM EdU Cell Proliferation Kit for Imaging, Alexa FluorTM 488 dye ThermoFisher #Cat C10337 Foxp3/Transcription Factor Staining Buffer Set ThermoFisher #Cat 00-5523-00 Deposited data Raw and analyzed data (Treg RNAseq) This paper GEO: GSE169024 Raw and analyzed data (NK RNAseq) This paper GEO: GSE169025 Experimental Models: Organisms/Strains Mus musculus: Strain: Wild-type FVB/N Janvier Laboratories FVB/N Mus musculus: Strain: K14-cre; Cdh1F/F;Trp53F/F (FVB/n) Netherlands Cancer Institute N/A Mus musculus: Strain Wap-cre; Cdh1F/F;Pik3caE545K (FVB/n) Netherlands Cancer Institute N/A Mus musculus: Strain Wap-cre; Cdh1F/F;AktE17K (FVB/n) Netherlands Cancer Institute N/A Mus musculus: Strain Cdh1F/F; Trp53F/F;Foxp3GFP-DTR(FVB/n) Netherlands Cancer Institute N/A Mus musculus: Strain Wap-cre; Cdh1F/F;PtenF/F (FVB/n) Netherlands Cancer Institute N/A Mus musculus: Strain Wap-cre; Cdh1F/F;Pik3caH1047R (FVB/n) Netherlands Cancer Institute N/A Mus musculus: Strain Brca1F/F; Trp53F/F (FVB/n) Netherlands Cancer Institute N/A Recombinant DNA Plasmid: IRES-DTR-GFP Gift from Alexander Rudensky (MSKCC) N/A Software and algorithms FlowJo v10.7 https://www.flowjo.com/solutions/flowjo N/A GSEA v4.0.3 https://www.gsea-msigdb.org/gsea/index.jsp N/A R statistical programming environment R Foundation for Statistical Computing https://www.r-project.org GraphPad Prism v8 https://www.graphpad.com/ scientific-software/prism/ N/A G*power software v3.1 https://www.psychologie.hhu.de/ arbeitsgruppen/allgemeine-psychologieund-arbeitspsychologie/gpower.html N/A Tophat 2.1.0 https://ccb.jhu.edu/software/ tophat/index.shtml N/A Itreecount (https://github.com/NKI-GCF/itreecount) N/A Hisat2 http://daehwankimlab.github.io/hisat2/ N/A
Purification:Article Title: Tumor-educated T regs drive organ-specific metastasis in breast cancer by impairing NK cells in the lymph node niche.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Armenian Hamster anti-CD3e, APC (clone 145-2C11) Invitrogen #Cat 17-0031-82 Armenian Hamster anti-CD3e, FITC (clone 145-2C11) Biolegend #Cat 100306 Armenian Hamster anti-CD3e, PE-Cy7 (clone 145-2C11) eBioscience #Cat 25-0031-82 Armenian Hamster anti-CD3e, PE (clone 145-2C11) Biolegend #Cat 100307 Rat anti-CD4, BV421 (clone GK1.5) BD #Cat 562891 Rat anti-CD4, BUV805 (clone GK1.5) BD #Cat 612900 Rat anti-CD4, PE (clone GK1.5) Invitrogen #Cat 12-0041-82 Rat anti-CD8, AF700 (clone 56-6.7) BioLegend #Cat 100730 Rat anti-CD8, BUV395 (clone 56-6.7) BD #Cat 563786 Rat anti-CD8, FITC (clone 56-6.7) eBioscience #Cat 11-0081-85 Rat anti-CD11b, APC (clone M1/70) eBioscience #Cat 17-01120-82 Rat anti-CD11b, BV786 (clone M1/70) BD #Cat 740861 Rat anti-CD25, PE (clone PC61) Biolegend #Cat 102008 Rat anti-CD25, APC (clone PC61) Biolegend #Cat 102011 Armenian Hamster anti-CD27, PerCP-eFluor 710 (clone LG.7F9) ThermoFisher #Cat 46-0271-82 Rat anti-CD44, BV605 (clone IM7) Biolegend #Cat 103047 Rat anti-CD45, BUV395 (clone 30F11) BD #Cat 564279 Rat anti-CD45, BUV563 (clone 30F11) BD #Cat 612924 Rat anti-CD45, APC-eF780 (clone 30F11) eBioscience #Cat 47-0451-82 Rat anti-CD49b, eF450 (clone DX5) ThermoFisher #Cat 48-5971-82 Rat anti-CD62L, AF700 (clone MEL-14) ThermoFisher #Cat 56-0621-82 Hamster anti-CD69, BUV737 (clone H1.2F3) BD #Cat 612793 Rat anti-CD103, BV711 (clone M290) BD #Cat 564320 Rat anti-mouse CD107a, PE (clone 1D4B) Biolegend #Cat 121611 Armenian hamster anti-CD152, PE-Cy7 (clone UC10-4B9) Biolegend #Cat 106313 Armenian hamster anti-CD278, PerCP-Cy5.5 (clone C398.4A) Biolegend #Cat 313517 Mouse anti-FOXP3, AF647 (clone 150D) Biolegend #Cat 320014 Mouse anti-Granzyme B, PE (clone QA16A02) Biolegend #Cat 372208 Rat anti-IFNy, eF450 (clone XMG1.2) ThermoFisher #Cat 48-7311-82 Rat anti-Ki67, PE (clone SOL-A15) ThermoFisher #Cat 12-5698-80 Mouse anti Ki-67, BV786 (clone B56) BD #Cat 563756 Mouse anti-NK1.1, APC-eFluor 780 (clone PK136) ThermoFisher #Cat 47-5941-82 Rat anti-NKp46, FITC (clone 29A1.4) ThermoFisher #Cat 11-3351-82 Rat anti-ST2, PE (clone RMST2-2) ThermoFisher #Cat 12-9335-82 Rat anti-TNFa, AF700 (clone MP6-XT22) Biolegend #Cat 506338 anti-CD25, mIgG2a (clone M2A) Gift from S. Quezada (under MTA), produced by Evitria N/A (Continued on next page) e1 Cell Reports 38, 110447, March 1, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER Mouse IgG2a isotype control (clone C1.18.4) BioXcell #Cat BE0085 InVivoPlus anti-mouse CD8a (clone 2.43) BioXcell #Cat BP0061 InVivoPlus anti-mouse NK1.1 (clone PK136) BioXcell #Cat BP0036 Purified Hamster Anti-Mouse CD3e BD #Cat 553058 Goat anti-IL-33 (polyclonal) R&D Systems #Cat AF3626 Goat IgG control (polyclonal) R&D Systems #Cat AB-108-C Rat anti-Keratine-8 (TROMA I) DSHB University of Iowa #Cat Troma I Rabbit anti-E-Cadherin (24E10) Cell Signaling #Cat 3195 Rat Anti-Mouse CD16/CD32, purified (clone 2.4G2) BD #Cat 553141 Armenian Hamster anti-CD3e, purified (clone 145-2C11) Biolegend #Cat 100302 Mouse anti-human CD3, APC (clone SK7) BD #Cat 340661 Mouse anti-human CD3, PerCP-cy5.5 (clone SK7) BD #Cat 340949 Mouse anti-human CD56, PE (clone B159) BD #Cat 561903 Mouse anti-human CD16, FITC (clone 3G8) BD #Cat 555406 Mouse anti-human IgG1, FITC (clone X40) BD #Cat 345815 Mouse anti-human CD25, APC (2A3) BD #Cat 340939 Mouse anti-human FoxP3, PE (PCH101) ThermoFisher #Cat 12-4776-42 Bacterial and virus strains pLenti#737-P2A-Cre Gift from Jos Jonkers (NKI) N/A Biological samples KEP tumor fragments This paper N/A Chemicals, peptides, and recombinant proteins Dynabeads mouse T-activator CD3/CD28 Thermofisher #Cat 11452D Recombinant murine IL-2 Peprotech #Cat 212-12 7-AAD Viability Staining Solution Thermofisher #Cat 00-6993-50 Ionomycin (calcium salt from Streptomyces conglobatus) Sigma #Cat I0634-1mg Phorbol 12-myristate 13-acetate (PMA) Sigma #Cat P1585-1MG UltraComp eBeads eBioscience #Cat 01-2222-42 DNAse I Invitrogen #Cat 18068-015 Collagenase A Roche #Cat 11088793001 BD Brilliant stain buffer BD #Cat 563794 Liberase TL Research Grade Roche #Cat 5401020001 Diphtheria Toxin from Corynebacterium diphtheriae Sigma-Aldrich #Cat D0564-1MG RLT Buffer Qiagen #Cat 79216 5-Ethynyl-2’-deoxyuridine Sigma #Cat 900584-50MG GolgiStop BD #Cat 554724 GolgiPlug BD #Cat 555029 IL-33 Trap Gift from Rudi Beyaert, VIB (under MTA) N/A Critical commercial assays LEGENDplexTM Mouse IL-33 Capture Bead B5, 13X Biolegend #Cat 740144 LEGENDplexTM Mouse Cytokine Panel 2 Standard Biolegend #Cat 740372 LEGENDplexTM Mouse Cytokine Panel 2 Detection Antibodies Biolegend #Cat 740149 LEGENDplexTM Buffer Set B Biolegend #Cat 740373 (Continued on next page) Cell Reports 38, 110447, March 1, 2022 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER LIVE/DEADTM Fixable Near-IR Dead Cell Stain Kit ThermoFisher #Cat L34975 LIVE/DEADTM Fixable Aqua Dead Cell Stain Kit ThermoFisher #Cat L34957 Zombie RedTM Fixable Viability Kit Biolegend #Cat 423109 Zombie NIRTM Fixable Viability Kit Biolegend #Cat 423105 CellTraceTM Violet Cell Proliferation Kit ThermoFisher #Cat C34557 Click-iTTM EdU Cell Proliferation Kit for Imaging, Alexa FluorTM 488 dye ThermoFisher #Cat C10337 Foxp3/Transcription Factor Staining Buffer Set ThermoFisher #Cat 00-5523-00 Deposited data Raw and analyzed data (Treg RNAseq) This paper GEO: GSE169024 Raw and analyzed data (NK RNAseq) This paper GEO: GSE169025 Experimental Models: Organisms/Strains Mus musculus: Strain: Wild-type FVB/N Janvier Laboratories FVB/N Mus musculus: Strain: K14-cre; Cdh1F/F;Trp53F/F (FVB/n) Netherlands Cancer Institute N/A Mus musculus: Strain Wap-cre; Cdh1F/F;Pik3caE545K (FVB/n) Netherlands Cancer Institute N/A Mus musculus: Strain Wap-cre; Cdh1F/F;AktE17K (FVB/n) Netherlands Cancer Institute N/A Mus musculus: Strain Cdh1F/F; Trp53F/F;Foxp3GFP-DTR(FVB/n) Netherlands Cancer Institute N/A Mus musculus: Strain Wap-cre; Cdh1F/F;PtenF/F (FVB/n) Netherlands Cancer Institute N/A Mus musculus: Strain Wap-cre; Cdh1F/F;Pik3caH1047R (FVB/n) Netherlands Cancer Institute N/A Mus musculus: Strain Brca1F/F; Trp53F/F (FVB/n) Netherlands Cancer Institute N/A Recombinant DNA Plasmid: IRES-DTR-GFP Gift from Alexander Rudensky (MSKCC) N/A Software and algorithms FlowJo v10.7 https://www.flowjo.com/solutions/flowjo N/A GSEA v4.0.3 https://www.gsea-msigdb.org/gsea/index.jsp N/A R statistical programming environment R Foundation for Statistical Computing https://www.r-project.org GraphPad Prism v8 https://www.graphpad.com/ scientific-software/prism/ N/A G*power software v3.1 https://www.psychologie.hhu.de/ arbeitsgruppen/allgemeine-psychologieund-arbeitspsychologie/gpower.html N/A Tophat 2.1.0 https://ccb.jhu.edu/software/ tophat/index.shtml N/A Itreecount (https://github.com/NKI-GCF/itreecount) N/A Hisat2 http://daehwankimlab.github.io/hisat2/ N/A
Virus:Article Title: Tumor-educated T regs drive organ-specific metastasis in breast cancer by impairing NK cells in the lymph node niche.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Armenian Hamster anti-CD3e, APC (clone 145-2C11) Invitrogen #Cat 17-0031-82 Armenian Hamster anti-CD3e, FITC (clone 145-2C11) Biolegend #Cat 100306 Armenian Hamster anti-CD3e, PE-Cy7 (clone 145-2C11) eBioscience #Cat 25-0031-82 Armenian Hamster anti-CD3e, PE (clone 145-2C11) Biolegend #Cat 100307 Rat anti-CD4, BV421 (clone GK1.5) BD #Cat 562891 Rat anti-CD4, BUV805 (clone GK1.5) BD #Cat 612900 Rat anti-CD4, PE (clone GK1.5) Invitrogen #Cat 12-0041-82 Rat anti-CD8, AF700 (clone 56-6.7) BioLegend #Cat 100730 Rat anti-CD8, BUV395 (clone 56-6.7) BD #Cat 563786 Rat anti-CD8, FITC (clone 56-6.7) eBioscience #Cat 11-0081-85 Rat anti-CD11b, APC (clone M1/70) eBioscience #Cat 17-01120-82 Rat anti-CD11b, BV786 (clone M1/70) BD #Cat 740861 Rat anti-CD25, PE (clone PC61) Biolegend #Cat 102008 Rat anti-CD25, APC (clone PC61) Biolegend #Cat 102011 Armenian Hamster anti-CD27, PerCP-eFluor 710 (clone LG.7F9) ThermoFisher #Cat 46-0271-82 Rat anti-CD44, BV605 (clone IM7) Biolegend #Cat 103047 Rat anti-CD45, BUV395 (clone 30F11) BD #Cat 564279 Rat anti-CD45, BUV563 (clone 30F11) BD #Cat 612924 Rat anti-CD45, APC-eF780 (clone 30F11) eBioscience #Cat 47-0451-82 Rat anti-CD49b, eF450 (clone DX5) ThermoFisher #Cat 48-5971-82 Rat anti-CD62L, AF700 (clone MEL-14) ThermoFisher #Cat 56-0621-82 Hamster anti-CD69, BUV737 (clone H1.2F3) BD #Cat 612793 Rat anti-CD103, BV711 (clone M290) BD #Cat 564320 Rat anti-mouse CD107a, PE (clone 1D4B) Biolegend #Cat 121611 Armenian hamster anti-CD152, PE-Cy7 (clone UC10-4B9) Biolegend #Cat 106313 Armenian hamster anti-CD278, PerCP-Cy5.5 (clone C398.4A) Biolegend #Cat 313517 Mouse anti-FOXP3, AF647 (clone 150D) Biolegend #Cat 320014 Mouse anti-Granzyme B, PE (clone QA16A02) Biolegend #Cat 372208 Rat anti-IFNy, eF450 (clone XMG1.2) ThermoFisher #Cat 48-7311-82 Rat anti-Ki67, PE (clone SOL-A15) ThermoFisher #Cat 12-5698-80 Mouse anti Ki-67, BV786 (clone B56) BD #Cat 563756 Mouse anti-NK1.1, APC-eFluor 780 (clone PK136) ThermoFisher #Cat 47-5941-82 Rat anti-NKp46, FITC (clone 29A1.4) ThermoFisher #Cat 11-3351-82 Rat anti-ST2, PE (clone RMST2-2) ThermoFisher #Cat 12-9335-82 Rat anti-TNFa, AF700 (clone MP6-XT22) Biolegend #Cat 506338 anti-CD25, mIgG2a (clone M2A) Gift from S. Quezada (under MTA), produced by Evitria N/A (Continued on next page) e1 Cell Reports 38, 110447, March 1, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER Mouse IgG2a isotype control (clone C1.18.4) BioXcell #Cat BE0085 InVivoPlus anti-mouse CD8a (clone 2.43) BioXcell #Cat BP0061 InVivoPlus anti-mouse NK1.1 (clone PK136) BioXcell #Cat BP0036 Purified Hamster Anti-Mouse CD3e BD #Cat 553058 Goat anti-IL-33 (polyclonal) R&D Systems #Cat AF3626 Goat IgG control (polyclonal) R&D Systems #Cat AB-108-C Rat anti-Keratine-8 (TROMA I) DSHB University of Iowa #Cat Troma I Rabbit anti-E-Cadherin (24E10) Cell Signaling #Cat 3195 Rat Anti-Mouse CD16/CD32, purified (clone 2.4G2) BD #Cat 553141 Armenian Hamster anti-CD3e, purified (clone 145-2C11) Biolegend #Cat 100302 Mouse anti-human CD3, APC (clone SK7) BD #Cat 340661 Mouse anti-human CD3, PerCP-cy5.5 (clone SK7) BD #Cat 340949 Mouse anti-human CD56, PE (clone B159) BD #Cat 561903 Mouse anti-human CD16, FITC (clone 3G8) BD #Cat 555406 Mouse anti-human IgG1, FITC (clone X40) BD #Cat 345815 Mouse anti-human CD25, APC (2A3) BD #Cat 340939 Mouse anti-human FoxP3, PE (PCH101) ThermoFisher #Cat 12-4776-42 Bacterial and virus strains pLenti#737-P2A-Cre Gift from Jos Jonkers (NKI) N/A Biological samples KEP tumor fragments This paper N/A Chemicals, peptides, and recombinant proteins Dynabeads mouse T-activator CD3/CD28 Thermofisher #Cat 11452D Recombinant murine IL-2 Peprotech #Cat 212-12 7-AAD Viability Staining Solution Thermofisher #Cat 00-6993-50 Ionomycin (calcium salt from Streptomyces conglobatus) Sigma #Cat I0634-1mg Phorbol 12-myristate 13-acetate (PMA) Sigma #Cat P1585-1MG UltraComp eBeads eBioscience #Cat 01-2222-42 DNAse I Invitrogen #Cat 18068-015 Collagenase A Roche #Cat 11088793001 BD Brilliant stain buffer BD #Cat 563794 Liberase TL Research Grade Roche #Cat 5401020001 Diphtheria Toxin from Corynebacterium diphtheriae Sigma-Aldrich #Cat D0564-1MG RLT Buffer Qiagen #Cat 79216 5-Ethynyl-2’-deoxyuridine Sigma #Cat 900584-50MG GolgiStop BD #Cat 554724 GolgiPlug BD #Cat 555029 IL-33 Trap Gift from Rudi Beyaert, VIB (under MTA) N/A Critical commercial assays LEGENDplexTM Mouse IL-33 Capture Bead B5, 13X Biolegend #Cat 740144 LEGENDplexTM Mouse Cytokine Panel 2 Standard Biolegend #Cat 740372 LEGENDplexTM Mouse Cytokine Panel 2 Detection Antibodies Biolegend #Cat 740149 LEGENDplexTM Buffer Set B Biolegend #Cat 740373 (Continued on next page) Cell Reports 38, 110447, March 1, 2022 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER LIVE/DEADTM Fixable Near-IR Dead Cell Stain Kit ThermoFisher #Cat L34975 LIVE/DEADTM Fixable Aqua Dead Cell Stain Kit ThermoFisher #Cat L34957 Zombie RedTM Fixable Viability Kit Biolegend #Cat 423109 Zombie NIRTM Fixable Viability Kit Biolegend #Cat 423105 CellTraceTM Violet Cell Proliferation Kit ThermoFisher #Cat C34557 Click-iTTM EdU Cell Proliferation Kit for Imaging, Alexa FluorTM 488 dye ThermoFisher #Cat C10337 Foxp3/Transcription Factor Staining Buffer Set ThermoFisher #Cat 00-5523-00 Deposited data Raw and analyzed data (Treg RNAseq) This paper GEO: GSE169024 Raw and analyzed data (NK RNAseq) This paper GEO: GSE169025 Experimental Models: Organisms/Strains Mus musculus: Strain: Wild-type FVB/N Janvier Laboratories FVB/N Mus musculus: Strain: K14-cre; Cdh1F/F;Trp53F/F (FVB/n) Netherlands Cancer Institute N/A Mus musculus: Strain Wap-cre; Cdh1F/F;Pik3caE545K (FVB/n) Netherlands Cancer Institute N/A Mus musculus: Strain Wap-cre; Cdh1F/F;AktE17K (FVB/n) Netherlands Cancer Institute N/A Mus musculus: Strain Cdh1F/F; Trp53F/F;Foxp3GFP-DTR(FVB/n) Netherlands Cancer Institute N/A Mus musculus: Strain Wap-cre; Cdh1F/F;PtenF/F (FVB/n) Netherlands Cancer Institute N/A Mus musculus: Strain Wap-cre; Cdh1F/F;Pik3caH1047R (FVB/n) Netherlands Cancer Institute N/A Mus musculus: Strain Brca1F/F; Trp53F/F (FVB/n) Netherlands Cancer Institute N/A Recombinant DNA Plasmid: IRES-DTR-GFP Gift from Alexander Rudensky (MSKCC) N/A Software and algorithms FlowJo v10.7 https://www.flowjo.com/solutions/flowjo N/A GSEA v4.0.3 https://www.gsea-msigdb.org/gsea/index.jsp N/A R statistical programming environment R Foundation for Statistical Computing https://www.r-project.org GraphPad Prism v8 https://www.graphpad.com/ scientific-software/prism/ N/A G*power software v3.1 https://www.psychologie.hhu.de/ arbeitsgruppen/allgemeine-psychologieund-arbeitspsychologie/gpower.html N/A Tophat 2.1.0 https://ccb.jhu.edu/software/ tophat/index.shtml N/A Itreecount (https://github.com/NKI-GCF/itreecount) N/A Hisat2 http://daehwankimlab.github.io/hisat2/ N/A
Recombinant:Article Title: Tumor-educated T regs drive organ-specific metastasis in breast cancer by impairing NK cells in the lymph node niche.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Armenian Hamster anti-CD3e, APC (clone 145-2C11) Invitrogen #Cat 17-0031-82 Armenian Hamster anti-CD3e, FITC (clone 145-2C11) Biolegend #Cat 100306 Armenian Hamster anti-CD3e, PE-Cy7 (clone 145-2C11) eBioscience #Cat 25-0031-82 Armenian Hamster anti-CD3e, PE (clone 145-2C11) Biolegend #Cat 100307 Rat anti-CD4, BV421 (clone GK1.5) BD #Cat 562891 Rat anti-CD4, BUV805 (clone GK1.5) BD #Cat 612900 Rat anti-CD4, PE (clone GK1.5) Invitrogen #Cat 12-0041-82 Rat anti-CD8, AF700 (clone 56-6.7) BioLegend #Cat 100730 Rat anti-CD8, BUV395 (clone 56-6.7) BD #Cat 563786 Rat anti-CD8, FITC (clone 56-6.7) eBioscience #Cat 11-0081-85 Rat anti-CD11b, APC (clone M1/70) eBioscience #Cat 17-01120-82 Rat anti-CD11b, BV786 (clone M1/70) BD #Cat 740861 Rat anti-CD25, PE (clone PC61) Biolegend #Cat 102008 Rat anti-CD25, APC (clone PC61) Biolegend #Cat 102011 Armenian Hamster anti-CD27, PerCP-eFluor 710 (clone LG.7F9) ThermoFisher #Cat 46-0271-82 Rat anti-CD44, BV605 (clone IM7) Biolegend #Cat 103047 Rat anti-CD45, BUV395 (clone 30F11) BD #Cat 564279 Rat anti-CD45, BUV563 (clone 30F11) BD #Cat 612924 Rat anti-CD45, APC-eF780 (clone 30F11) eBioscience #Cat 47-0451-82 Rat anti-CD49b, eF450 (clone DX5) ThermoFisher #Cat 48-5971-82 Rat anti-CD62L, AF700 (clone MEL-14) ThermoFisher #Cat 56-0621-82 Hamster anti-CD69, BUV737 (clone H1.2F3) BD #Cat 612793 Rat anti-CD103, BV711 (clone M290) BD #Cat 564320 Rat anti-mouse CD107a, PE (clone 1D4B) Biolegend #Cat 121611 Armenian hamster anti-CD152, PE-Cy7 (clone UC10-4B9) Biolegend #Cat 106313 Armenian hamster anti-CD278, PerCP-Cy5.5 (clone C398.4A) Biolegend #Cat 313517 Mouse anti-FOXP3, AF647 (clone 150D) Biolegend #Cat 320014 Mouse anti-Granzyme B, PE (clone QA16A02) Biolegend #Cat 372208 Rat anti-IFNy, eF450 (clone XMG1.2) ThermoFisher #Cat 48-7311-82 Rat anti-Ki67, PE (clone SOL-A15) ThermoFisher #Cat 12-5698-80 Mouse anti Ki-67, BV786 (clone B56) BD #Cat 563756 Mouse anti-NK1.1, APC-eFluor 780 (clone PK136) ThermoFisher #Cat 47-5941-82 Rat anti-NKp46, FITC (clone 29A1.4) ThermoFisher #Cat 11-3351-82 Rat anti-ST2, PE (clone RMST2-2) ThermoFisher #Cat 12-9335-82 Rat anti-TNFa, AF700 (clone MP6-XT22) Biolegend #Cat 506338 anti-CD25, mIgG2a (clone M2A) Gift from S. Quezada (under MTA), produced by Evitria N/A (Continued on next page) e1 Cell Reports 38, 110447, March 1, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER Mouse IgG2a isotype control (clone C1.18.4) BioXcell #Cat BE0085 InVivoPlus anti-mouse CD8a (clone 2.43) BioXcell #Cat BP0061 InVivoPlus anti-mouse NK1.1 (clone PK136) BioXcell #Cat BP0036 Purified Hamster Anti-Mouse CD3e BD #Cat 553058 Goat anti-IL-33 (polyclonal) R&D Systems #Cat AF3626 Goat IgG control (polyclonal) R&D Systems #Cat AB-108-C Rat anti-Keratine-8 (TROMA I) DSHB University of Iowa #Cat Troma I Rabbit anti-E-Cadherin (24E10) Cell Signaling #Cat 3195 Rat Anti-Mouse CD16/CD32, purified (clone 2.4G2) BD #Cat 553141 Armenian Hamster anti-CD3e, purified (clone 145-2C11) Biolegend #Cat 100302 Mouse anti-human CD3, APC (clone SK7) BD #Cat 340661 Mouse anti-human CD3, PerCP-cy5.5 (clone SK7) BD #Cat 340949 Mouse anti-human CD56, PE (clone B159) BD #Cat 561903 Mouse anti-human CD16, FITC (clone 3G8) BD #Cat 555406 Mouse anti-human IgG1, FITC (clone X40) BD #Cat 345815 Mouse anti-human CD25, APC (2A3) BD #Cat 340939 Mouse anti-human FoxP3, PE (PCH101) ThermoFisher #Cat 12-4776-42 Bacterial and virus strains pLenti#737-P2A-Cre Gift from Jos Jonkers (NKI) N/A Biological samples KEP tumor fragments This paper N/A Chemicals, peptides, and recombinant proteins Dynabeads mouse T-activator CD3/CD28 Thermofisher #Cat 11452D Recombinant murine IL-2 Peprotech #Cat 212-12 7-AAD Viability Staining Solution Thermofisher #Cat 00-6993-50 Ionomycin (calcium salt from Streptomyces conglobatus) Sigma #Cat I0634-1mg Phorbol 12-myristate 13-acetate (PMA) Sigma #Cat P1585-1MG UltraComp eBeads eBioscience #Cat 01-2222-42 DNAse I Invitrogen #Cat 18068-015 Collagenase A Roche #Cat 11088793001 BD Brilliant stain buffer BD #Cat 563794 Liberase TL Research Grade Roche #Cat 5401020001 Diphtheria Toxin from Corynebacterium diphtheriae Sigma-Aldrich #Cat D0564-1MG RLT Buffer Qiagen #Cat 79216 5-Ethynyl-2’-deoxyuridine Sigma #Cat 900584-50MG GolgiStop BD #Cat 554724 GolgiPlug BD #Cat 555029 IL-33 Trap Gift from Rudi Beyaert, VIB (under MTA) N/A Critical commercial assays LEGENDplexTM Mouse IL-33 Capture Bead B5, 13X Biolegend #Cat 740144 LEGENDplexTM Mouse Cytokine Panel 2 Standard Biolegend #Cat 740372 LEGENDplexTM Mouse Cytokine Panel 2 Detection Antibodies Biolegend #Cat 740149 LEGENDplexTM Buffer Set B Biolegend #Cat 740373 (Continued on next page) Cell Reports 38, 110447, March 1, 2022 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER LIVE/DEADTM Fixable Near-IR Dead Cell Stain Kit ThermoFisher #Cat L34975 LIVE/DEADTM Fixable Aqua Dead Cell Stain Kit ThermoFisher #Cat L34957 Zombie RedTM Fixable Viability Kit Biolegend #Cat 423109 Zombie NIRTM Fixable Viability Kit Biolegend #Cat 423105 CellTraceTM Violet Cell Proliferation Kit ThermoFisher #Cat C34557 Click-iTTM EdU Cell Proliferation Kit for Imaging, Alexa FluorTM 488 dye ThermoFisher #Cat C10337 Foxp3/Transcription Factor Staining Buffer Set ThermoFisher #Cat 00-5523-00 Deposited data Raw and analyzed data (Treg RNAseq) This paper GEO: GSE169024 Raw and analyzed data (NK RNAseq) This paper GEO: GSE169025 Experimental Models: Organisms/Strains Mus musculus: Strain: Wild-type FVB/N Janvier Laboratories FVB/N Mus musculus: Strain: K14-cre; Cdh1F/F;Trp53F/F (FVB/n) Netherlands Cancer Institute N/A Mus musculus: Strain Wap-cre; Cdh1F/F;Pik3caE545K (FVB/n) Netherlands Cancer Institute N/A Mus musculus: Strain Wap-cre; Cdh1F/F;AktE17K (FVB/n) Netherlands Cancer Institute N/A Mus musculus: Strain Cdh1F/F; Trp53F/F;Foxp3GFP-DTR(FVB/n) Netherlands Cancer Institute N/A Mus musculus: Strain Wap-cre; Cdh1F/F;PtenF/F (FVB/n) Netherlands Cancer Institute N/A Mus musculus: Strain Wap-cre; Cdh1F/F;Pik3caH1047R (FVB/n) Netherlands Cancer Institute N/A Mus musculus: Strain Brca1F/F; Trp53F/F (FVB/n) Netherlands Cancer Institute N/A Recombinant DNA Plasmid: IRES-DTR-GFP Gift from Alexander Rudensky (MSKCC) N/A Software and algorithms FlowJo v10.7 https://www.flowjo.com/solutions/flowjo N/A GSEA v4.0.3 https://www.gsea-msigdb.org/gsea/index.jsp N/A R statistical programming environment R Foundation for Statistical Computing https://www.r-project.org GraphPad Prism v8 https://www.graphpad.com/ scientific-software/prism/ N/A G*power software v3.1 https://www.psychologie.hhu.de/ arbeitsgruppen/allgemeine-psychologieund-arbeitspsychologie/gpower.html N/A Tophat 2.1.0 https://ccb.jhu.edu/software/ tophat/index.shtml N/A Itreecount (https://github.com/NKI-GCF/itreecount) N/A Hisat2 http://daehwankimlab.github.io/hisat2/ N/A
Staining:Article Title: Tumor-educated T regs drive organ-specific metastasis in breast cancer by impairing NK cells in the lymph node niche.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Armenian Hamster anti-CD3e, APC (clone 145-2C11) Invitrogen #Cat 17-0031-82 Armenian Hamster anti-CD3e, FITC (clone 145-2C11) Biolegend #Cat 100306 Armenian Hamster anti-CD3e, PE-Cy7 (clone 145-2C11) eBioscience #Cat 25-0031-82 Armenian Hamster anti-CD3e, PE (clone 145-2C11) Biolegend #Cat 100307 Rat anti-CD4, BV421 (clone GK1.5) BD #Cat 562891 Rat anti-CD4, BUV805 (clone GK1.5) BD #Cat 612900 Rat anti-CD4, PE (clone GK1.5) Invitrogen #Cat 12-0041-82 Rat anti-CD8, AF700 (clone 56-6.7) BioLegend #Cat 100730 Rat anti-CD8, BUV395 (clone 56-6.7) BD #Cat 563786 Rat anti-CD8, FITC (clone 56-6.7) eBioscience #Cat 11-0081-85 Rat anti-CD11b, APC (clone M1/70) eBioscience #Cat 17-01120-82 Rat anti-CD11b, BV786 (clone M1/70) BD #Cat 740861 Rat anti-CD25, PE (clone PC61) Biolegend #Cat 102008 Rat anti-CD25, APC (clone PC61) Biolegend #Cat 102011 Armenian Hamster anti-CD27, PerCP-eFluor 710 (clone LG.7F9) ThermoFisher #Cat 46-0271-82 Rat anti-CD44, BV605 (clone IM7) Biolegend #Cat 103047 Rat anti-CD45, BUV395 (clone 30F11) BD #Cat 564279 Rat anti-CD45, BUV563 (clone 30F11) BD #Cat 612924 Rat anti-CD45, APC-eF780 (clone 30F11) eBioscience #Cat 47-0451-82 Rat anti-CD49b, eF450 (clone DX5) ThermoFisher #Cat 48-5971-82 Rat anti-CD62L, AF700 (clone MEL-14) ThermoFisher #Cat 56-0621-82 Hamster anti-CD69, BUV737 (clone H1.2F3) BD #Cat 612793 Rat anti-CD103, BV711 (clone M290) BD #Cat 564320 Rat anti-mouse CD107a, PE (clone 1D4B) Biolegend #Cat 121611 Armenian hamster anti-CD152, PE-Cy7 (clone UC10-4B9) Biolegend #Cat 106313 Armenian hamster anti-CD278, PerCP-Cy5.5 (clone C398.4A) Biolegend #Cat 313517 Mouse anti-FOXP3, AF647 (clone 150D) Biolegend #Cat 320014 Mouse anti-Granzyme B, PE (clone QA16A02) Biolegend #Cat 372208 Rat anti-IFNy, eF450 (clone XMG1.2) ThermoFisher #Cat 48-7311-82 Rat anti-Ki67, PE (clone SOL-A15) ThermoFisher #Cat 12-5698-80 Mouse anti Ki-67, BV786 (clone B56) BD #Cat 563756 Mouse anti-NK1.1, APC-eFluor 780 (clone PK136) ThermoFisher #Cat 47-5941-82 Rat anti-NKp46, FITC (clone 29A1.4) ThermoFisher #Cat 11-3351-82 Rat anti-ST2, PE (clone RMST2-2) ThermoFisher #Cat 12-9335-82 Rat anti-TNFa, AF700 (clone MP6-XT22) Biolegend #Cat 506338 anti-CD25, mIgG2a (clone M2A) Gift from S. Quezada (under MTA), produced by Evitria N/A (Continued on next page) e1 Cell Reports 38, 110447, March 1, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER Mouse IgG2a isotype control (clone C1.18.4) BioXcell #Cat BE0085 InVivoPlus anti-mouse CD8a (clone 2.43) BioXcell #Cat BP0061 InVivoPlus anti-mouse NK1.1 (clone PK136) BioXcell #Cat BP0036 Purified Hamster Anti-Mouse CD3e BD #Cat 553058 Goat anti-IL-33 (polyclonal) R&D Systems #Cat AF3626 Goat IgG control (polyclonal) R&D Systems #Cat AB-108-C Rat anti-Keratine-8 (TROMA I) DSHB University of Iowa #Cat Troma I Rabbit anti-E-Cadherin (24E10) Cell Signaling #Cat 3195 Rat Anti-Mouse CD16/CD32, purified (clone 2.4G2) BD #Cat 553141 Armenian Hamster anti-CD3e, purified (clone 145-2C11) Biolegend #Cat 100302 Mouse anti-human CD3, APC (clone SK7) BD #Cat 340661 Mouse anti-human CD3, PerCP-cy5.5 (clone SK7) BD #Cat 340949 Mouse anti-human CD56, PE (clone B159) BD #Cat 561903 Mouse anti-human CD16, FITC (clone 3G8) BD #Cat 555406 Mouse anti-human IgG1, FITC (clone X40) BD #Cat 345815 Mouse anti-human CD25, APC (2A3) BD #Cat 340939 Mouse anti-human FoxP3, PE (PCH101) ThermoFisher #Cat 12-4776-42 Bacterial and virus strains pLenti#737-P2A-Cre Gift from Jos Jonkers (NKI) N/A Biological samples KEP tumor fragments This paper N/A Chemicals, peptides, and recombinant proteins Dynabeads mouse T-activator CD3/CD28 Thermofisher #Cat 11452D Recombinant murine IL-2 Peprotech #Cat 212-12 7-AAD Viability Staining Solution Thermofisher #Cat 00-6993-50 Ionomycin (calcium salt from Streptomyces conglobatus) Sigma #Cat I0634-1mg Phorbol 12-myristate 13-acetate (PMA) Sigma #Cat P1585-1MG UltraComp eBeads eBioscience #Cat 01-2222-42 DNAse I Invitrogen #Cat 18068-015 Collagenase A Roche #Cat 11088793001 BD Brilliant stain buffer BD #Cat 563794 Liberase TL Research Grade Roche #Cat 5401020001 Diphtheria Toxin from Corynebacterium diphtheriae Sigma-Aldrich #Cat D0564-1MG RLT Buffer Qiagen #Cat 79216 5-Ethynyl-2’-deoxyuridine Sigma #Cat 900584-50MG GolgiStop BD #Cat 554724 GolgiPlug BD #Cat 555029 IL-33 Trap Gift from Rudi Beyaert, VIB (under MTA) N/A Critical commercial assays LEGENDplexTM Mouse IL-33 Capture Bead B5, 13X Biolegend #Cat 740144 LEGENDplexTM Mouse Cytokine Panel 2 Standard Biolegend #Cat 740372 LEGENDplexTM Mouse Cytokine Panel 2 Detection Antibodies Biolegend #Cat 740149 LEGENDplexTM Buffer Set B Biolegend #Cat 740373 (Continued on next page) Cell Reports 38, 110447, March 1, 2022 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER LIVE/DEADTM Fixable Near-IR Dead Cell Stain Kit ThermoFisher #Cat L34975 LIVE/DEADTM Fixable Aqua Dead Cell Stain Kit ThermoFisher #Cat L34957 Zombie RedTM Fixable Viability Kit Biolegend #Cat 423109 Zombie NIRTM Fixable Viability Kit Biolegend #Cat 423105 CellTraceTM Violet Cell Proliferation Kit ThermoFisher #Cat C34557 Click-iTTM EdU Cell Proliferation Kit for Imaging, Alexa FluorTM 488 dye ThermoFisher #Cat C10337 Foxp3/Transcription Factor Staining Buffer Set ThermoFisher #Cat 00-5523-00 Deposited data Raw and analyzed data (Treg RNAseq) This paper GEO: GSE169024 Raw and analyzed data (NK RNAseq) This paper GEO: GSE169025 Experimental Models: Organisms/Strains Mus musculus: Strain: Wild-type FVB/N Janvier Laboratories FVB/N Mus musculus: Strain: K14-cre; Cdh1F/F;Trp53F/F (FVB/n) Netherlands Cancer Institute N/A Mus musculus: Strain Wap-cre; Cdh1F/F;Pik3caE545K (FVB/n) Netherlands Cancer Institute N/A Mus musculus: Strain Wap-cre; Cdh1F/F;AktE17K (FVB/n) Netherlands Cancer Institute N/A Mus musculus: Strain Cdh1F/F; Trp53F/F;Foxp3GFP-DTR(FVB/n) Netherlands Cancer Institute N/A Mus musculus: Strain Wap-cre; Cdh1F/F;PtenF/F (FVB/n) Netherlands Cancer Institute N/A Mus musculus: Strain Wap-cre; Cdh1F/F;Pik3caH1047R (FVB/n) Netherlands Cancer Institute N/A Mus musculus: Strain Brca1F/F; Trp53F/F (FVB/n) Netherlands Cancer Institute N/A Recombinant DNA Plasmid: IRES-DTR-GFP Gift from Alexander Rudensky (MSKCC) N/A Software and algorithms FlowJo v10.7 https://www.flowjo.com/solutions/flowjo N/A GSEA v4.0.3 https://www.gsea-msigdb.org/gsea/index.jsp N/A R statistical programming environment R Foundation for Statistical Computing https://www.r-project.org GraphPad Prism v8 https://www.graphpad.com/ scientific-software/prism/ N/A G*power software v3.1 https://www.psychologie.hhu.de/ arbeitsgruppen/allgemeine-psychologieund-arbeitspsychologie/gpower.html N/A Tophat 2.1.0 https://ccb.jhu.edu/software/ tophat/index.shtml N/A Itreecount (https://github.com/NKI-GCF/itreecount) N/A Hisat2 http://daehwankimlab.github.io/hisat2/ N/A
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