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    Tree Star Inc algorithms graphpad prism version 9 5 1 graphpad
    Algorithms Graphpad Prism Version 9 5 1 Graphpad, supplied by Tree Star Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/prism+version+9/flowjo10/pm42166330-192-5-19
    Average 86 stars, based on 1 article reviews
    algorithms graphpad prism version 9 5 1 graphpad - by Bioz Stars, 2026-11
    86/100 stars

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    Software:

    Article Title: 5' UTR introns reduce nuclear transgene silencing and enable robust protein expression in Chlamydomonas reinhardtii.
    Article Snippet: .. This paper N/A Software and algorithms GraphPad Prism version 9.5.1 GraphPad https://www.graphpad.com/ R version 4.2.2 R https://cran.r-project.org/bin/windows/base/ FlowJo v10 TreeStar https://www.flowjo.com/solutions/flowjo/downloads QuantStudioTM Design & Analysis Software Thermo Fisher https://www.thermofisher.cn/cn/zh/home/technical- resources/software-downloads/quantstudio-3-5real-time-pcr-systems.html Fiji Schindelin et al.34 https://imagej.net/software/fiji/downloads Other LSM 980 Confocal Microscope Zeiss LSM 980 BD LSR II flow cytometer BD biosciences N/A SapphireTM Biomolecular Imager Azure Biosystems N/A Cell Reports 45, 117424, June 23, 2026 13 ..

    Article Title: Regulatory T cell depletion promotes myeloid cell activation and glioblastoma response to anti-PD1 and tumor-targeting antibodies.
    Article Snippet: Male, 76 years Patient 6 This study Glioblastoma, IDH-wildtype, CNS WHO grade 4 Patient 7 This study Glioblastoma, IDH-wildtype, CNS WHO grade 4 Patient 8 This study Glioblastoma, IDH-wildtype, CNS WHO grade 4 Patient 9 This study Glioblastoma, IDH-wildtype, CNS WHO grade 4 Chemicals, peptides, and recombinant proteins EGF, final concentration 10 ng/mL Peprotech Cat #315-09 FGF, final concentration 10 ng/mL Peprotech Cat #100-18B Laminin Cultrex Cat #3446-005-01 Liberase TL Roche Cat #05401119001 DNAse Sigma Cat #101041590001 Diphteria toxin from Corynebacterium diphteriae Merck Cat #322326 Viability dye eFluor780 ThermoFisher Cat #65-865-14 2mM Glutamine Sigma (Merck) Cat #G1272-10mL 1x MEM NEAA (100x) Gibco Cat #11140-035 100mL 1 mM Sodium Pyruvate Sigma (Merck) Cat #S8636-100mL Matrigel Matrix Corning Cat #356234 Collagen I Corning Cat #354249 Sodium Bicarbonate 1.1% Sigma Cat #102399192 Collagenase IV (1 mg/mL) Thermo Fisher Scientific Cat #17104019 Pen/Strep 1% Sigma Cat #P0781-100mL 2mM EDTA Sigma (Merck) Cat #03690-100mL Recombinant Human IFN-g PeproTech Cat #300-02 CFSE Thermo Fisher Scientific Cat #C34554 (Continued on next page) Immunity 58, 1–18.e1–e8, May 13, 2025 e3 .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays BD CytoFix/Cytoperm BD Biosciences Cat #554714 Foxp3 Transcription Factor Staining Buffer set eBioscience Cat #00-5523-00 Deposited data Single-cell RNAseq data This study GSE218013 Experimental models: Cell lines NPE-IE cells Gift Steven Pollard, University of Edinburgh, United Kingdom GL261-EGFRvIII Gift Martin Pule, UCL, United Kingdom MC38-B7-H3 Made in house N/A Experimental models: Organisms/strains C57BL/6 Charles Rivers N/A B6.129(Cg)-Foxp3tm3(DTR/GFP)Ayr/J Charles Rivers N/A Lysm-Cre-Fcgr4KO Gift Jeffrey Ravetch, Rockefeller University, USA Software and algorithms FlowJo v.10.8.1 TreeStar https://www.flowjo.com/solutions/flowjo R version 3.6.2 Cran r-project.org GraphPad Prism 9 GraphPad www.graphpad.com Other NeuroCult Basal Medium StemCell Technologies Cat #05700 NeuroCult Proliferation Supplement StemCell Technologies Cat #05701 100 UI/mL penicillin, 100 mg/mL streptomycin Gibco Cat #15140-122 Accutase Life Technologies-eBioscience Cat #00-4555-56 Lacrilube/Xaline gel Lacri-Lube Cat #0345520 0.25% Marcaine National Veterinary Service Cat #115095 10% Rymadyl National Veterinary Service Cat #91649 5 ml Hamilton micro-syringe Hamilton Cat #7641-01 Fine step stereotactic device Harvard Apparatus Digital, Single mouse Stereotaxic U frame Cat #75-1828, Cat #75-1883, Cat #75- 4507, Cat #75-1887, Cat #72-6066 6-0 Vicryl Ethicon Cat #ETW9913 Metacam National Veterinary Service Cat #45755 CountBrightTM Absolute counting Beads Invitrogen Cat #C36950 UW media, Cold storage solution Belzer Cat #BUWC FBS PAN-Biotech Cat #P40-37500 DMEM Sigma (Merck) Cat #D6546-500mL MEM Non-Essential Amino Acids Solution (100X) ThermoFisher Scientific Cat #11140050 Trypsin ThermoFisher Scientific Cat #108444 ..

    Article Title: Clonal hematopoiesis driven by chromosome 1q/MDM4 trisomy defines a canonical route toward leukemia in Fanconi anemia.
    Article Snippet: Article Clonal hematopoiesis driven by chromosome1q/MDM4 trisomy defines a canonical route toward leukemia in

    Article Title: Tissue-specific transcriptional profiles and heterogeneity of natural killer cells and group 1 innate lymphoid cells.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies PeCy5 anti-mouse CD3 (145-2C11) BD Biosciences Cat# 553065; RRID:AB_394598 PeCy5 anti-mouse TCRb (H57-597) BD Biosciences Cat# 553173; RRID:AB_394685 BV650 anti-mouse CD226/DNAM-1 (10E5) BD Biosciences Cat# 750916; RRID:AB_2875003 BUV805 anti-mouse CD45 (104) BD Biosciences Cat# 741957; RRID:AB_2871265 BV785 anti-mouse CD49a (Ha31/8) BD Biosciences Cat# 740919; RRID:AB_2740560 BUV395 anti-mouse CD49b (HMa2) BD Biosciences Cat# 740250; RRID:AB_2739996 A700 anti-mouse NKp46 (29A1.4) BD Biosciences Cat# 561169; RRID:AB_10561840 BV510 anti-mouse NK1.1 (PK136) BD Biosciences Cat# 563096; RRID:AB_2738002 APC.Cy7 anti-mouse CD90.2 (53-2.1) BD Biosciences Cat# 561641; RRID:AB_10898013 BUV661 anti-mouse CD122 (5H4) BD Biosciences Cat# 741537; RRID:AB_2870975 BV421 anti-mouse CD223/LAG-3 (C9B7W) BD Biosciences Cat# 740072; RRID:AB_2739836 BV650 anti-mouse Ly49D (4E5) BD Biosciences Cat# 742558; RRID:AB_2740868 BV605 anti-mouse VISTA/PD-1H (MIH64) BD Biosciences Cat# 742722; RRID:AB_2740998 PeCy5 anti-mouse Ter-119 (Ter-119) eBiosciences Cat# 15-5921-83; RRID:AB_468811 PerCP-eFluor 710 anti-mouse CD200R (OX110) eBiosciences Cat# 46-5201-82; RRID:AB_10804765 PeCy7 anti-mouse CD127 (A7R34) eBiosciences Cat# 25-1271-82; RRID:AB_469649 eFluor660 anti-mouse Eomes (Dan11mag) eBiosciences Cat# 50-4875-82; RRID:AB_2574227 APC anti-mouse CD253/TRAIL (N2B2) eBiosciences Cat# 17-5951-82; RRID:AB_2573248 PeCy5 anti-mouse TCRgd (GL3) eBiosciences Cat# 15-5711-82; RRID:AB_468804 FITC anti-mouse Ly49H (3D10) eBiosciences Cat# 11-5886-82; RRID:AB_1257159 PeCy5 anti-mouse CD19 (1D3) eBiosciences Cat# 15-0193-82; RRID:AB_657672 APC anti-mouse SDC4 (REA640) Miltenyi Biotec Cat# 130-109-831; RRID:AB_2653641 PE/Dazzle 594 CXCR6 (SA051D1) BioLegend Cat# 151117; RRID:AB_2721700 A700 anti-mouse CD11b (M1/70) BioLegend Cat# 101222; RRID:AB_493705 (Continued on next page) Cell Reports Medicine 3, 100812, November 15, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Healthy liver, spleen, salivary glands and lamina propria from adult mice N/A Human ILC single-cell dataset Mazzurana et al., 20219 Downloaded from the NCBI GEO depository (GSE150050) Chemicals, peptides, and recombinant proteins Collagenase IV Sigma Aldrich C5138 Collagenase VIII Sigma Aldrich C2139 DNase Sigma Aldrich DN25 Fetal bovine serum Thermo Fisher scientific 10437028 RPMI1640 Corning 10-041-CV Phosphate Buffered Saline Corning 21-040-CMR EDTA Invitrogen AM9260G Foxp3 transcription factor staining buffer kit Invitrogen 00-5523-00 LIVE/DEAD Fixable Near-IR dead cell stain kit Life technologies L10119 Critical commercial assays Easysep Mouse NK Cell Isolation Kit Stemcell technologies 19855 103 Genomics Chromium Next GEM Single Cell 30 v3.1 kit Fisher scientific NC1690752 Qubit High Sensitivity assay kit Invitrogen Q32854 Deposited data Raw and analyzed data (scRNA-seq) This paper GEO: GSE189807 Experimental models: Organisms/strains Mouse: C57BL/6JR Janvier Labs https://janvier-labs.com/fiche_produit/2-c57bl-6jrj/ Software and algorithms Flowjo software v10 Tree Star https://www.flowjo.com/RRID: SCR_008520 Graph Pad Prism Version 9 Graphpad https://www.graphpad.com/RRID: SCR_002798 CellRanger software v4.0.0 103 Genomics https://support.10xgenomics.com/single-cell-gene- expression/software/pipelines/latest/what-is-cell-ranger CITE-seq-Count 1.4.3 https://hoohm.github.io/CITE-seq-Count/ Seurat v4.0.0 Hao et al., 202143 https://satijalab.org/seurat/ Monocle 0.3.1 N/A https://cole-trapnell-lab.github.io/monocle3/ ClusterProfiler 3.18.1 N/A https://guangchuangyu.github.io/software/ clusterProfiler/ Harmony 0.1.0 Korsunsky, I et al. Nat Methods, 201922 https://portals.broadinstitute.org/harmony/articles/ quickstart.html ..

    Article Title: Potent neutralization of SARS-CoV-2 variants of concern by an antibody with an uncommon genetic signature and structural mode of spike recognition
    Article Snippet: N/A Software and algorithms Cell Ranger 10X Genomics https://support.10xgenomics.com/ single-cell-gene-expression/ software/downloads/latest (Continued on next page) e2 Cell Reports 37, 109784, October 5, 2021 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER HighV-Quest Alamyar et al., 2012 http://www.imgt.org/IMGTindex/ IMGTHighV-QUEST.php ChangeO Gupta et al., 2015 https://changeo.readthedocs.io/en/stable/ Geneious 11.1.5 https://www.geneious.com N/A PyMOL The PyMOL Molecular Graphics System, Version 2.3.5 Schrödinger, LLC N/A Flowjo v10 TreeStar https://www.flowjo.com/ GraphPad Prism 9.0.0 https://www.graphpad.com:443/ N/A Biacore X100 Evaluation Software GE Healthcare V2.0.1 SerialEM Mastronarde, 2003 https://bio3d.colorado.edu/SerialEM/ cryoSPARC v3.2.0 Punjani et al., 2017 https://cryosparc.com/ SAbPred Dunbar et al., 2016 http://opig.stats.ox.ac.uk/ webapps/newsabdab/sabpred/ COOT Emsley and Cowtan, 2004 http://bernhardcl.github.io/coot/ Phenix Adams et al., 2002; Afonine et al., 2018 https://phenix-online.org/ ISOLDE Croll, 2018 http://preview.cgl.ucsf.edu/ chimerax/download.html ChimeraX Goddard et al., 2018 https://www.rbvi.ucsf.edu/chimerax/ Other Galanthus nivalis lectin Vector Laboratories Cat # AL-1243-5 1-Step Ultra TMB-ELISA Substrate Solution ThermoFisher Scientific Cat#34029 Costar High Binding Microplates Corning Cat#9018 Saponin VWR TCS0019-025G Paraformaldehyde VWR 100496-496 Donor Goat Serum Atlanta Biologicals S13150 DPBS(++) Cytiva SH30264.02 Article ll OPEN ACCESS ..

    Microscopy:

    Article Title: 5' UTR introns reduce nuclear transgene silencing and enable robust protein expression in Chlamydomonas reinhardtii.
    Article Snippet: .. This paper N/A Software and algorithms GraphPad Prism version 9.5.1 GraphPad https://www.graphpad.com/ R version 4.2.2 R https://cran.r-project.org/bin/windows/base/ FlowJo v10 TreeStar https://www.flowjo.com/solutions/flowjo/downloads QuantStudioTM Design & Analysis Software Thermo Fisher https://www.thermofisher.cn/cn/zh/home/technical- resources/software-downloads/quantstudio-3-5real-time-pcr-systems.html Fiji Schindelin et al.34 https://imagej.net/software/fiji/downloads Other LSM 980 Confocal Microscope Zeiss LSM 980 BD LSR II flow cytometer BD biosciences N/A SapphireTM Biomolecular Imager Azure Biosystems N/A Cell Reports 45, 117424, June 23, 2026 13 ..

    Flow Cytometry:

    Article Title: 5' UTR introns reduce nuclear transgene silencing and enable robust protein expression in Chlamydomonas reinhardtii.
    Article Snippet: .. This paper N/A Software and algorithms GraphPad Prism version 9.5.1 GraphPad https://www.graphpad.com/ R version 4.2.2 R https://cran.r-project.org/bin/windows/base/ FlowJo v10 TreeStar https://www.flowjo.com/solutions/flowjo/downloads QuantStudioTM Design & Analysis Software Thermo Fisher https://www.thermofisher.cn/cn/zh/home/technical- resources/software-downloads/quantstudio-3-5real-time-pcr-systems.html Fiji Schindelin et al.34 https://imagej.net/software/fiji/downloads Other LSM 980 Confocal Microscope Zeiss LSM 980 BD LSR II flow cytometer BD biosciences N/A SapphireTM Biomolecular Imager Azure Biosystems N/A Cell Reports 45, 117424, June 23, 2026 13 ..

    Staining:

    Article Title: Regulatory T cell depletion promotes myeloid cell activation and glioblastoma response to anti-PD1 and tumor-targeting antibodies.
    Article Snippet: Male, 76 years Patient 6 This study Glioblastoma, IDH-wildtype, CNS WHO grade 4 Patient 7 This study Glioblastoma, IDH-wildtype, CNS WHO grade 4 Patient 8 This study Glioblastoma, IDH-wildtype, CNS WHO grade 4 Patient 9 This study Glioblastoma, IDH-wildtype, CNS WHO grade 4 Chemicals, peptides, and recombinant proteins EGF, final concentration 10 ng/mL Peprotech Cat #315-09 FGF, final concentration 10 ng/mL Peprotech Cat #100-18B Laminin Cultrex Cat #3446-005-01 Liberase TL Roche Cat #05401119001 DNAse Sigma Cat #101041590001 Diphteria toxin from Corynebacterium diphteriae Merck Cat #322326 Viability dye eFluor780 ThermoFisher Cat #65-865-14 2mM Glutamine Sigma (Merck) Cat #G1272-10mL 1x MEM NEAA (100x) Gibco Cat #11140-035 100mL 1 mM Sodium Pyruvate Sigma (Merck) Cat #S8636-100mL Matrigel Matrix Corning Cat #356234 Collagen I Corning Cat #354249 Sodium Bicarbonate 1.1% Sigma Cat #102399192 Collagenase IV (1 mg/mL) Thermo Fisher Scientific Cat #17104019 Pen/Strep 1% Sigma Cat #P0781-100mL 2mM EDTA Sigma (Merck) Cat #03690-100mL Recombinant Human IFN-g PeproTech Cat #300-02 CFSE Thermo Fisher Scientific Cat #C34554 (Continued on next page) Immunity 58, 1–18.e1–e8, May 13, 2025 e3 .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays BD CytoFix/Cytoperm BD Biosciences Cat #554714 Foxp3 Transcription Factor Staining Buffer set eBioscience Cat #00-5523-00 Deposited data Single-cell RNAseq data This study GSE218013 Experimental models: Cell lines NPE-IE cells Gift Steven Pollard, University of Edinburgh, United Kingdom GL261-EGFRvIII Gift Martin Pule, UCL, United Kingdom MC38-B7-H3 Made in house N/A Experimental models: Organisms/strains C57BL/6 Charles Rivers N/A B6.129(Cg)-Foxp3tm3(DTR/GFP)Ayr/J Charles Rivers N/A Lysm-Cre-Fcgr4KO Gift Jeffrey Ravetch, Rockefeller University, USA Software and algorithms FlowJo v.10.8.1 TreeStar https://www.flowjo.com/solutions/flowjo R version 3.6.2 Cran r-project.org GraphPad Prism 9 GraphPad www.graphpad.com Other NeuroCult Basal Medium StemCell Technologies Cat #05700 NeuroCult Proliferation Supplement StemCell Technologies Cat #05701 100 UI/mL penicillin, 100 mg/mL streptomycin Gibco Cat #15140-122 Accutase Life Technologies-eBioscience Cat #00-4555-56 Lacrilube/Xaline gel Lacri-Lube Cat #0345520 0.25% Marcaine National Veterinary Service Cat #115095 10% Rymadyl National Veterinary Service Cat #91649 5 ml Hamilton micro-syringe Hamilton Cat #7641-01 Fine step stereotactic device Harvard Apparatus Digital, Single mouse Stereotaxic U frame Cat #75-1828, Cat #75-1883, Cat #75- 4507, Cat #75-1887, Cat #72-6066 6-0 Vicryl Ethicon Cat #ETW9913 Metacam National Veterinary Service Cat #45755 CountBrightTM Absolute counting Beads Invitrogen Cat #C36950 UW media, Cold storage solution Belzer Cat #BUWC FBS PAN-Biotech Cat #P40-37500 DMEM Sigma (Merck) Cat #D6546-500mL MEM Non-Essential Amino Acids Solution (100X) ThermoFisher Scientific Cat #11140050 Trypsin ThermoFisher Scientific Cat #108444 ..

    Article Title: Tissue-specific transcriptional profiles and heterogeneity of natural killer cells and group 1 innate lymphoid cells.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies PeCy5 anti-mouse CD3 (145-2C11) BD Biosciences Cat# 553065; RRID:AB_394598 PeCy5 anti-mouse TCRb (H57-597) BD Biosciences Cat# 553173; RRID:AB_394685 BV650 anti-mouse CD226/DNAM-1 (10E5) BD Biosciences Cat# 750916; RRID:AB_2875003 BUV805 anti-mouse CD45 (104) BD Biosciences Cat# 741957; RRID:AB_2871265 BV785 anti-mouse CD49a (Ha31/8) BD Biosciences Cat# 740919; RRID:AB_2740560 BUV395 anti-mouse CD49b (HMa2) BD Biosciences Cat# 740250; RRID:AB_2739996 A700 anti-mouse NKp46 (29A1.4) BD Biosciences Cat# 561169; RRID:AB_10561840 BV510 anti-mouse NK1.1 (PK136) BD Biosciences Cat# 563096; RRID:AB_2738002 APC.Cy7 anti-mouse CD90.2 (53-2.1) BD Biosciences Cat# 561641; RRID:AB_10898013 BUV661 anti-mouse CD122 (5H4) BD Biosciences Cat# 741537; RRID:AB_2870975 BV421 anti-mouse CD223/LAG-3 (C9B7W) BD Biosciences Cat# 740072; RRID:AB_2739836 BV650 anti-mouse Ly49D (4E5) BD Biosciences Cat# 742558; RRID:AB_2740868 BV605 anti-mouse VISTA/PD-1H (MIH64) BD Biosciences Cat# 742722; RRID:AB_2740998 PeCy5 anti-mouse Ter-119 (Ter-119) eBiosciences Cat# 15-5921-83; RRID:AB_468811 PerCP-eFluor 710 anti-mouse CD200R (OX110) eBiosciences Cat# 46-5201-82; RRID:AB_10804765 PeCy7 anti-mouse CD127 (A7R34) eBiosciences Cat# 25-1271-82; RRID:AB_469649 eFluor660 anti-mouse Eomes (Dan11mag) eBiosciences Cat# 50-4875-82; RRID:AB_2574227 APC anti-mouse CD253/TRAIL (N2B2) eBiosciences Cat# 17-5951-82; RRID:AB_2573248 PeCy5 anti-mouse TCRgd (GL3) eBiosciences Cat# 15-5711-82; RRID:AB_468804 FITC anti-mouse Ly49H (3D10) eBiosciences Cat# 11-5886-82; RRID:AB_1257159 PeCy5 anti-mouse CD19 (1D3) eBiosciences Cat# 15-0193-82; RRID:AB_657672 APC anti-mouse SDC4 (REA640) Miltenyi Biotec Cat# 130-109-831; RRID:AB_2653641 PE/Dazzle 594 CXCR6 (SA051D1) BioLegend Cat# 151117; RRID:AB_2721700 A700 anti-mouse CD11b (M1/70) BioLegend Cat# 101222; RRID:AB_493705 (Continued on next page) Cell Reports Medicine 3, 100812, November 15, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Healthy liver, spleen, salivary glands and lamina propria from adult mice N/A Human ILC single-cell dataset Mazzurana et al., 20219 Downloaded from the NCBI GEO depository (GSE150050) Chemicals, peptides, and recombinant proteins Collagenase IV Sigma Aldrich C5138 Collagenase VIII Sigma Aldrich C2139 DNase Sigma Aldrich DN25 Fetal bovine serum Thermo Fisher scientific 10437028 RPMI1640 Corning 10-041-CV Phosphate Buffered Saline Corning 21-040-CMR EDTA Invitrogen AM9260G Foxp3 transcription factor staining buffer kit Invitrogen 00-5523-00 LIVE/DEAD Fixable Near-IR dead cell stain kit Life technologies L10119 Critical commercial assays Easysep Mouse NK Cell Isolation Kit Stemcell technologies 19855 103 Genomics Chromium Next GEM Single Cell 30 v3.1 kit Fisher scientific NC1690752 Qubit High Sensitivity assay kit Invitrogen Q32854 Deposited data Raw and analyzed data (scRNA-seq) This paper GEO: GSE189807 Experimental models: Organisms/strains Mouse: C57BL/6JR Janvier Labs https://janvier-labs.com/fiche_produit/2-c57bl-6jrj/ Software and algorithms Flowjo software v10 Tree Star https://www.flowjo.com/RRID: SCR_008520 Graph Pad Prism Version 9 Graphpad https://www.graphpad.com/RRID: SCR_002798 CellRanger software v4.0.0 103 Genomics https://support.10xgenomics.com/single-cell-gene- expression/software/pipelines/latest/what-is-cell-ranger CITE-seq-Count 1.4.3 https://hoohm.github.io/CITE-seq-Count/ Seurat v4.0.0 Hao et al., 202143 https://satijalab.org/seurat/ Monocle 0.3.1 N/A https://cole-trapnell-lab.github.io/monocle3/ ClusterProfiler 3.18.1 N/A https://guangchuangyu.github.io/software/ clusterProfiler/ Harmony 0.1.0 Korsunsky, I et al. Nat Methods, 201922 https://portals.broadinstitute.org/harmony/articles/ quickstart.html ..

    Single Cell:

    Article Title: Regulatory T cell depletion promotes myeloid cell activation and glioblastoma response to anti-PD1 and tumor-targeting antibodies.
    Article Snippet: Male, 76 years Patient 6 This study Glioblastoma, IDH-wildtype, CNS WHO grade 4 Patient 7 This study Glioblastoma, IDH-wildtype, CNS WHO grade 4 Patient 8 This study Glioblastoma, IDH-wildtype, CNS WHO grade 4 Patient 9 This study Glioblastoma, IDH-wildtype, CNS WHO grade 4 Chemicals, peptides, and recombinant proteins EGF, final concentration 10 ng/mL Peprotech Cat #315-09 FGF, final concentration 10 ng/mL Peprotech Cat #100-18B Laminin Cultrex Cat #3446-005-01 Liberase TL Roche Cat #05401119001 DNAse Sigma Cat #101041590001 Diphteria toxin from Corynebacterium diphteriae Merck Cat #322326 Viability dye eFluor780 ThermoFisher Cat #65-865-14 2mM Glutamine Sigma (Merck) Cat #G1272-10mL 1x MEM NEAA (100x) Gibco Cat #11140-035 100mL 1 mM Sodium Pyruvate Sigma (Merck) Cat #S8636-100mL Matrigel Matrix Corning Cat #356234 Collagen I Corning Cat #354249 Sodium Bicarbonate 1.1% Sigma Cat #102399192 Collagenase IV (1 mg/mL) Thermo Fisher Scientific Cat #17104019 Pen/Strep 1% Sigma Cat #P0781-100mL 2mM EDTA Sigma (Merck) Cat #03690-100mL Recombinant Human IFN-g PeproTech Cat #300-02 CFSE Thermo Fisher Scientific Cat #C34554 (Continued on next page) Immunity 58, 1–18.e1–e8, May 13, 2025 e3 .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays BD CytoFix/Cytoperm BD Biosciences Cat #554714 Foxp3 Transcription Factor Staining Buffer set eBioscience Cat #00-5523-00 Deposited data Single-cell RNAseq data This study GSE218013 Experimental models: Cell lines NPE-IE cells Gift Steven Pollard, University of Edinburgh, United Kingdom GL261-EGFRvIII Gift Martin Pule, UCL, United Kingdom MC38-B7-H3 Made in house N/A Experimental models: Organisms/strains C57BL/6 Charles Rivers N/A B6.129(Cg)-Foxp3tm3(DTR/GFP)Ayr/J Charles Rivers N/A Lysm-Cre-Fcgr4KO Gift Jeffrey Ravetch, Rockefeller University, USA Software and algorithms FlowJo v.10.8.1 TreeStar https://www.flowjo.com/solutions/flowjo R version 3.6.2 Cran r-project.org GraphPad Prism 9 GraphPad www.graphpad.com Other NeuroCult Basal Medium StemCell Technologies Cat #05700 NeuroCult Proliferation Supplement StemCell Technologies Cat #05701 100 UI/mL penicillin, 100 mg/mL streptomycin Gibco Cat #15140-122 Accutase Life Technologies-eBioscience Cat #00-4555-56 Lacrilube/Xaline gel Lacri-Lube Cat #0345520 0.25% Marcaine National Veterinary Service Cat #115095 10% Rymadyl National Veterinary Service Cat #91649 5 ml Hamilton micro-syringe Hamilton Cat #7641-01 Fine step stereotactic device Harvard Apparatus Digital, Single mouse Stereotaxic U frame Cat #75-1828, Cat #75-1883, Cat #75- 4507, Cat #75-1887, Cat #72-6066 6-0 Vicryl Ethicon Cat #ETW9913 Metacam National Veterinary Service Cat #45755 CountBrightTM Absolute counting Beads Invitrogen Cat #C36950 UW media, Cold storage solution Belzer Cat #BUWC FBS PAN-Biotech Cat #P40-37500 DMEM Sigma (Merck) Cat #D6546-500mL MEM Non-Essential Amino Acids Solution (100X) ThermoFisher Scientific Cat #11140050 Trypsin ThermoFisher Scientific Cat #108444 ..

    Article Title: Tissue-specific transcriptional profiles and heterogeneity of natural killer cells and group 1 innate lymphoid cells.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies PeCy5 anti-mouse CD3 (145-2C11) BD Biosciences Cat# 553065; RRID:AB_394598 PeCy5 anti-mouse TCRb (H57-597) BD Biosciences Cat# 553173; RRID:AB_394685 BV650 anti-mouse CD226/DNAM-1 (10E5) BD Biosciences Cat# 750916; RRID:AB_2875003 BUV805 anti-mouse CD45 (104) BD Biosciences Cat# 741957; RRID:AB_2871265 BV785 anti-mouse CD49a (Ha31/8) BD Biosciences Cat# 740919; RRID:AB_2740560 BUV395 anti-mouse CD49b (HMa2) BD Biosciences Cat# 740250; RRID:AB_2739996 A700 anti-mouse NKp46 (29A1.4) BD Biosciences Cat# 561169; RRID:AB_10561840 BV510 anti-mouse NK1.1 (PK136) BD Biosciences Cat# 563096; RRID:AB_2738002 APC.Cy7 anti-mouse CD90.2 (53-2.1) BD Biosciences Cat# 561641; RRID:AB_10898013 BUV661 anti-mouse CD122 (5H4) BD Biosciences Cat# 741537; RRID:AB_2870975 BV421 anti-mouse CD223/LAG-3 (C9B7W) BD Biosciences Cat# 740072; RRID:AB_2739836 BV650 anti-mouse Ly49D (4E5) BD Biosciences Cat# 742558; RRID:AB_2740868 BV605 anti-mouse VISTA/PD-1H (MIH64) BD Biosciences Cat# 742722; RRID:AB_2740998 PeCy5 anti-mouse Ter-119 (Ter-119) eBiosciences Cat# 15-5921-83; RRID:AB_468811 PerCP-eFluor 710 anti-mouse CD200R (OX110) eBiosciences Cat# 46-5201-82; RRID:AB_10804765 PeCy7 anti-mouse CD127 (A7R34) eBiosciences Cat# 25-1271-82; RRID:AB_469649 eFluor660 anti-mouse Eomes (Dan11mag) eBiosciences Cat# 50-4875-82; RRID:AB_2574227 APC anti-mouse CD253/TRAIL (N2B2) eBiosciences Cat# 17-5951-82; RRID:AB_2573248 PeCy5 anti-mouse TCRgd (GL3) eBiosciences Cat# 15-5711-82; RRID:AB_468804 FITC anti-mouse Ly49H (3D10) eBiosciences Cat# 11-5886-82; RRID:AB_1257159 PeCy5 anti-mouse CD19 (1D3) eBiosciences Cat# 15-0193-82; RRID:AB_657672 APC anti-mouse SDC4 (REA640) Miltenyi Biotec Cat# 130-109-831; RRID:AB_2653641 PE/Dazzle 594 CXCR6 (SA051D1) BioLegend Cat# 151117; RRID:AB_2721700 A700 anti-mouse CD11b (M1/70) BioLegend Cat# 101222; RRID:AB_493705 (Continued on next page) Cell Reports Medicine 3, 100812, November 15, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Healthy liver, spleen, salivary glands and lamina propria from adult mice N/A Human ILC single-cell dataset Mazzurana et al., 20219 Downloaded from the NCBI GEO depository (GSE150050) Chemicals, peptides, and recombinant proteins Collagenase IV Sigma Aldrich C5138 Collagenase VIII Sigma Aldrich C2139 DNase Sigma Aldrich DN25 Fetal bovine serum Thermo Fisher scientific 10437028 RPMI1640 Corning 10-041-CV Phosphate Buffered Saline Corning 21-040-CMR EDTA Invitrogen AM9260G Foxp3 transcription factor staining buffer kit Invitrogen 00-5523-00 LIVE/DEAD Fixable Near-IR dead cell stain kit Life technologies L10119 Critical commercial assays Easysep Mouse NK Cell Isolation Kit Stemcell technologies 19855 103 Genomics Chromium Next GEM Single Cell 30 v3.1 kit Fisher scientific NC1690752 Qubit High Sensitivity assay kit Invitrogen Q32854 Deposited data Raw and analyzed data (scRNA-seq) This paper GEO: GSE189807 Experimental models: Organisms/strains Mouse: C57BL/6JR Janvier Labs https://janvier-labs.com/fiche_produit/2-c57bl-6jrj/ Software and algorithms Flowjo software v10 Tree Star https://www.flowjo.com/RRID: SCR_008520 Graph Pad Prism Version 9 Graphpad https://www.graphpad.com/RRID: SCR_002798 CellRanger software v4.0.0 103 Genomics https://support.10xgenomics.com/single-cell-gene- expression/software/pipelines/latest/what-is-cell-ranger CITE-seq-Count 1.4.3 https://hoohm.github.io/CITE-seq-Count/ Seurat v4.0.0 Hao et al., 202143 https://satijalab.org/seurat/ Monocle 0.3.1 N/A https://cole-trapnell-lab.github.io/monocle3/ ClusterProfiler 3.18.1 N/A https://guangchuangyu.github.io/software/ clusterProfiler/ Harmony 0.1.0 Korsunsky, I et al. Nat Methods, 201922 https://portals.broadinstitute.org/harmony/articles/ quickstart.html ..

    RNA sequencing:

    Article Title: Regulatory T cell depletion promotes myeloid cell activation and glioblastoma response to anti-PD1 and tumor-targeting antibodies.
    Article Snippet: Male, 76 years Patient 6 This study Glioblastoma, IDH-wildtype, CNS WHO grade 4 Patient 7 This study Glioblastoma, IDH-wildtype, CNS WHO grade 4 Patient 8 This study Glioblastoma, IDH-wildtype, CNS WHO grade 4 Patient 9 This study Glioblastoma, IDH-wildtype, CNS WHO grade 4 Chemicals, peptides, and recombinant proteins EGF, final concentration 10 ng/mL Peprotech Cat #315-09 FGF, final concentration 10 ng/mL Peprotech Cat #100-18B Laminin Cultrex Cat #3446-005-01 Liberase TL Roche Cat #05401119001 DNAse Sigma Cat #101041590001 Diphteria toxin from Corynebacterium diphteriae Merck Cat #322326 Viability dye eFluor780 ThermoFisher Cat #65-865-14 2mM Glutamine Sigma (Merck) Cat #G1272-10mL 1x MEM NEAA (100x) Gibco Cat #11140-035 100mL 1 mM Sodium Pyruvate Sigma (Merck) Cat #S8636-100mL Matrigel Matrix Corning Cat #356234 Collagen I Corning Cat #354249 Sodium Bicarbonate 1.1% Sigma Cat #102399192 Collagenase IV (1 mg/mL) Thermo Fisher Scientific Cat #17104019 Pen/Strep 1% Sigma Cat #P0781-100mL 2mM EDTA Sigma (Merck) Cat #03690-100mL Recombinant Human IFN-g PeproTech Cat #300-02 CFSE Thermo Fisher Scientific Cat #C34554 (Continued on next page) Immunity 58, 1–18.e1–e8, May 13, 2025 e3 .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays BD CytoFix/Cytoperm BD Biosciences Cat #554714 Foxp3 Transcription Factor Staining Buffer set eBioscience Cat #00-5523-00 Deposited data Single-cell RNAseq data This study GSE218013 Experimental models: Cell lines NPE-IE cells Gift Steven Pollard, University of Edinburgh, United Kingdom GL261-EGFRvIII Gift Martin Pule, UCL, United Kingdom MC38-B7-H3 Made in house N/A Experimental models: Organisms/strains C57BL/6 Charles Rivers N/A B6.129(Cg)-Foxp3tm3(DTR/GFP)Ayr/J Charles Rivers N/A Lysm-Cre-Fcgr4KO Gift Jeffrey Ravetch, Rockefeller University, USA Software and algorithms FlowJo v.10.8.1 TreeStar https://www.flowjo.com/solutions/flowjo R version 3.6.2 Cran r-project.org GraphPad Prism 9 GraphPad www.graphpad.com Other NeuroCult Basal Medium StemCell Technologies Cat #05700 NeuroCult Proliferation Supplement StemCell Technologies Cat #05701 100 UI/mL penicillin, 100 mg/mL streptomycin Gibco Cat #15140-122 Accutase Life Technologies-eBioscience Cat #00-4555-56 Lacrilube/Xaline gel Lacri-Lube Cat #0345520 0.25% Marcaine National Veterinary Service Cat #115095 10% Rymadyl National Veterinary Service Cat #91649 5 ml Hamilton micro-syringe Hamilton Cat #7641-01 Fine step stereotactic device Harvard Apparatus Digital, Single mouse Stereotaxic U frame Cat #75-1828, Cat #75-1883, Cat #75- 4507, Cat #75-1887, Cat #72-6066 6-0 Vicryl Ethicon Cat #ETW9913 Metacam National Veterinary Service Cat #45755 CountBrightTM Absolute counting Beads Invitrogen Cat #C36950 UW media, Cold storage solution Belzer Cat #BUWC FBS PAN-Biotech Cat #P40-37500 DMEM Sigma (Merck) Cat #D6546-500mL MEM Non-Essential Amino Acids Solution (100X) ThermoFisher Scientific Cat #11140050 Trypsin ThermoFisher Scientific Cat #108444 ..

    other:

    Article Title: Mast cell tolerance in the skin microenvironment to commensal bacteria is controlled by fibroblasts.
    Article Snippet: STAR+METHODS Detailed methods are provided in the online version of this paper and include the following: d KEY RESOURCES TABLE d RESOURCE AVAILABILITY B Lead contact B Materials availability B Data and code availability d EXPERIMENTAL MODEL AND SUBJECT DETAILS B Animal model B Human model B Microbe (bacteria) strain B Primary cell cultures d METHOD DETAILS B Human cells B Bacterial supernatant stock preparation B Bacterial supernatant cell treatments B Mice B RNA sequencing B Single cell RNA sequencing B Real-time quantitative RT-qPCR B Fluorescence-activated cell sorting (FACS) B Elisa and luminex assay B Genoskin B Immunofluorescence of skin and HMCs d QUANTIFICATION AND STATISTICAL ANALYSIS SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j.

    Recombinant:

    Article Title: Clonal hematopoiesis driven by chromosome 1q/MDM4 trisomy defines a canonical route toward leukemia in Fanconi anemia.
    Article Snippet: Article Clonal hematopoiesis driven by chromosome1q/MDM4 trisomy defines a canonical route toward leukemia in

    Article Title: Tissue-specific transcriptional profiles and heterogeneity of natural killer cells and group 1 innate lymphoid cells.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies PeCy5 anti-mouse CD3 (145-2C11) BD Biosciences Cat# 553065; RRID:AB_394598 PeCy5 anti-mouse TCRb (H57-597) BD Biosciences Cat# 553173; RRID:AB_394685 BV650 anti-mouse CD226/DNAM-1 (10E5) BD Biosciences Cat# 750916; RRID:AB_2875003 BUV805 anti-mouse CD45 (104) BD Biosciences Cat# 741957; RRID:AB_2871265 BV785 anti-mouse CD49a (Ha31/8) BD Biosciences Cat# 740919; RRID:AB_2740560 BUV395 anti-mouse CD49b (HMa2) BD Biosciences Cat# 740250; RRID:AB_2739996 A700 anti-mouse NKp46 (29A1.4) BD Biosciences Cat# 561169; RRID:AB_10561840 BV510 anti-mouse NK1.1 (PK136) BD Biosciences Cat# 563096; RRID:AB_2738002 APC.Cy7 anti-mouse CD90.2 (53-2.1) BD Biosciences Cat# 561641; RRID:AB_10898013 BUV661 anti-mouse CD122 (5H4) BD Biosciences Cat# 741537; RRID:AB_2870975 BV421 anti-mouse CD223/LAG-3 (C9B7W) BD Biosciences Cat# 740072; RRID:AB_2739836 BV650 anti-mouse Ly49D (4E5) BD Biosciences Cat# 742558; RRID:AB_2740868 BV605 anti-mouse VISTA/PD-1H (MIH64) BD Biosciences Cat# 742722; RRID:AB_2740998 PeCy5 anti-mouse Ter-119 (Ter-119) eBiosciences Cat# 15-5921-83; RRID:AB_468811 PerCP-eFluor 710 anti-mouse CD200R (OX110) eBiosciences Cat# 46-5201-82; RRID:AB_10804765 PeCy7 anti-mouse CD127 (A7R34) eBiosciences Cat# 25-1271-82; RRID:AB_469649 eFluor660 anti-mouse Eomes (Dan11mag) eBiosciences Cat# 50-4875-82; RRID:AB_2574227 APC anti-mouse CD253/TRAIL (N2B2) eBiosciences Cat# 17-5951-82; RRID:AB_2573248 PeCy5 anti-mouse TCRgd (GL3) eBiosciences Cat# 15-5711-82; RRID:AB_468804 FITC anti-mouse Ly49H (3D10) eBiosciences Cat# 11-5886-82; RRID:AB_1257159 PeCy5 anti-mouse CD19 (1D3) eBiosciences Cat# 15-0193-82; RRID:AB_657672 APC anti-mouse SDC4 (REA640) Miltenyi Biotec Cat# 130-109-831; RRID:AB_2653641 PE/Dazzle 594 CXCR6 (SA051D1) BioLegend Cat# 151117; RRID:AB_2721700 A700 anti-mouse CD11b (M1/70) BioLegend Cat# 101222; RRID:AB_493705 (Continued on next page) Cell Reports Medicine 3, 100812, November 15, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Healthy liver, spleen, salivary glands and lamina propria from adult mice N/A Human ILC single-cell dataset Mazzurana et al., 20219 Downloaded from the NCBI GEO depository (GSE150050) Chemicals, peptides, and recombinant proteins Collagenase IV Sigma Aldrich C5138 Collagenase VIII Sigma Aldrich C2139 DNase Sigma Aldrich DN25 Fetal bovine serum Thermo Fisher scientific 10437028 RPMI1640 Corning 10-041-CV Phosphate Buffered Saline Corning 21-040-CMR EDTA Invitrogen AM9260G Foxp3 transcription factor staining buffer kit Invitrogen 00-5523-00 LIVE/DEAD Fixable Near-IR dead cell stain kit Life technologies L10119 Critical commercial assays Easysep Mouse NK Cell Isolation Kit Stemcell technologies 19855 103 Genomics Chromium Next GEM Single Cell 30 v3.1 kit Fisher scientific NC1690752 Qubit High Sensitivity assay kit Invitrogen Q32854 Deposited data Raw and analyzed data (scRNA-seq) This paper GEO: GSE189807 Experimental models: Organisms/strains Mouse: C57BL/6JR Janvier Labs https://janvier-labs.com/fiche_produit/2-c57bl-6jrj/ Software and algorithms Flowjo software v10 Tree Star https://www.flowjo.com/RRID: SCR_008520 Graph Pad Prism Version 9 Graphpad https://www.graphpad.com/RRID: SCR_002798 CellRanger software v4.0.0 103 Genomics https://support.10xgenomics.com/single-cell-gene- expression/software/pipelines/latest/what-is-cell-ranger CITE-seq-Count 1.4.3 https://hoohm.github.io/CITE-seq-Count/ Seurat v4.0.0 Hao et al., 202143 https://satijalab.org/seurat/ Monocle 0.3.1 N/A https://cole-trapnell-lab.github.io/monocle3/ ClusterProfiler 3.18.1 N/A https://guangchuangyu.github.io/software/ clusterProfiler/ Harmony 0.1.0 Korsunsky, I et al. Nat Methods, 201922 https://portals.broadinstitute.org/harmony/articles/ quickstart.html ..

    shRNA:

    Article Title: Clonal hematopoiesis driven by chromosome 1q/MDM4 trisomy defines a canonical route toward leukemia in Fanconi anemia.
    Article Snippet: Article Clonal hematopoiesis driven by chromosome1q/MDM4 trisomy defines a canonical route toward leukemia in

    Generated:

    Article Title: Clonal hematopoiesis driven by chromosome 1q/MDM4 trisomy defines a canonical route toward leukemia in Fanconi anemia.
    Article Snippet: Article Clonal hematopoiesis driven by chromosome1q/MDM4 trisomy defines a canonical route toward leukemia in

    Whole Complete genome sequencing:

    Article Title: Clonal hematopoiesis driven by chromosome 1q/MDM4 trisomy defines a canonical route toward leukemia in Fanconi anemia.
    Article Snippet: Article Clonal hematopoiesis driven by chromosome1q/MDM4 trisomy defines a canonical route toward leukemia in

    Saline:

    Article Title: Tissue-specific transcriptional profiles and heterogeneity of natural killer cells and group 1 innate lymphoid cells.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies PeCy5 anti-mouse CD3 (145-2C11) BD Biosciences Cat# 553065; RRID:AB_394598 PeCy5 anti-mouse TCRb (H57-597) BD Biosciences Cat# 553173; RRID:AB_394685 BV650 anti-mouse CD226/DNAM-1 (10E5) BD Biosciences Cat# 750916; RRID:AB_2875003 BUV805 anti-mouse CD45 (104) BD Biosciences Cat# 741957; RRID:AB_2871265 BV785 anti-mouse CD49a (Ha31/8) BD Biosciences Cat# 740919; RRID:AB_2740560 BUV395 anti-mouse CD49b (HMa2) BD Biosciences Cat# 740250; RRID:AB_2739996 A700 anti-mouse NKp46 (29A1.4) BD Biosciences Cat# 561169; RRID:AB_10561840 BV510 anti-mouse NK1.1 (PK136) BD Biosciences Cat# 563096; RRID:AB_2738002 APC.Cy7 anti-mouse CD90.2 (53-2.1) BD Biosciences Cat# 561641; RRID:AB_10898013 BUV661 anti-mouse CD122 (5H4) BD Biosciences Cat# 741537; RRID:AB_2870975 BV421 anti-mouse CD223/LAG-3 (C9B7W) BD Biosciences Cat# 740072; RRID:AB_2739836 BV650 anti-mouse Ly49D (4E5) BD Biosciences Cat# 742558; RRID:AB_2740868 BV605 anti-mouse VISTA/PD-1H (MIH64) BD Biosciences Cat# 742722; RRID:AB_2740998 PeCy5 anti-mouse Ter-119 (Ter-119) eBiosciences Cat# 15-5921-83; RRID:AB_468811 PerCP-eFluor 710 anti-mouse CD200R (OX110) eBiosciences Cat# 46-5201-82; RRID:AB_10804765 PeCy7 anti-mouse CD127 (A7R34) eBiosciences Cat# 25-1271-82; RRID:AB_469649 eFluor660 anti-mouse Eomes (Dan11mag) eBiosciences Cat# 50-4875-82; RRID:AB_2574227 APC anti-mouse CD253/TRAIL (N2B2) eBiosciences Cat# 17-5951-82; RRID:AB_2573248 PeCy5 anti-mouse TCRgd (GL3) eBiosciences Cat# 15-5711-82; RRID:AB_468804 FITC anti-mouse Ly49H (3D10) eBiosciences Cat# 11-5886-82; RRID:AB_1257159 PeCy5 anti-mouse CD19 (1D3) eBiosciences Cat# 15-0193-82; RRID:AB_657672 APC anti-mouse SDC4 (REA640) Miltenyi Biotec Cat# 130-109-831; RRID:AB_2653641 PE/Dazzle 594 CXCR6 (SA051D1) BioLegend Cat# 151117; RRID:AB_2721700 A700 anti-mouse CD11b (M1/70) BioLegend Cat# 101222; RRID:AB_493705 (Continued on next page) Cell Reports Medicine 3, 100812, November 15, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Healthy liver, spleen, salivary glands and lamina propria from adult mice N/A Human ILC single-cell dataset Mazzurana et al., 20219 Downloaded from the NCBI GEO depository (GSE150050) Chemicals, peptides, and recombinant proteins Collagenase IV Sigma Aldrich C5138 Collagenase VIII Sigma Aldrich C2139 DNase Sigma Aldrich DN25 Fetal bovine serum Thermo Fisher scientific 10437028 RPMI1640 Corning 10-041-CV Phosphate Buffered Saline Corning 21-040-CMR EDTA Invitrogen AM9260G Foxp3 transcription factor staining buffer kit Invitrogen 00-5523-00 LIVE/DEAD Fixable Near-IR dead cell stain kit Life technologies L10119 Critical commercial assays Easysep Mouse NK Cell Isolation Kit Stemcell technologies 19855 103 Genomics Chromium Next GEM Single Cell 30 v3.1 kit Fisher scientific NC1690752 Qubit High Sensitivity assay kit Invitrogen Q32854 Deposited data Raw and analyzed data (scRNA-seq) This paper GEO: GSE189807 Experimental models: Organisms/strains Mouse: C57BL/6JR Janvier Labs https://janvier-labs.com/fiche_produit/2-c57bl-6jrj/ Software and algorithms Flowjo software v10 Tree Star https://www.flowjo.com/RRID: SCR_008520 Graph Pad Prism Version 9 Graphpad https://www.graphpad.com/RRID: SCR_002798 CellRanger software v4.0.0 103 Genomics https://support.10xgenomics.com/single-cell-gene- expression/software/pipelines/latest/what-is-cell-ranger CITE-seq-Count 1.4.3 https://hoohm.github.io/CITE-seq-Count/ Seurat v4.0.0 Hao et al., 202143 https://satijalab.org/seurat/ Monocle 0.3.1 N/A https://cole-trapnell-lab.github.io/monocle3/ ClusterProfiler 3.18.1 N/A https://guangchuangyu.github.io/software/ clusterProfiler/ Harmony 0.1.0 Korsunsky, I et al. Nat Methods, 201922 https://portals.broadinstitute.org/harmony/articles/ quickstart.html ..

    Cell Isolation:

    Article Title: Tissue-specific transcriptional profiles and heterogeneity of natural killer cells and group 1 innate lymphoid cells.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies PeCy5 anti-mouse CD3 (145-2C11) BD Biosciences Cat# 553065; RRID:AB_394598 PeCy5 anti-mouse TCRb (H57-597) BD Biosciences Cat# 553173; RRID:AB_394685 BV650 anti-mouse CD226/DNAM-1 (10E5) BD Biosciences Cat# 750916; RRID:AB_2875003 BUV805 anti-mouse CD45 (104) BD Biosciences Cat# 741957; RRID:AB_2871265 BV785 anti-mouse CD49a (Ha31/8) BD Biosciences Cat# 740919; RRID:AB_2740560 BUV395 anti-mouse CD49b (HMa2) BD Biosciences Cat# 740250; RRID:AB_2739996 A700 anti-mouse NKp46 (29A1.4) BD Biosciences Cat# 561169; RRID:AB_10561840 BV510 anti-mouse NK1.1 (PK136) BD Biosciences Cat# 563096; RRID:AB_2738002 APC.Cy7 anti-mouse CD90.2 (53-2.1) BD Biosciences Cat# 561641; RRID:AB_10898013 BUV661 anti-mouse CD122 (5H4) BD Biosciences Cat# 741537; RRID:AB_2870975 BV421 anti-mouse CD223/LAG-3 (C9B7W) BD Biosciences Cat# 740072; RRID:AB_2739836 BV650 anti-mouse Ly49D (4E5) BD Biosciences Cat# 742558; RRID:AB_2740868 BV605 anti-mouse VISTA/PD-1H (MIH64) BD Biosciences Cat# 742722; RRID:AB_2740998 PeCy5 anti-mouse Ter-119 (Ter-119) eBiosciences Cat# 15-5921-83; RRID:AB_468811 PerCP-eFluor 710 anti-mouse CD200R (OX110) eBiosciences Cat# 46-5201-82; RRID:AB_10804765 PeCy7 anti-mouse CD127 (A7R34) eBiosciences Cat# 25-1271-82; RRID:AB_469649 eFluor660 anti-mouse Eomes (Dan11mag) eBiosciences Cat# 50-4875-82; RRID:AB_2574227 APC anti-mouse CD253/TRAIL (N2B2) eBiosciences Cat# 17-5951-82; RRID:AB_2573248 PeCy5 anti-mouse TCRgd (GL3) eBiosciences Cat# 15-5711-82; RRID:AB_468804 FITC anti-mouse Ly49H (3D10) eBiosciences Cat# 11-5886-82; RRID:AB_1257159 PeCy5 anti-mouse CD19 (1D3) eBiosciences Cat# 15-0193-82; RRID:AB_657672 APC anti-mouse SDC4 (REA640) Miltenyi Biotec Cat# 130-109-831; RRID:AB_2653641 PE/Dazzle 594 CXCR6 (SA051D1) BioLegend Cat# 151117; RRID:AB_2721700 A700 anti-mouse CD11b (M1/70) BioLegend Cat# 101222; RRID:AB_493705 (Continued on next page) Cell Reports Medicine 3, 100812, November 15, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Healthy liver, spleen, salivary glands and lamina propria from adult mice N/A Human ILC single-cell dataset Mazzurana et al., 20219 Downloaded from the NCBI GEO depository (GSE150050) Chemicals, peptides, and recombinant proteins Collagenase IV Sigma Aldrich C5138 Collagenase VIII Sigma Aldrich C2139 DNase Sigma Aldrich DN25 Fetal bovine serum Thermo Fisher scientific 10437028 RPMI1640 Corning 10-041-CV Phosphate Buffered Saline Corning 21-040-CMR EDTA Invitrogen AM9260G Foxp3 transcription factor staining buffer kit Invitrogen 00-5523-00 LIVE/DEAD Fixable Near-IR dead cell stain kit Life technologies L10119 Critical commercial assays Easysep Mouse NK Cell Isolation Kit Stemcell technologies 19855 103 Genomics Chromium Next GEM Single Cell 30 v3.1 kit Fisher scientific NC1690752 Qubit High Sensitivity assay kit Invitrogen Q32854 Deposited data Raw and analyzed data (scRNA-seq) This paper GEO: GSE189807 Experimental models: Organisms/strains Mouse: C57BL/6JR Janvier Labs https://janvier-labs.com/fiche_produit/2-c57bl-6jrj/ Software and algorithms Flowjo software v10 Tree Star https://www.flowjo.com/RRID: SCR_008520 Graph Pad Prism Version 9 Graphpad https://www.graphpad.com/RRID: SCR_002798 CellRanger software v4.0.0 103 Genomics https://support.10xgenomics.com/single-cell-gene- expression/software/pipelines/latest/what-is-cell-ranger CITE-seq-Count 1.4.3 https://hoohm.github.io/CITE-seq-Count/ Seurat v4.0.0 Hao et al., 202143 https://satijalab.org/seurat/ Monocle 0.3.1 N/A https://cole-trapnell-lab.github.io/monocle3/ ClusterProfiler 3.18.1 N/A https://guangchuangyu.github.io/software/ clusterProfiler/ Harmony 0.1.0 Korsunsky, I et al. Nat Methods, 201922 https://portals.broadinstitute.org/harmony/articles/ quickstart.html ..

    Sensitive Assay:

    Article Title: Tissue-specific transcriptional profiles and heterogeneity of natural killer cells and group 1 innate lymphoid cells.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies PeCy5 anti-mouse CD3 (145-2C11) BD Biosciences Cat# 553065; RRID:AB_394598 PeCy5 anti-mouse TCRb (H57-597) BD Biosciences Cat# 553173; RRID:AB_394685 BV650 anti-mouse CD226/DNAM-1 (10E5) BD Biosciences Cat# 750916; RRID:AB_2875003 BUV805 anti-mouse CD45 (104) BD Biosciences Cat# 741957; RRID:AB_2871265 BV785 anti-mouse CD49a (Ha31/8) BD Biosciences Cat# 740919; RRID:AB_2740560 BUV395 anti-mouse CD49b (HMa2) BD Biosciences Cat# 740250; RRID:AB_2739996 A700 anti-mouse NKp46 (29A1.4) BD Biosciences Cat# 561169; RRID:AB_10561840 BV510 anti-mouse NK1.1 (PK136) BD Biosciences Cat# 563096; RRID:AB_2738002 APC.Cy7 anti-mouse CD90.2 (53-2.1) BD Biosciences Cat# 561641; RRID:AB_10898013 BUV661 anti-mouse CD122 (5H4) BD Biosciences Cat# 741537; RRID:AB_2870975 BV421 anti-mouse CD223/LAG-3 (C9B7W) BD Biosciences Cat# 740072; RRID:AB_2739836 BV650 anti-mouse Ly49D (4E5) BD Biosciences Cat# 742558; RRID:AB_2740868 BV605 anti-mouse VISTA/PD-1H (MIH64) BD Biosciences Cat# 742722; RRID:AB_2740998 PeCy5 anti-mouse Ter-119 (Ter-119) eBiosciences Cat# 15-5921-83; RRID:AB_468811 PerCP-eFluor 710 anti-mouse CD200R (OX110) eBiosciences Cat# 46-5201-82; RRID:AB_10804765 PeCy7 anti-mouse CD127 (A7R34) eBiosciences Cat# 25-1271-82; RRID:AB_469649 eFluor660 anti-mouse Eomes (Dan11mag) eBiosciences Cat# 50-4875-82; RRID:AB_2574227 APC anti-mouse CD253/TRAIL (N2B2) eBiosciences Cat# 17-5951-82; RRID:AB_2573248 PeCy5 anti-mouse TCRgd (GL3) eBiosciences Cat# 15-5711-82; RRID:AB_468804 FITC anti-mouse Ly49H (3D10) eBiosciences Cat# 11-5886-82; RRID:AB_1257159 PeCy5 anti-mouse CD19 (1D3) eBiosciences Cat# 15-0193-82; RRID:AB_657672 APC anti-mouse SDC4 (REA640) Miltenyi Biotec Cat# 130-109-831; RRID:AB_2653641 PE/Dazzle 594 CXCR6 (SA051D1) BioLegend Cat# 151117; RRID:AB_2721700 A700 anti-mouse CD11b (M1/70) BioLegend Cat# 101222; RRID:AB_493705 (Continued on next page) Cell Reports Medicine 3, 100812, November 15, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Healthy liver, spleen, salivary glands and lamina propria from adult mice N/A Human ILC single-cell dataset Mazzurana et al., 20219 Downloaded from the NCBI GEO depository (GSE150050) Chemicals, peptides, and recombinant proteins Collagenase IV Sigma Aldrich C5138 Collagenase VIII Sigma Aldrich C2139 DNase Sigma Aldrich DN25 Fetal bovine serum Thermo Fisher scientific 10437028 RPMI1640 Corning 10-041-CV Phosphate Buffered Saline Corning 21-040-CMR EDTA Invitrogen AM9260G Foxp3 transcription factor staining buffer kit Invitrogen 00-5523-00 LIVE/DEAD Fixable Near-IR dead cell stain kit Life technologies L10119 Critical commercial assays Easysep Mouse NK Cell Isolation Kit Stemcell technologies 19855 103 Genomics Chromium Next GEM Single Cell 30 v3.1 kit Fisher scientific NC1690752 Qubit High Sensitivity assay kit Invitrogen Q32854 Deposited data Raw and analyzed data (scRNA-seq) This paper GEO: GSE189807 Experimental models: Organisms/strains Mouse: C57BL/6JR Janvier Labs https://janvier-labs.com/fiche_produit/2-c57bl-6jrj/ Software and algorithms Flowjo software v10 Tree Star https://www.flowjo.com/RRID: SCR_008520 Graph Pad Prism Version 9 Graphpad https://www.graphpad.com/RRID: SCR_002798 CellRanger software v4.0.0 103 Genomics https://support.10xgenomics.com/single-cell-gene- expression/software/pipelines/latest/what-is-cell-ranger CITE-seq-Count 1.4.3 https://hoohm.github.io/CITE-seq-Count/ Seurat v4.0.0 Hao et al., 202143 https://satijalab.org/seurat/ Monocle 0.3.1 N/A https://cole-trapnell-lab.github.io/monocle3/ ClusterProfiler 3.18.1 N/A https://guangchuangyu.github.io/software/ clusterProfiler/ Harmony 0.1.0 Korsunsky, I et al. Nat Methods, 201922 https://portals.broadinstitute.org/harmony/articles/ quickstart.html ..

    Expressing:

    Article Title: Tissue-specific transcriptional profiles and heterogeneity of natural killer cells and group 1 innate lymphoid cells.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies PeCy5 anti-mouse CD3 (145-2C11) BD Biosciences Cat# 553065; RRID:AB_394598 PeCy5 anti-mouse TCRb (H57-597) BD Biosciences Cat# 553173; RRID:AB_394685 BV650 anti-mouse CD226/DNAM-1 (10E5) BD Biosciences Cat# 750916; RRID:AB_2875003 BUV805 anti-mouse CD45 (104) BD Biosciences Cat# 741957; RRID:AB_2871265 BV785 anti-mouse CD49a (Ha31/8) BD Biosciences Cat# 740919; RRID:AB_2740560 BUV395 anti-mouse CD49b (HMa2) BD Biosciences Cat# 740250; RRID:AB_2739996 A700 anti-mouse NKp46 (29A1.4) BD Biosciences Cat# 561169; RRID:AB_10561840 BV510 anti-mouse NK1.1 (PK136) BD Biosciences Cat# 563096; RRID:AB_2738002 APC.Cy7 anti-mouse CD90.2 (53-2.1) BD Biosciences Cat# 561641; RRID:AB_10898013 BUV661 anti-mouse CD122 (5H4) BD Biosciences Cat# 741537; RRID:AB_2870975 BV421 anti-mouse CD223/LAG-3 (C9B7W) BD Biosciences Cat# 740072; RRID:AB_2739836 BV650 anti-mouse Ly49D (4E5) BD Biosciences Cat# 742558; RRID:AB_2740868 BV605 anti-mouse VISTA/PD-1H (MIH64) BD Biosciences Cat# 742722; RRID:AB_2740998 PeCy5 anti-mouse Ter-119 (Ter-119) eBiosciences Cat# 15-5921-83; RRID:AB_468811 PerCP-eFluor 710 anti-mouse CD200R (OX110) eBiosciences Cat# 46-5201-82; RRID:AB_10804765 PeCy7 anti-mouse CD127 (A7R34) eBiosciences Cat# 25-1271-82; RRID:AB_469649 eFluor660 anti-mouse Eomes (Dan11mag) eBiosciences Cat# 50-4875-82; RRID:AB_2574227 APC anti-mouse CD253/TRAIL (N2B2) eBiosciences Cat# 17-5951-82; RRID:AB_2573248 PeCy5 anti-mouse TCRgd (GL3) eBiosciences Cat# 15-5711-82; RRID:AB_468804 FITC anti-mouse Ly49H (3D10) eBiosciences Cat# 11-5886-82; RRID:AB_1257159 PeCy5 anti-mouse CD19 (1D3) eBiosciences Cat# 15-0193-82; RRID:AB_657672 APC anti-mouse SDC4 (REA640) Miltenyi Biotec Cat# 130-109-831; RRID:AB_2653641 PE/Dazzle 594 CXCR6 (SA051D1) BioLegend Cat# 151117; RRID:AB_2721700 A700 anti-mouse CD11b (M1/70) BioLegend Cat# 101222; RRID:AB_493705 (Continued on next page) Cell Reports Medicine 3, 100812, November 15, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Healthy liver, spleen, salivary glands and lamina propria from adult mice N/A Human ILC single-cell dataset Mazzurana et al., 20219 Downloaded from the NCBI GEO depository (GSE150050) Chemicals, peptides, and recombinant proteins Collagenase IV Sigma Aldrich C5138 Collagenase VIII Sigma Aldrich C2139 DNase Sigma Aldrich DN25 Fetal bovine serum Thermo Fisher scientific 10437028 RPMI1640 Corning 10-041-CV Phosphate Buffered Saline Corning 21-040-CMR EDTA Invitrogen AM9260G Foxp3 transcription factor staining buffer kit Invitrogen 00-5523-00 LIVE/DEAD Fixable Near-IR dead cell stain kit Life technologies L10119 Critical commercial assays Easysep Mouse NK Cell Isolation Kit Stemcell technologies 19855 103 Genomics Chromium Next GEM Single Cell 30 v3.1 kit Fisher scientific NC1690752 Qubit High Sensitivity assay kit Invitrogen Q32854 Deposited data Raw and analyzed data (scRNA-seq) This paper GEO: GSE189807 Experimental models: Organisms/strains Mouse: C57BL/6JR Janvier Labs https://janvier-labs.com/fiche_produit/2-c57bl-6jrj/ Software and algorithms Flowjo software v10 Tree Star https://www.flowjo.com/RRID: SCR_008520 Graph Pad Prism Version 9 Graphpad https://www.graphpad.com/RRID: SCR_002798 CellRanger software v4.0.0 103 Genomics https://support.10xgenomics.com/single-cell-gene- expression/software/pipelines/latest/what-is-cell-ranger CITE-seq-Count 1.4.3 https://hoohm.github.io/CITE-seq-Count/ Seurat v4.0.0 Hao et al., 202143 https://satijalab.org/seurat/ Monocle 0.3.1 N/A https://cole-trapnell-lab.github.io/monocle3/ ClusterProfiler 3.18.1 N/A https://guangchuangyu.github.io/software/ clusterProfiler/ Harmony 0.1.0 Korsunsky, I et al. Nat Methods, 201922 https://portals.broadinstitute.org/harmony/articles/ quickstart.html ..

    Binding Assay:

    Article Title: Potent neutralization of SARS-CoV-2 variants of concern by an antibody with an uncommon genetic signature and structural mode of spike recognition
    Article Snippet: N/A Software and algorithms Cell Ranger 10X Genomics https://support.10xgenomics.com/ single-cell-gene-expression/ software/downloads/latest (Continued on next page) e2 Cell Reports 37, 109784, October 5, 2021 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER HighV-Quest Alamyar et al., 2012 http://www.imgt.org/IMGTindex/ IMGTHighV-QUEST.php ChangeO Gupta et al., 2015 https://changeo.readthedocs.io/en/stable/ Geneious 11.1.5 https://www.geneious.com N/A PyMOL The PyMOL Molecular Graphics System, Version 2.3.5 Schrödinger, LLC N/A Flowjo v10 TreeStar https://www.flowjo.com/ GraphPad Prism 9.0.0 https://www.graphpad.com:443/ N/A Biacore X100 Evaluation Software GE Healthcare V2.0.1 SerialEM Mastronarde, 2003 https://bio3d.colorado.edu/SerialEM/ cryoSPARC v3.2.0 Punjani et al., 2017 https://cryosparc.com/ SAbPred Dunbar et al., 2016 http://opig.stats.ox.ac.uk/ webapps/newsabdab/sabpred/ COOT Emsley and Cowtan, 2004 http://bernhardcl.github.io/coot/ Phenix Adams et al., 2002; Afonine et al., 2018 https://phenix-online.org/ ISOLDE Croll, 2018 http://preview.cgl.ucsf.edu/ chimerax/download.html ChimeraX Goddard et al., 2018 https://www.rbvi.ucsf.edu/chimerax/ Other Galanthus nivalis lectin Vector Laboratories Cat # AL-1243-5 1-Step Ultra TMB-ELISA Substrate Solution ThermoFisher Scientific Cat#34029 Costar High Binding Microplates Corning Cat#9018 Saponin VWR TCS0019-025G Paraformaldehyde VWR 100496-496 Donor Goat Serum Atlanta Biologicals S13150 DPBS(++) Cytiva SH30264.02 Article ll OPEN ACCESS ..



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