other:Article Title: Integrated Cross-Species Analysis Identifies a Conserved Transitional Dendritic Cell Population
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Software and Algorithms GraphPad Prism 6 GraphPad Software, Inc. https://www.graphpad.com/ scientific-software/prism/ MATLAB N/A https://www.mathworks.com/ products/matlab.html Cytofkit N/A https://bioconductor.riken.jp/packages/ 3.7/bioc/html/cytofkit.html ViSNE (CYT) Amir et al., 2013. https://dpeerlab.github.io/dpeerlab-website/ cyt-download.html FlowJo Software v10.0.8 TreeStar, Inc. https://www.flowjo.com/solutions/flowjo UMAP Becht et al., 2018 https://github.com/lmcinnes/umap R N/A https://www.R-project.org/ rgl v0.98.1 N/A https://r-forge.r-project.org/projects/rgl/ ggplot2 v2.2.1 N/A https://github.com/tidyverse/ggplot2 viridis N/A https://github.com/sjmgarnier/viridis limma N/A https://bioconductor.org/packages/ release/bioc/html/limma.html DESeq2 N/A https://bioconductor.org/packages/ release/bioc/html/DESeq2.html
Virus:Article Title: Spatio-Temporal Characteristics of Tropospheric Ozone and Its Precursors in Guangxi, South China
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Anti-FLAG APC Biolegend Cat#: 637308; RRID: AB_2561497 Alexa Fluor 647 Goat Anti-Human IgG (H+L) Invitrogen Cat#: A-21445; RRID: AB_2535862 Anti-mouse IgG APC Biolegend Cat#: 405308; RRID: AB_315011 TruStain fcX (anti-mouse CD16/32) Antibody Biolegend Cat#: 101320; RRID: AB_1574975 Anti-mouse IgG HRP Sigma Cat#: A9044-2ML; RRID: AB_258431 Bacterial and Virus Strains Lenti-virus packaging kit GeneCopoeia Cat#: LT001 GeneCopoeia GCI-L3 chemically competent cells GeneCopoeia Cat#: STK-300-10 pLenti CMV Puro DEST (w118-1) Addgene Cat#: 17452 Chemicals, Peptides, and Recombinant Proteins Collagenase from Clostridium Histolyticum, Type IV Sigma-Aldrich Cat#: C5138 DNase, Type I Sigma-Aldrich Cat#: D4527 Cell-ID Intercalator-Ir—125 mM Fluidigm Cat#: 201192A Cell-ID Cisplatin Fluidigm Cat#: 201064 16% Paraformaldehyde Aqueous Solution, EM Grade EMS Cat#: 15710 TSA Plus Cy3 System Perkin Elmer Cat#: NEL744001KT TSA Cy5-tyramide Perkin Elmer Cat#: SAT705A001EA Biotinylated Tyramide Perkin Elmer Cat#: SAT700001EA Streptavidin Alexa-750 Thermo Fisher Cat # S-21384 DAPI (4’,6-Diamidino-2-Phenylindole, Dihydrochloride) Thermo Fisher Cat # D1306 I-Ak HEL peptide MBL international Cat# TS-M708-P OVA 257-264 peptide GenScript Cat#: RP10611 Lipofectamine 2000 Invitrogen Cat#:11668019 Critical Commercial Assays Mass cytometry antibody conjugation kits Fluidigm Cat#: 201300 Foxp3 / Transcription Factor Fixation/Permeabilization Concentrate and Diluent Thermo Fisher Cat#: 00-5521-00 EQTM Four Element Calibration Beads Fluidigm Cat#: 201078 Permeabilization Buffer (10X) Thermo Fisher Cat#: 00-8333-56 BD CBA mouse Inflammation/Th1,2,17 kit BD Biosciences Cat#:552364;560485 Mouse anti-dsDNA IgG specific ELISA kit Alpha diagnostic International Cat#: 5120 Octet Protein A Biosensor PALL https://www.fortebio.com/biosensors-Protein-A.html Deposited Data CyTOF data for MC38 tumor from WT/FGL1-KO mice This paper Mendeley Data, see STAR Methods. .. CyTOF data for PBMCs from WT/FGL1-KO mice This paper Mendeley Data, see STAR Methods.
Recombinant:Article Title: Spatio-Temporal Characteristics of Tropospheric Ozone and Its Precursors in Guangxi, South China
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Anti-FLAG APC Biolegend Cat#: 637308; RRID: AB_2561497 Alexa Fluor 647 Goat Anti-Human IgG (H+L) Invitrogen Cat#: A-21445; RRID: AB_2535862 Anti-mouse IgG APC Biolegend Cat#: 405308; RRID: AB_315011 TruStain fcX (anti-mouse CD16/32) Antibody Biolegend Cat#: 101320; RRID: AB_1574975 Anti-mouse IgG HRP Sigma Cat#: A9044-2ML; RRID: AB_258431 Bacterial and Virus Strains Lenti-virus packaging kit GeneCopoeia Cat#: LT001 GeneCopoeia GCI-L3 chemically competent cells GeneCopoeia Cat#: STK-300-10 pLenti CMV Puro DEST (w118-1) Addgene Cat#: 17452 Chemicals, Peptides, and Recombinant Proteins Collagenase from Clostridium Histolyticum, Type IV Sigma-Aldrich Cat#: C5138 DNase, Type I Sigma-Aldrich Cat#: D4527 Cell-ID Intercalator-Ir—125 mM Fluidigm Cat#: 201192A Cell-ID Cisplatin Fluidigm Cat#: 201064 16% Paraformaldehyde Aqueous Solution, EM Grade EMS Cat#: 15710 TSA Plus Cy3 System Perkin Elmer Cat#: NEL744001KT TSA Cy5-tyramide Perkin Elmer Cat#: SAT705A001EA Biotinylated Tyramide Perkin Elmer Cat#: SAT700001EA Streptavidin Alexa-750 Thermo Fisher Cat # S-21384 DAPI (4’,6-Diamidino-2-Phenylindole, Dihydrochloride) Thermo Fisher Cat # D1306 I-Ak HEL peptide MBL international Cat# TS-M708-P OVA 257-264 peptide GenScript Cat#: RP10611 Lipofectamine 2000 Invitrogen Cat#:11668019 Critical Commercial Assays Mass cytometry antibody conjugation kits Fluidigm Cat#: 201300 Foxp3 / Transcription Factor Fixation/Permeabilization Concentrate and Diluent Thermo Fisher Cat#: 00-5521-00 EQTM Four Element Calibration Beads Fluidigm Cat#: 201078 Permeabilization Buffer (10X) Thermo Fisher Cat#: 00-8333-56 BD CBA mouse Inflammation/Th1,2,17 kit BD Biosciences Cat#:552364;560485 Mouse anti-dsDNA IgG specific ELISA kit Alpha diagnostic International Cat#: 5120 Octet Protein A Biosensor PALL https://www.fortebio.com/biosensors-Protein-A.html Deposited Data CyTOF data for MC38 tumor from WT/FGL1-KO mice This paper Mendeley Data, see STAR Methods. .. CyTOF data for PBMCs from WT/FGL1-KO mice This paper Mendeley Data, see STAR Methods.
Article Title: An Integrated Multi-omic Single-Cell Atlas of Human B Cell Identity
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Goat F(ab’)2 Anti-Human Kappa-UNLB Southern Biotech Cat#2062-01; RRID: AB_2795736 All antibodies used for cytometry Various Table S1 Biological Samples Leukocyte reduction chamber from human blood Stanford Blood Center stanfordbloodcenter.org Whole blood from healthy donors Obtained under informed consent with IRB approval n/a Human tonsil Stanford Hospital, adult tonsilectomy from adults with obstructive sleep apnea stanfordhealthcare.org Human lymph node Stanford Hosptial, biopsy sample of recovered lymphoma patient stanfordhealthcare.org Human bone marrow from healthy donors AllCells allcells.com Chemicals, Peptides, and Recombinant Proteins Ficoll-Paque Plus GE Healthcare Cat#300-25 RPMI 1640 media Thermo Fisher Scientific Cat#21-870-092 GlutaMAX supplement Thermo Fisher Scientific Cat#35050-061 Fetal bovine serum USDA approved lot Omega Scientific, Inc. Cat#FB-01 Benzonase nuclease Sigma-Aldrich Cat#E1014-25KU Recombinant human CD40L BioLegend Cat#591704 Human TruStain FcX (Fc Receptor Blocking Solution) BioLegend Cat#422302 Bovine Serum Album (BSA) Heat-shock Treated Thermo Fisher Scientific Cat#BP1600-100 Cell-ID Intercalator-Ir Fluidigm Cat201192A Cell-ID Cisplatin Fluidigm Cat#201064 Saponin from quillaja bark Sigma-Aldrich Cat#S7900-25G Calibration Beads, EQ, Four Element Fluidigm Cat#201078 7-AAD Viability Staining Solution BioLegend Cat#420404 Streptavidin Particles Plus BD Biosciences Cat#557812 Critical Commercial Assays Cell-ID 20-Plex Pd Barcoding Kit Fluidigm Cat#201060 Maxpar X8 Antibody Labeling Kit Fluidigm Cat#201176B IMag Cell Separation Magnet BD Biosciences Cat#552311 QIAamp DNA Micro Kit QIAGEN Cat#56304 immunoSeq Human B Cell - survey resolution Adaptive adaptivebiotech.com Deposited Data Mass cytometry data This study flowrepository.org/id/FR-FCM-Z2MA flowrepository.org/id/FR-FCM-Z2MC Software and Algorithms RStudio Rstudio rstudio.com MATLAB MathWorks mathworks.com/products/MATLAB.html Cytobank Cytobank cytobank.org CellEngine Primity Bio cellengine.com Other Custom code for analysis This study github.com/davidrglass/atlas Immunity 53, 217–232.e1–e5, July 14, 2020 e1 ll OPEN ACCESS Resource ..
Article Title: Chromatin Landscape Underpinning Human Dendritic Cell Heterogeneity
Article Snippet: .. N/A Chemicals, Peptides, and Recombinant Proteins Ficoll-Paque PLUS GE Healthcare Cat# 300-25 1M Tris-HCl, pH 7.4 VWR Cat# 100216-458 NaCl ThermoFisher Scientific Cat# AM9760G MgCl2 ThermoFisher Scientific Cat# AM9530G Tween-20 Millipore-Sigma Cat# 11332465001 Digitonin VWR Cat# PAG9441 Nonidet P40 Substitute Millipore-Sigma Cat# 11332473001 IGEPAL CA-630 Millipore-Sigma Cat# 18896 Tn5 transposase Produced as described in Picelli et al., 2014 N/A SYBR Green I Nucleic Acid Gel ThermoFisher Scientific Cat# S7563 Dulbecco’s Phosphate Buffered Saline Corning Cat# 21-031-CV Fetal Bovine Serum, qualified, US origin GIBCO Cat# 26140079 RPMI 1640 with L- Glutamine Corning Cat# 10040CV L-glutamine Solution Corning Cat# 25005CI Sodium Pyruvate Solution Corning Cat# 25000CI Penicillin-Streptomycin Corning Cat# 30002CI HEPES solution Corning Cat# 25060CI MEM Nonessential Amino Acid Solution Corning Cat# 25025CI Recombinant Human IL-3 R&D Systems Cat# 203IL010CF EDTA 0.5M pH 8.0 Corning Cat# 46034CI ACK Lysis Buffer Lonza Cat# 10-548E Benzonase Nuclease Millipore-Sigma Cat# E1014-25KU Cell-ID Intercalator-Ir Fluidigm Cat# 201192A Cell-ID Cisplatin Fluidigm Cat# 201064 5(6)-Carboxyfluorescein diacetate N-succinimidyl ester Millipore-Sigma Cat# 21888-25MG-F CellTrace Violet Cell Proliferation Kit ThermoFisher Scientific Cat# C34557 Bovine Serum Albumin solution 30% ± 2% in 0.85% sodium chloride, aseptically filled Millipore-Sigma Cat# A7284-50ML Dimethyl sulfoxide > 95% Millipore-Sigma Cat# D4540 Paraformaldehyde 16% aqueous solution Electron Microscopy Sciences Cat# 15710 Indium 113 metal chloride Trace Sciences International In-113 Indium 115 metal chloride Trace Sciences International In-115 CpG-A ODN 2216 Invivogen Cat# tlrl-2216-1 Imiquimod Invivogen Cat# tlrl-imqs Recombinant Human CD40 Ligand R&D Systems Cat# 6420CL025CF Critical Commercial Assays Foxp3 / Transcription Factor Fixation/ Permeabilization Concentrate and Diluent ThermoFisher Scientific Cat# 00-5521-00 Permeabilization Buffer (10X) ThermoFisher Scientific Cat# 00-8333-56 (Continued on next page) e3 Cell Reports 32, 108180, September 22, 2020 Resource ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Maxpar X8 Multimetal Labeling Kit Fluidigm Fluidigm Cat# 201300 LIVE/DEAD Fixable Dead Cell Stain Sampler Kit ThermoFisher Scientific Cat# L34960 Dynabeads Pan Mouse IgG ThermoFisher Scientific Cat# 11042 Plasmacytoid Dendritic Cell Isolation Kit II, human MACS, Miltenyi Biotec Cat# 130-097-415 Pan T cell Isolation Kit, human MACS, Miltenyi Biotec Cat# 130-096-535 Human IFN Alpha Multi-Subtype ELISA Kit (TCM) PBL Assay Science Cat# 41105-1 BD Cytometric Bead Array Human Enhanced Sensitivity Master Buffer Kit BD Biosciences Cat# 561521 BD Cytometric Bead Array Human IL-6 Enhanced Sensitivity Flex Set BD Biosciences Cat# 561512 BD Cytometric Bead Array Human TNF Enhanced Sensitivity Flex Set BD Biosciences Cat# 561516 BD CompBead Anti-Mouse Ig, k/Negative Control Compensation Particles Set BD Biosciences Cat# 552843 Alexa Fluor 647 Antibody Labeling Kit ThermoFisher Scientific Cat# A20186 NucleoSpin RNA XS kit Takara Bio Cat# 740902.10 NEBNext High Fidelity 2X PCR Master Mix New England Biolabs Cat# M0541S iScript Reverse Transcription Supermix Bio-Rad Laboratories Cat# 1708840 iTaq Universal SYBRGreen Supermix Bio-Rad Laboratories Cat# 1725120 QIAGEN MinElute PCR Purification Kit QIAGEN Cat# 28004 Nextera DNA Library Preparation Kit Illumina Cat# FC-121-1030 Zymo DNA Clean and Concentrator-5 Kit Zymo Research Corporation Cat# D4013 PrimeFlow RNA Assay Kit ThermoFisher Scientific Cat# 88-18005-204 ID2 PrimeFlow Probe Set (A488) ThermoFisher Scientific Cat# PF210; Assay ID: VA4-3086868-PF Deposited Data ATAC-seq data (generated here) NCBI GEO GEO: GSE146896 Human DC scRNA-seq https://singlecell.broadinstitute. org/single_cell/study/atlas-ofhuman-blood-dendritic-cellsand-monocytes Broad Single Cell Portal study ‘‘Atlas of human blood dendritic cells and monocytes’’ Mouse DC RNA-seq NCBI GEO GEO: GSE76132 Other Immune Lineage ATAC-seq NCBI GEO GEO: GSE118189 TCF4 ChIP-seq NCBI GEO GEO: GSE76147 TCF4 silencing microarray NCBI GEO GEO: GSE75650 Zbtb18 silencing microarray NCBI GEO GEO: GSE12993 Klf12 / mouse RNA-seq NCBI GEO GEO: GSE128962 Software and Algorithms GraphPad Prism 6 GraphPad Software, Inc. https://www.graphpad.com/scientific- software/prism/ MATLAB N/A https://www.mathworks.com/products/ matlab.html Cytofkit N/A https://bioconductor.riken.jp/packages/3.7/ bioc/html/cytofkit.html FlowJo Software v10.0.8 TreeStar, Inc https://www.flowjo.com/solutions/flowjo R N/A https://www.R-project.org/ ggplot2 v2.2.1 N/A https://github.com/tidyverse/ggplot2 viridis v0.3.0 N/A https://github.com/sjmgarnier/viridis limma v3.44.3 N/A https://bioconductor.org/packages/ release/bioc/html/limma.html (Continued on next page) Cell Reports 32, 108180, September 22, 2020 e4 Resource ll OPEN ACCESS
Mass Cytometry:Article Title: Spatio-Temporal Characteristics of Tropospheric Ozone and Its Precursors in Guangxi, South China
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Anti-FLAG APC Biolegend Cat#: 637308; RRID: AB_2561497 Alexa Fluor 647 Goat Anti-Human IgG (H+L) Invitrogen Cat#: A-21445; RRID: AB_2535862 Anti-mouse IgG APC Biolegend Cat#: 405308; RRID: AB_315011 TruStain fcX (anti-mouse CD16/32) Antibody Biolegend Cat#: 101320; RRID: AB_1574975 Anti-mouse IgG HRP Sigma Cat#: A9044-2ML; RRID: AB_258431 Bacterial and Virus Strains Lenti-virus packaging kit GeneCopoeia Cat#: LT001 GeneCopoeia GCI-L3 chemically competent cells GeneCopoeia Cat#: STK-300-10 pLenti CMV Puro DEST (w118-1) Addgene Cat#: 17452 Chemicals, Peptides, and Recombinant Proteins Collagenase from Clostridium Histolyticum, Type IV Sigma-Aldrich Cat#: C5138 DNase, Type I Sigma-Aldrich Cat#: D4527 Cell-ID Intercalator-Ir—125 mM Fluidigm Cat#: 201192A Cell-ID Cisplatin Fluidigm Cat#: 201064 16% Paraformaldehyde Aqueous Solution, EM Grade EMS Cat#: 15710 TSA Plus Cy3 System Perkin Elmer Cat#: NEL744001KT TSA Cy5-tyramide Perkin Elmer Cat#: SAT705A001EA Biotinylated Tyramide Perkin Elmer Cat#: SAT700001EA Streptavidin Alexa-750 Thermo Fisher Cat # S-21384 DAPI (4’,6-Diamidino-2-Phenylindole, Dihydrochloride) Thermo Fisher Cat # D1306 I-Ak HEL peptide MBL international Cat# TS-M708-P OVA 257-264 peptide GenScript Cat#: RP10611 Lipofectamine 2000 Invitrogen Cat#:11668019 Critical Commercial Assays Mass cytometry antibody conjugation kits Fluidigm Cat#: 201300 Foxp3 / Transcription Factor Fixation/Permeabilization Concentrate and Diluent Thermo Fisher Cat#: 00-5521-00 EQTM Four Element Calibration Beads Fluidigm Cat#: 201078 Permeabilization Buffer (10X) Thermo Fisher Cat#: 00-8333-56 BD CBA mouse Inflammation/Th1,2,17 kit BD Biosciences Cat#:552364;560485 Mouse anti-dsDNA IgG specific ELISA kit Alpha diagnostic International Cat#: 5120 Octet Protein A Biosensor PALL https://www.fortebio.com/biosensors-Protein-A.html Deposited Data CyTOF data for MC38 tumor from WT/FGL1-KO mice This paper Mendeley Data, see STAR Methods. .. CyTOF data for PBMCs from WT/FGL1-KO mice This paper Mendeley Data, see STAR Methods.
Article Title: An Integrated Multi-omic Single-Cell Atlas of Human B Cell Identity
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Goat F(ab’)2 Anti-Human Kappa-UNLB Southern Biotech Cat#2062-01; RRID: AB_2795736 All antibodies used for cytometry Various Table S1 Biological Samples Leukocyte reduction chamber from human blood Stanford Blood Center stanfordbloodcenter.org Whole blood from healthy donors Obtained under informed consent with IRB approval n/a Human tonsil Stanford Hospital, adult tonsilectomy from adults with obstructive sleep apnea stanfordhealthcare.org Human lymph node Stanford Hosptial, biopsy sample of recovered lymphoma patient stanfordhealthcare.org Human bone marrow from healthy donors AllCells allcells.com Chemicals, Peptides, and Recombinant Proteins Ficoll-Paque Plus GE Healthcare Cat#300-25 RPMI 1640 media Thermo Fisher Scientific Cat#21-870-092 GlutaMAX supplement Thermo Fisher Scientific Cat#35050-061 Fetal bovine serum USDA approved lot Omega Scientific, Inc. Cat#FB-01 Benzonase nuclease Sigma-Aldrich Cat#E1014-25KU Recombinant human CD40L BioLegend Cat#591704 Human TruStain FcX (Fc Receptor Blocking Solution) BioLegend Cat#422302 Bovine Serum Album (BSA) Heat-shock Treated Thermo Fisher Scientific Cat#BP1600-100 Cell-ID Intercalator-Ir Fluidigm Cat201192A Cell-ID Cisplatin Fluidigm Cat#201064 Saponin from quillaja bark Sigma-Aldrich Cat#S7900-25G Calibration Beads, EQ, Four Element Fluidigm Cat#201078 7-AAD Viability Staining Solution BioLegend Cat#420404 Streptavidin Particles Plus BD Biosciences Cat#557812 Critical Commercial Assays Cell-ID 20-Plex Pd Barcoding Kit Fluidigm Cat#201060 Maxpar X8 Antibody Labeling Kit Fluidigm Cat#201176B IMag Cell Separation Magnet BD Biosciences Cat#552311 QIAamp DNA Micro Kit QIAGEN Cat#56304 immunoSeq Human B Cell - survey resolution Adaptive adaptivebiotech.com Deposited Data Mass cytometry data This study flowrepository.org/id/FR-FCM-Z2MA flowrepository.org/id/FR-FCM-Z2MC Software and Algorithms RStudio Rstudio rstudio.com MATLAB MathWorks mathworks.com/products/MATLAB.html Cytobank Cytobank cytobank.org CellEngine Primity Bio cellengine.com Other Custom code for analysis This study github.com/davidrglass/atlas Immunity 53, 217–232.e1–e5, July 14, 2020 e1 ll OPEN ACCESS Resource ..
Conjugation Assay:Article Title: Spatio-Temporal Characteristics of Tropospheric Ozone and Its Precursors in Guangxi, South China
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Anti-FLAG APC Biolegend Cat#: 637308; RRID: AB_2561497 Alexa Fluor 647 Goat Anti-Human IgG (H+L) Invitrogen Cat#: A-21445; RRID: AB_2535862 Anti-mouse IgG APC Biolegend Cat#: 405308; RRID: AB_315011 TruStain fcX (anti-mouse CD16/32) Antibody Biolegend Cat#: 101320; RRID: AB_1574975 Anti-mouse IgG HRP Sigma Cat#: A9044-2ML; RRID: AB_258431 Bacterial and Virus Strains Lenti-virus packaging kit GeneCopoeia Cat#: LT001 GeneCopoeia GCI-L3 chemically competent cells GeneCopoeia Cat#: STK-300-10 pLenti CMV Puro DEST (w118-1) Addgene Cat#: 17452 Chemicals, Peptides, and Recombinant Proteins Collagenase from Clostridium Histolyticum, Type IV Sigma-Aldrich Cat#: C5138 DNase, Type I Sigma-Aldrich Cat#: D4527 Cell-ID Intercalator-Ir—125 mM Fluidigm Cat#: 201192A Cell-ID Cisplatin Fluidigm Cat#: 201064 16% Paraformaldehyde Aqueous Solution, EM Grade EMS Cat#: 15710 TSA Plus Cy3 System Perkin Elmer Cat#: NEL744001KT TSA Cy5-tyramide Perkin Elmer Cat#: SAT705A001EA Biotinylated Tyramide Perkin Elmer Cat#: SAT700001EA Streptavidin Alexa-750 Thermo Fisher Cat # S-21384 DAPI (4’,6-Diamidino-2-Phenylindole, Dihydrochloride) Thermo Fisher Cat # D1306 I-Ak HEL peptide MBL international Cat# TS-M708-P OVA 257-264 peptide GenScript Cat#: RP10611 Lipofectamine 2000 Invitrogen Cat#:11668019 Critical Commercial Assays Mass cytometry antibody conjugation kits Fluidigm Cat#: 201300 Foxp3 / Transcription Factor Fixation/Permeabilization Concentrate and Diluent Thermo Fisher Cat#: 00-5521-00 EQTM Four Element Calibration Beads Fluidigm Cat#: 201078 Permeabilization Buffer (10X) Thermo Fisher Cat#: 00-8333-56 BD CBA mouse Inflammation/Th1,2,17 kit BD Biosciences Cat#:552364;560485 Mouse anti-dsDNA IgG specific ELISA kit Alpha diagnostic International Cat#: 5120 Octet Protein A Biosensor PALL https://www.fortebio.com/biosensors-Protein-A.html Deposited Data CyTOF data for MC38 tumor from WT/FGL1-KO mice This paper Mendeley Data, see STAR Methods. .. CyTOF data for PBMCs from WT/FGL1-KO mice This paper Mendeley Data, see STAR Methods.
Crocin Bleaching Assay:Article Title: Spatio-Temporal Characteristics of Tropospheric Ozone and Its Precursors in Guangxi, South China
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Anti-FLAG APC Biolegend Cat#: 637308; RRID: AB_2561497 Alexa Fluor 647 Goat Anti-Human IgG (H+L) Invitrogen Cat#: A-21445; RRID: AB_2535862 Anti-mouse IgG APC Biolegend Cat#: 405308; RRID: AB_315011 TruStain fcX (anti-mouse CD16/32) Antibody Biolegend Cat#: 101320; RRID: AB_1574975 Anti-mouse IgG HRP Sigma Cat#: A9044-2ML; RRID: AB_258431 Bacterial and Virus Strains Lenti-virus packaging kit GeneCopoeia Cat#: LT001 GeneCopoeia GCI-L3 chemically competent cells GeneCopoeia Cat#: STK-300-10 pLenti CMV Puro DEST (w118-1) Addgene Cat#: 17452 Chemicals, Peptides, and Recombinant Proteins Collagenase from Clostridium Histolyticum, Type IV Sigma-Aldrich Cat#: C5138 DNase, Type I Sigma-Aldrich Cat#: D4527 Cell-ID Intercalator-Ir—125 mM Fluidigm Cat#: 201192A Cell-ID Cisplatin Fluidigm Cat#: 201064 16% Paraformaldehyde Aqueous Solution, EM Grade EMS Cat#: 15710 TSA Plus Cy3 System Perkin Elmer Cat#: NEL744001KT TSA Cy5-tyramide Perkin Elmer Cat#: SAT705A001EA Biotinylated Tyramide Perkin Elmer Cat#: SAT700001EA Streptavidin Alexa-750 Thermo Fisher Cat # S-21384 DAPI (4’,6-Diamidino-2-Phenylindole, Dihydrochloride) Thermo Fisher Cat # D1306 I-Ak HEL peptide MBL international Cat# TS-M708-P OVA 257-264 peptide GenScript Cat#: RP10611 Lipofectamine 2000 Invitrogen Cat#:11668019 Critical Commercial Assays Mass cytometry antibody conjugation kits Fluidigm Cat#: 201300 Foxp3 / Transcription Factor Fixation/Permeabilization Concentrate and Diluent Thermo Fisher Cat#: 00-5521-00 EQTM Four Element Calibration Beads Fluidigm Cat#: 201078 Permeabilization Buffer (10X) Thermo Fisher Cat#: 00-8333-56 BD CBA mouse Inflammation/Th1,2,17 kit BD Biosciences Cat#:552364;560485 Mouse anti-dsDNA IgG specific ELISA kit Alpha diagnostic International Cat#: 5120 Octet Protein A Biosensor PALL https://www.fortebio.com/biosensors-Protein-A.html Deposited Data CyTOF data for MC38 tumor from WT/FGL1-KO mice This paper Mendeley Data, see STAR Methods. .. CyTOF data for PBMCs from WT/FGL1-KO mice This paper Mendeley Data, see STAR Methods.
Enzyme-linked Immunosorbent Assay:Article Title: Spatio-Temporal Characteristics of Tropospheric Ozone and Its Precursors in Guangxi, South China
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Anti-FLAG APC Biolegend Cat#: 637308; RRID: AB_2561497 Alexa Fluor 647 Goat Anti-Human IgG (H+L) Invitrogen Cat#: A-21445; RRID: AB_2535862 Anti-mouse IgG APC Biolegend Cat#: 405308; RRID: AB_315011 TruStain fcX (anti-mouse CD16/32) Antibody Biolegend Cat#: 101320; RRID: AB_1574975 Anti-mouse IgG HRP Sigma Cat#: A9044-2ML; RRID: AB_258431 Bacterial and Virus Strains Lenti-virus packaging kit GeneCopoeia Cat#: LT001 GeneCopoeia GCI-L3 chemically competent cells GeneCopoeia Cat#: STK-300-10 pLenti CMV Puro DEST (w118-1) Addgene Cat#: 17452 Chemicals, Peptides, and Recombinant Proteins Collagenase from Clostridium Histolyticum, Type IV Sigma-Aldrich Cat#: C5138 DNase, Type I Sigma-Aldrich Cat#: D4527 Cell-ID Intercalator-Ir—125 mM Fluidigm Cat#: 201192A Cell-ID Cisplatin Fluidigm Cat#: 201064 16% Paraformaldehyde Aqueous Solution, EM Grade EMS Cat#: 15710 TSA Plus Cy3 System Perkin Elmer Cat#: NEL744001KT TSA Cy5-tyramide Perkin Elmer Cat#: SAT705A001EA Biotinylated Tyramide Perkin Elmer Cat#: SAT700001EA Streptavidin Alexa-750 Thermo Fisher Cat # S-21384 DAPI (4’,6-Diamidino-2-Phenylindole, Dihydrochloride) Thermo Fisher Cat # D1306 I-Ak HEL peptide MBL international Cat# TS-M708-P OVA 257-264 peptide GenScript Cat#: RP10611 Lipofectamine 2000 Invitrogen Cat#:11668019 Critical Commercial Assays Mass cytometry antibody conjugation kits Fluidigm Cat#: 201300 Foxp3 / Transcription Factor Fixation/Permeabilization Concentrate and Diluent Thermo Fisher Cat#: 00-5521-00 EQTM Four Element Calibration Beads Fluidigm Cat#: 201078 Permeabilization Buffer (10X) Thermo Fisher Cat#: 00-8333-56 BD CBA mouse Inflammation/Th1,2,17 kit BD Biosciences Cat#:552364;560485 Mouse anti-dsDNA IgG specific ELISA kit Alpha diagnostic International Cat#: 5120 Octet Protein A Biosensor PALL https://www.fortebio.com/biosensors-Protein-A.html Deposited Data CyTOF data for MC38 tumor from WT/FGL1-KO mice This paper Mendeley Data, see STAR Methods. .. CyTOF data for PBMCs from WT/FGL1-KO mice This paper Mendeley Data, see STAR Methods.
Cytometry:Article Title: An Integrated Multi-omic Single-Cell Atlas of Human B Cell Identity
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Goat F(ab’)2 Anti-Human Kappa-UNLB Southern Biotech Cat#2062-01; RRID: AB_2795736 All antibodies used for cytometry Various Table S1 Biological Samples Leukocyte reduction chamber from human blood Stanford Blood Center stanfordbloodcenter.org Whole blood from healthy donors Obtained under informed consent with IRB approval n/a Human tonsil Stanford Hospital, adult tonsilectomy from adults with obstructive sleep apnea stanfordhealthcare.org Human lymph node Stanford Hosptial, biopsy sample of recovered lymphoma patient stanfordhealthcare.org Human bone marrow from healthy donors AllCells allcells.com Chemicals, Peptides, and Recombinant Proteins Ficoll-Paque Plus GE Healthcare Cat#300-25 RPMI 1640 media Thermo Fisher Scientific Cat#21-870-092 GlutaMAX supplement Thermo Fisher Scientific Cat#35050-061 Fetal bovine serum USDA approved lot Omega Scientific, Inc. Cat#FB-01 Benzonase nuclease Sigma-Aldrich Cat#E1014-25KU Recombinant human CD40L BioLegend Cat#591704 Human TruStain FcX (Fc Receptor Blocking Solution) BioLegend Cat#422302 Bovine Serum Album (BSA) Heat-shock Treated Thermo Fisher Scientific Cat#BP1600-100 Cell-ID Intercalator-Ir Fluidigm Cat201192A Cell-ID Cisplatin Fluidigm Cat#201064 Saponin from quillaja bark Sigma-Aldrich Cat#S7900-25G Calibration Beads, EQ, Four Element Fluidigm Cat#201078 7-AAD Viability Staining Solution BioLegend Cat#420404 Streptavidin Particles Plus BD Biosciences Cat#557812 Critical Commercial Assays Cell-ID 20-Plex Pd Barcoding Kit Fluidigm Cat#201060 Maxpar X8 Antibody Labeling Kit Fluidigm Cat#201176B IMag Cell Separation Magnet BD Biosciences Cat#552311 QIAamp DNA Micro Kit QIAGEN Cat#56304 immunoSeq Human B Cell - survey resolution Adaptive adaptivebiotech.com Deposited Data Mass cytometry data This study flowrepository.org/id/FR-FCM-Z2MA flowrepository.org/id/FR-FCM-Z2MC Software and Algorithms RStudio Rstudio rstudio.com MATLAB MathWorks mathworks.com/products/MATLAB.html Cytobank Cytobank cytobank.org CellEngine Primity Bio cellengine.com Other Custom code for analysis This study github.com/davidrglass/atlas Immunity 53, 217–232.e1–e5, July 14, 2020 e1 ll OPEN ACCESS Resource ..
Blocking Assay:Article Title: An Integrated Multi-omic Single-Cell Atlas of Human B Cell Identity
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Goat F(ab’)2 Anti-Human Kappa-UNLB Southern Biotech Cat#2062-01; RRID: AB_2795736 All antibodies used for cytometry Various Table S1 Biological Samples Leukocyte reduction chamber from human blood Stanford Blood Center stanfordbloodcenter.org Whole blood from healthy donors Obtained under informed consent with IRB approval n/a Human tonsil Stanford Hospital, adult tonsilectomy from adults with obstructive sleep apnea stanfordhealthcare.org Human lymph node Stanford Hosptial, biopsy sample of recovered lymphoma patient stanfordhealthcare.org Human bone marrow from healthy donors AllCells allcells.com Chemicals, Peptides, and Recombinant Proteins Ficoll-Paque Plus GE Healthcare Cat#300-25 RPMI 1640 media Thermo Fisher Scientific Cat#21-870-092 GlutaMAX supplement Thermo Fisher Scientific Cat#35050-061 Fetal bovine serum USDA approved lot Omega Scientific, Inc. Cat#FB-01 Benzonase nuclease Sigma-Aldrich Cat#E1014-25KU Recombinant human CD40L BioLegend Cat#591704 Human TruStain FcX (Fc Receptor Blocking Solution) BioLegend Cat#422302 Bovine Serum Album (BSA) Heat-shock Treated Thermo Fisher Scientific Cat#BP1600-100 Cell-ID Intercalator-Ir Fluidigm Cat201192A Cell-ID Cisplatin Fluidigm Cat#201064 Saponin from quillaja bark Sigma-Aldrich Cat#S7900-25G Calibration Beads, EQ, Four Element Fluidigm Cat#201078 7-AAD Viability Staining Solution BioLegend Cat#420404 Streptavidin Particles Plus BD Biosciences Cat#557812 Critical Commercial Assays Cell-ID 20-Plex Pd Barcoding Kit Fluidigm Cat#201060 Maxpar X8 Antibody Labeling Kit Fluidigm Cat#201176B IMag Cell Separation Magnet BD Biosciences Cat#552311 QIAamp DNA Micro Kit QIAGEN Cat#56304 immunoSeq Human B Cell - survey resolution Adaptive adaptivebiotech.com Deposited Data Mass cytometry data This study flowrepository.org/id/FR-FCM-Z2MA flowrepository.org/id/FR-FCM-Z2MC Software and Algorithms RStudio Rstudio rstudio.com MATLAB MathWorks mathworks.com/products/MATLAB.html Cytobank Cytobank cytobank.org CellEngine Primity Bio cellengine.com Other Custom code for analysis This study github.com/davidrglass/atlas Immunity 53, 217–232.e1–e5, July 14, 2020 e1 ll OPEN ACCESS Resource ..
Staining:Article Title: An Integrated Multi-omic Single-Cell Atlas of Human B Cell Identity
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Goat F(ab’)2 Anti-Human Kappa-UNLB Southern Biotech Cat#2062-01; RRID: AB_2795736 All antibodies used for cytometry Various Table S1 Biological Samples Leukocyte reduction chamber from human blood Stanford Blood Center stanfordbloodcenter.org Whole blood from healthy donors Obtained under informed consent with IRB approval n/a Human tonsil Stanford Hospital, adult tonsilectomy from adults with obstructive sleep apnea stanfordhealthcare.org Human lymph node Stanford Hosptial, biopsy sample of recovered lymphoma patient stanfordhealthcare.org Human bone marrow from healthy donors AllCells allcells.com Chemicals, Peptides, and Recombinant Proteins Ficoll-Paque Plus GE Healthcare Cat#300-25 RPMI 1640 media Thermo Fisher Scientific Cat#21-870-092 GlutaMAX supplement Thermo Fisher Scientific Cat#35050-061 Fetal bovine serum USDA approved lot Omega Scientific, Inc. Cat#FB-01 Benzonase nuclease Sigma-Aldrich Cat#E1014-25KU Recombinant human CD40L BioLegend Cat#591704 Human TruStain FcX (Fc Receptor Blocking Solution) BioLegend Cat#422302 Bovine Serum Album (BSA) Heat-shock Treated Thermo Fisher Scientific Cat#BP1600-100 Cell-ID Intercalator-Ir Fluidigm Cat201192A Cell-ID Cisplatin Fluidigm Cat#201064 Saponin from quillaja bark Sigma-Aldrich Cat#S7900-25G Calibration Beads, EQ, Four Element Fluidigm Cat#201078 7-AAD Viability Staining Solution BioLegend Cat#420404 Streptavidin Particles Plus BD Biosciences Cat#557812 Critical Commercial Assays Cell-ID 20-Plex Pd Barcoding Kit Fluidigm Cat#201060 Maxpar X8 Antibody Labeling Kit Fluidigm Cat#201176B IMag Cell Separation Magnet BD Biosciences Cat#552311 QIAamp DNA Micro Kit QIAGEN Cat#56304 immunoSeq Human B Cell - survey resolution Adaptive adaptivebiotech.com Deposited Data Mass cytometry data This study flowrepository.org/id/FR-FCM-Z2MA flowrepository.org/id/FR-FCM-Z2MC Software and Algorithms RStudio Rstudio rstudio.com MATLAB MathWorks mathworks.com/products/MATLAB.html Cytobank Cytobank cytobank.org CellEngine Primity Bio cellengine.com Other Custom code for analysis This study github.com/davidrglass/atlas Immunity 53, 217–232.e1–e5, July 14, 2020 e1 ll OPEN ACCESS Resource ..
Antibody Labeling:Article Title: An Integrated Multi-omic Single-Cell Atlas of Human B Cell Identity
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Goat F(ab’)2 Anti-Human Kappa-UNLB Southern Biotech Cat#2062-01; RRID: AB_2795736 All antibodies used for cytometry Various Table S1 Biological Samples Leukocyte reduction chamber from human blood Stanford Blood Center stanfordbloodcenter.org Whole blood from healthy donors Obtained under informed consent with IRB approval n/a Human tonsil Stanford Hospital, adult tonsilectomy from adults with obstructive sleep apnea stanfordhealthcare.org Human lymph node Stanford Hosptial, biopsy sample of recovered lymphoma patient stanfordhealthcare.org Human bone marrow from healthy donors AllCells allcells.com Chemicals, Peptides, and Recombinant Proteins Ficoll-Paque Plus GE Healthcare Cat#300-25 RPMI 1640 media Thermo Fisher Scientific Cat#21-870-092 GlutaMAX supplement Thermo Fisher Scientific Cat#35050-061 Fetal bovine serum USDA approved lot Omega Scientific, Inc. Cat#FB-01 Benzonase nuclease Sigma-Aldrich Cat#E1014-25KU Recombinant human CD40L BioLegend Cat#591704 Human TruStain FcX (Fc Receptor Blocking Solution) BioLegend Cat#422302 Bovine Serum Album (BSA) Heat-shock Treated Thermo Fisher Scientific Cat#BP1600-100 Cell-ID Intercalator-Ir Fluidigm Cat201192A Cell-ID Cisplatin Fluidigm Cat#201064 Saponin from quillaja bark Sigma-Aldrich Cat#S7900-25G Calibration Beads, EQ, Four Element Fluidigm Cat#201078 7-AAD Viability Staining Solution BioLegend Cat#420404 Streptavidin Particles Plus BD Biosciences Cat#557812 Critical Commercial Assays Cell-ID 20-Plex Pd Barcoding Kit Fluidigm Cat#201060 Maxpar X8 Antibody Labeling Kit Fluidigm Cat#201176B IMag Cell Separation Magnet BD Biosciences Cat#552311 QIAamp DNA Micro Kit QIAGEN Cat#56304 immunoSeq Human B Cell - survey resolution Adaptive adaptivebiotech.com Deposited Data Mass cytometry data This study flowrepository.org/id/FR-FCM-Z2MA flowrepository.org/id/FR-FCM-Z2MC Software and Algorithms RStudio Rstudio rstudio.com MATLAB MathWorks mathworks.com/products/MATLAB.html Cytobank Cytobank cytobank.org CellEngine Primity Bio cellengine.com Other Custom code for analysis This study github.com/davidrglass/atlas Immunity 53, 217–232.e1–e5, July 14, 2020 e1 ll OPEN ACCESS Resource ..
Software:Article Title: An Integrated Multi-omic Single-Cell Atlas of Human B Cell Identity
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Goat F(ab’)2 Anti-Human Kappa-UNLB Southern Biotech Cat#2062-01; RRID: AB_2795736 All antibodies used for cytometry Various Table S1 Biological Samples Leukocyte reduction chamber from human blood Stanford Blood Center stanfordbloodcenter.org Whole blood from healthy donors Obtained under informed consent with IRB approval n/a Human tonsil Stanford Hospital, adult tonsilectomy from adults with obstructive sleep apnea stanfordhealthcare.org Human lymph node Stanford Hosptial, biopsy sample of recovered lymphoma patient stanfordhealthcare.org Human bone marrow from healthy donors AllCells allcells.com Chemicals, Peptides, and Recombinant Proteins Ficoll-Paque Plus GE Healthcare Cat#300-25 RPMI 1640 media Thermo Fisher Scientific Cat#21-870-092 GlutaMAX supplement Thermo Fisher Scientific Cat#35050-061 Fetal bovine serum USDA approved lot Omega Scientific, Inc. Cat#FB-01 Benzonase nuclease Sigma-Aldrich Cat#E1014-25KU Recombinant human CD40L BioLegend Cat#591704 Human TruStain FcX (Fc Receptor Blocking Solution) BioLegend Cat#422302 Bovine Serum Album (BSA) Heat-shock Treated Thermo Fisher Scientific Cat#BP1600-100 Cell-ID Intercalator-Ir Fluidigm Cat201192A Cell-ID Cisplatin Fluidigm Cat#201064 Saponin from quillaja bark Sigma-Aldrich Cat#S7900-25G Calibration Beads, EQ, Four Element Fluidigm Cat#201078 7-AAD Viability Staining Solution BioLegend Cat#420404 Streptavidin Particles Plus BD Biosciences Cat#557812 Critical Commercial Assays Cell-ID 20-Plex Pd Barcoding Kit Fluidigm Cat#201060 Maxpar X8 Antibody Labeling Kit Fluidigm Cat#201176B IMag Cell Separation Magnet BD Biosciences Cat#552311 QIAamp DNA Micro Kit QIAGEN Cat#56304 immunoSeq Human B Cell - survey resolution Adaptive adaptivebiotech.com Deposited Data Mass cytometry data This study flowrepository.org/id/FR-FCM-Z2MA flowrepository.org/id/FR-FCM-Z2MC Software and Algorithms RStudio Rstudio rstudio.com MATLAB MathWorks mathworks.com/products/MATLAB.html Cytobank Cytobank cytobank.org CellEngine Primity Bio cellengine.com Other Custom code for analysis This study github.com/davidrglass/atlas Immunity 53, 217–232.e1–e5, July 14, 2020 e1 ll OPEN ACCESS Resource ..
Produced:Article Title: Chromatin Landscape Underpinning Human Dendritic Cell Heterogeneity
Article Snippet: .. N/A Chemicals, Peptides, and Recombinant Proteins Ficoll-Paque PLUS GE Healthcare Cat# 300-25 1M Tris-HCl, pH 7.4 VWR Cat# 100216-458 NaCl ThermoFisher Scientific Cat# AM9760G MgCl2 ThermoFisher Scientific Cat# AM9530G Tween-20 Millipore-Sigma Cat# 11332465001 Digitonin VWR Cat# PAG9441 Nonidet P40 Substitute Millipore-Sigma Cat# 11332473001 IGEPAL CA-630 Millipore-Sigma Cat# 18896 Tn5 transposase Produced as described in Picelli et al., 2014 N/A SYBR Green I Nucleic Acid Gel ThermoFisher Scientific Cat# S7563 Dulbecco’s Phosphate Buffered Saline Corning Cat# 21-031-CV Fetal Bovine Serum, qualified, US origin GIBCO Cat# 26140079 RPMI 1640 with L- Glutamine Corning Cat# 10040CV L-glutamine Solution Corning Cat# 25005CI Sodium Pyruvate Solution Corning Cat# 25000CI Penicillin-Streptomycin Corning Cat# 30002CI HEPES solution Corning Cat# 25060CI MEM Nonessential Amino Acid Solution Corning Cat# 25025CI Recombinant Human IL-3 R&D Systems Cat# 203IL010CF EDTA 0.5M pH 8.0 Corning Cat# 46034CI ACK Lysis Buffer Lonza Cat# 10-548E Benzonase Nuclease Millipore-Sigma Cat# E1014-25KU Cell-ID Intercalator-Ir Fluidigm Cat# 201192A Cell-ID Cisplatin Fluidigm Cat# 201064 5(6)-Carboxyfluorescein diacetate N-succinimidyl ester Millipore-Sigma Cat# 21888-25MG-F CellTrace Violet Cell Proliferation Kit ThermoFisher Scientific Cat# C34557 Bovine Serum Albumin solution 30% ± 2% in 0.85% sodium chloride, aseptically filled Millipore-Sigma Cat# A7284-50ML Dimethyl sulfoxide > 95% Millipore-Sigma Cat# D4540 Paraformaldehyde 16% aqueous solution Electron Microscopy Sciences Cat# 15710 Indium 113 metal chloride Trace Sciences International In-113 Indium 115 metal chloride Trace Sciences International In-115 CpG-A ODN 2216 Invivogen Cat# tlrl-2216-1 Imiquimod Invivogen Cat# tlrl-imqs Recombinant Human CD40 Ligand R&D Systems Cat# 6420CL025CF Critical Commercial Assays Foxp3 / Transcription Factor Fixation/ Permeabilization Concentrate and Diluent ThermoFisher Scientific Cat# 00-5521-00 Permeabilization Buffer (10X) ThermoFisher Scientific Cat# 00-8333-56 (Continued on next page) e3 Cell Reports 32, 108180, September 22, 2020 Resource ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Maxpar X8 Multimetal Labeling Kit Fluidigm Fluidigm Cat# 201300 LIVE/DEAD Fixable Dead Cell Stain Sampler Kit ThermoFisher Scientific Cat# L34960 Dynabeads Pan Mouse IgG ThermoFisher Scientific Cat# 11042 Plasmacytoid Dendritic Cell Isolation Kit II, human MACS, Miltenyi Biotec Cat# 130-097-415 Pan T cell Isolation Kit, human MACS, Miltenyi Biotec Cat# 130-096-535 Human IFN Alpha Multi-Subtype ELISA Kit (TCM) PBL Assay Science Cat# 41105-1 BD Cytometric Bead Array Human Enhanced Sensitivity Master Buffer Kit BD Biosciences Cat# 561521 BD Cytometric Bead Array Human IL-6 Enhanced Sensitivity Flex Set BD Biosciences Cat# 561512 BD Cytometric Bead Array Human TNF Enhanced Sensitivity Flex Set BD Biosciences Cat# 561516 BD CompBead Anti-Mouse Ig, k/Negative Control Compensation Particles Set BD Biosciences Cat# 552843 Alexa Fluor 647 Antibody Labeling Kit ThermoFisher Scientific Cat# A20186 NucleoSpin RNA XS kit Takara Bio Cat# 740902.10 NEBNext High Fidelity 2X PCR Master Mix New England Biolabs Cat# M0541S iScript Reverse Transcription Supermix Bio-Rad Laboratories Cat# 1708840 iTaq Universal SYBRGreen Supermix Bio-Rad Laboratories Cat# 1725120 QIAGEN MinElute PCR Purification Kit QIAGEN Cat# 28004 Nextera DNA Library Preparation Kit Illumina Cat# FC-121-1030 Zymo DNA Clean and Concentrator-5 Kit Zymo Research Corporation Cat# D4013 PrimeFlow RNA Assay Kit ThermoFisher Scientific Cat# 88-18005-204 ID2 PrimeFlow Probe Set (A488) ThermoFisher Scientific Cat# PF210; Assay ID: VA4-3086868-PF Deposited Data ATAC-seq data (generated here) NCBI GEO GEO: GSE146896 Human DC scRNA-seq https://singlecell.broadinstitute. org/single_cell/study/atlas-ofhuman-blood-dendritic-cellsand-monocytes Broad Single Cell Portal study ‘‘Atlas of human blood dendritic cells and monocytes’’ Mouse DC RNA-seq NCBI GEO GEO: GSE76132 Other Immune Lineage ATAC-seq NCBI GEO GEO: GSE118189 TCF4 ChIP-seq NCBI GEO GEO: GSE76147 TCF4 silencing microarray NCBI GEO GEO: GSE75650 Zbtb18 silencing microarray NCBI GEO GEO: GSE12993 Klf12 / mouse RNA-seq NCBI GEO GEO: GSE128962 Software and Algorithms GraphPad Prism 6 GraphPad Software, Inc. https://www.graphpad.com/scientific- software/prism/ MATLAB N/A https://www.mathworks.com/products/ matlab.html Cytofkit N/A https://bioconductor.riken.jp/packages/3.7/ bioc/html/cytofkit.html FlowJo Software v10.0.8 TreeStar, Inc https://www.flowjo.com/solutions/flowjo R N/A https://www.R-project.org/ ggplot2 v2.2.1 N/A https://github.com/tidyverse/ggplot2 viridis v0.3.0 N/A https://github.com/sjmgarnier/viridis limma v3.44.3 N/A https://bioconductor.org/packages/ release/bioc/html/limma.html (Continued on next page) Cell Reports 32, 108180, September 22, 2020 e4 Resource ll OPEN ACCESS
SYBR Green Assay:Article Title: Chromatin Landscape Underpinning Human Dendritic Cell Heterogeneity
Article Snippet: .. N/A Chemicals, Peptides, and Recombinant Proteins Ficoll-Paque PLUS GE Healthcare Cat# 300-25 1M Tris-HCl, pH 7.4 VWR Cat# 100216-458 NaCl ThermoFisher Scientific Cat# AM9760G MgCl2 ThermoFisher Scientific Cat# AM9530G Tween-20 Millipore-Sigma Cat# 11332465001 Digitonin VWR Cat# PAG9441 Nonidet P40 Substitute Millipore-Sigma Cat# 11332473001 IGEPAL CA-630 Millipore-Sigma Cat# 18896 Tn5 transposase Produced as described in Picelli et al., 2014 N/A SYBR Green I Nucleic Acid Gel ThermoFisher Scientific Cat# S7563 Dulbecco’s Phosphate Buffered Saline Corning Cat# 21-031-CV Fetal Bovine Serum, qualified, US origin GIBCO Cat# 26140079 RPMI 1640 with L- Glutamine Corning Cat# 10040CV L-glutamine Solution Corning Cat# 25005CI Sodium Pyruvate Solution Corning Cat# 25000CI Penicillin-Streptomycin Corning Cat# 30002CI HEPES solution Corning Cat# 25060CI MEM Nonessential Amino Acid Solution Corning Cat# 25025CI Recombinant Human IL-3 R&D Systems Cat# 203IL010CF EDTA 0.5M pH 8.0 Corning Cat# 46034CI ACK Lysis Buffer Lonza Cat# 10-548E Benzonase Nuclease Millipore-Sigma Cat# E1014-25KU Cell-ID Intercalator-Ir Fluidigm Cat# 201192A Cell-ID Cisplatin Fluidigm Cat# 201064 5(6)-Carboxyfluorescein diacetate N-succinimidyl ester Millipore-Sigma Cat# 21888-25MG-F CellTrace Violet Cell Proliferation Kit ThermoFisher Scientific Cat# C34557 Bovine Serum Albumin solution 30% ± 2% in 0.85% sodium chloride, aseptically filled Millipore-Sigma Cat# A7284-50ML Dimethyl sulfoxide > 95% Millipore-Sigma Cat# D4540 Paraformaldehyde 16% aqueous solution Electron Microscopy Sciences Cat# 15710 Indium 113 metal chloride Trace Sciences International In-113 Indium 115 metal chloride Trace Sciences International In-115 CpG-A ODN 2216 Invivogen Cat# tlrl-2216-1 Imiquimod Invivogen Cat# tlrl-imqs Recombinant Human CD40 Ligand R&D Systems Cat# 6420CL025CF Critical Commercial Assays Foxp3 / Transcription Factor Fixation/ Permeabilization Concentrate and Diluent ThermoFisher Scientific Cat# 00-5521-00 Permeabilization Buffer (10X) ThermoFisher Scientific Cat# 00-8333-56 (Continued on next page) e3 Cell Reports 32, 108180, September 22, 2020 Resource ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Maxpar X8 Multimetal Labeling Kit Fluidigm Fluidigm Cat# 201300 LIVE/DEAD Fixable Dead Cell Stain Sampler Kit ThermoFisher Scientific Cat# L34960 Dynabeads Pan Mouse IgG ThermoFisher Scientific Cat# 11042 Plasmacytoid Dendritic Cell Isolation Kit II, human MACS, Miltenyi Biotec Cat# 130-097-415 Pan T cell Isolation Kit, human MACS, Miltenyi Biotec Cat# 130-096-535 Human IFN Alpha Multi-Subtype ELISA Kit (TCM) PBL Assay Science Cat# 41105-1 BD Cytometric Bead Array Human Enhanced Sensitivity Master Buffer Kit BD Biosciences Cat# 561521 BD Cytometric Bead Array Human IL-6 Enhanced Sensitivity Flex Set BD Biosciences Cat# 561512 BD Cytometric Bead Array Human TNF Enhanced Sensitivity Flex Set BD Biosciences Cat# 561516 BD CompBead Anti-Mouse Ig, k/Negative Control Compensation Particles Set BD Biosciences Cat# 552843 Alexa Fluor 647 Antibody Labeling Kit ThermoFisher Scientific Cat# A20186 NucleoSpin RNA XS kit Takara Bio Cat# 740902.10 NEBNext High Fidelity 2X PCR Master Mix New England Biolabs Cat# M0541S iScript Reverse Transcription Supermix Bio-Rad Laboratories Cat# 1708840 iTaq Universal SYBRGreen Supermix Bio-Rad Laboratories Cat# 1725120 QIAGEN MinElute PCR Purification Kit QIAGEN Cat# 28004 Nextera DNA Library Preparation Kit Illumina Cat# FC-121-1030 Zymo DNA Clean and Concentrator-5 Kit Zymo Research Corporation Cat# D4013 PrimeFlow RNA Assay Kit ThermoFisher Scientific Cat# 88-18005-204 ID2 PrimeFlow Probe Set (A488) ThermoFisher Scientific Cat# PF210; Assay ID: VA4-3086868-PF Deposited Data ATAC-seq data (generated here) NCBI GEO GEO: GSE146896 Human DC scRNA-seq https://singlecell.broadinstitute. org/single_cell/study/atlas-ofhuman-blood-dendritic-cellsand-monocytes Broad Single Cell Portal study ‘‘Atlas of human blood dendritic cells and monocytes’’ Mouse DC RNA-seq NCBI GEO GEO: GSE76132 Other Immune Lineage ATAC-seq NCBI GEO GEO: GSE118189 TCF4 ChIP-seq NCBI GEO GEO: GSE76147 TCF4 silencing microarray NCBI GEO GEO: GSE75650 Zbtb18 silencing microarray NCBI GEO GEO: GSE12993 Klf12 / mouse RNA-seq NCBI GEO GEO: GSE128962 Software and Algorithms GraphPad Prism 6 GraphPad Software, Inc. https://www.graphpad.com/scientific- software/prism/ MATLAB N/A https://www.mathworks.com/products/ matlab.html Cytofkit N/A https://bioconductor.riken.jp/packages/3.7/ bioc/html/cytofkit.html FlowJo Software v10.0.8 TreeStar, Inc https://www.flowjo.com/solutions/flowjo R N/A https://www.R-project.org/ ggplot2 v2.2.1 N/A https://github.com/tidyverse/ggplot2 viridis v0.3.0 N/A https://github.com/sjmgarnier/viridis limma v3.44.3 N/A https://bioconductor.org/packages/ release/bioc/html/limma.html (Continued on next page) Cell Reports 32, 108180, September 22, 2020 e4 Resource ll OPEN ACCESS
Saline:Article Title: Chromatin Landscape Underpinning Human Dendritic Cell Heterogeneity
Article Snippet: .. N/A Chemicals, Peptides, and Recombinant Proteins Ficoll-Paque PLUS GE Healthcare Cat# 300-25 1M Tris-HCl, pH 7.4 VWR Cat# 100216-458 NaCl ThermoFisher Scientific Cat# AM9760G MgCl2 ThermoFisher Scientific Cat# AM9530G Tween-20 Millipore-Sigma Cat# 11332465001 Digitonin VWR Cat# PAG9441 Nonidet P40 Substitute Millipore-Sigma Cat# 11332473001 IGEPAL CA-630 Millipore-Sigma Cat# 18896 Tn5 transposase Produced as described in Picelli et al., 2014 N/A SYBR Green I Nucleic Acid Gel ThermoFisher Scientific Cat# S7563 Dulbecco’s Phosphate Buffered Saline Corning Cat# 21-031-CV Fetal Bovine Serum, qualified, US origin GIBCO Cat# 26140079 RPMI 1640 with L- Glutamine Corning Cat# 10040CV L-glutamine Solution Corning Cat# 25005CI Sodium Pyruvate Solution Corning Cat# 25000CI Penicillin-Streptomycin Corning Cat# 30002CI HEPES solution Corning Cat# 25060CI MEM Nonessential Amino Acid Solution Corning Cat# 25025CI Recombinant Human IL-3 R&D Systems Cat# 203IL010CF EDTA 0.5M pH 8.0 Corning Cat# 46034CI ACK Lysis Buffer Lonza Cat# 10-548E Benzonase Nuclease Millipore-Sigma Cat# E1014-25KU Cell-ID Intercalator-Ir Fluidigm Cat# 201192A Cell-ID Cisplatin Fluidigm Cat# 201064 5(6)-Carboxyfluorescein diacetate N-succinimidyl ester Millipore-Sigma Cat# 21888-25MG-F CellTrace Violet Cell Proliferation Kit ThermoFisher Scientific Cat# C34557 Bovine Serum Albumin solution 30% ± 2% in 0.85% sodium chloride, aseptically filled Millipore-Sigma Cat# A7284-50ML Dimethyl sulfoxide > 95% Millipore-Sigma Cat# D4540 Paraformaldehyde 16% aqueous solution Electron Microscopy Sciences Cat# 15710 Indium 113 metal chloride Trace Sciences International In-113 Indium 115 metal chloride Trace Sciences International In-115 CpG-A ODN 2216 Invivogen Cat# tlrl-2216-1 Imiquimod Invivogen Cat# tlrl-imqs Recombinant Human CD40 Ligand R&D Systems Cat# 6420CL025CF Critical Commercial Assays Foxp3 / Transcription Factor Fixation/ Permeabilization Concentrate and Diluent ThermoFisher Scientific Cat# 00-5521-00 Permeabilization Buffer (10X) ThermoFisher Scientific Cat# 00-8333-56 (Continued on next page) e3 Cell Reports 32, 108180, September 22, 2020 Resource ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Maxpar X8 Multimetal Labeling Kit Fluidigm Fluidigm Cat# 201300 LIVE/DEAD Fixable Dead Cell Stain Sampler Kit ThermoFisher Scientific Cat# L34960 Dynabeads Pan Mouse IgG ThermoFisher Scientific Cat# 11042 Plasmacytoid Dendritic Cell Isolation Kit II, human MACS, Miltenyi Biotec Cat# 130-097-415 Pan T cell Isolation Kit, human MACS, Miltenyi Biotec Cat# 130-096-535 Human IFN Alpha Multi-Subtype ELISA Kit (TCM) PBL Assay Science Cat# 41105-1 BD Cytometric Bead Array Human Enhanced Sensitivity Master Buffer Kit BD Biosciences Cat# 561521 BD Cytometric Bead Array Human IL-6 Enhanced Sensitivity Flex Set BD Biosciences Cat# 561512 BD Cytometric Bead Array Human TNF Enhanced Sensitivity Flex Set BD Biosciences Cat# 561516 BD CompBead Anti-Mouse Ig, k/Negative Control Compensation Particles Set BD Biosciences Cat# 552843 Alexa Fluor 647 Antibody Labeling Kit ThermoFisher Scientific Cat# A20186 NucleoSpin RNA XS kit Takara Bio Cat# 740902.10 NEBNext High Fidelity 2X PCR Master Mix New England Biolabs Cat# M0541S iScript Reverse Transcription Supermix Bio-Rad Laboratories Cat# 1708840 iTaq Universal SYBRGreen Supermix Bio-Rad Laboratories Cat# 1725120 QIAGEN MinElute PCR Purification Kit QIAGEN Cat# 28004 Nextera DNA Library Preparation Kit Illumina Cat# FC-121-1030 Zymo DNA Clean and Concentrator-5 Kit Zymo Research Corporation Cat# D4013 PrimeFlow RNA Assay Kit ThermoFisher Scientific Cat# 88-18005-204 ID2 PrimeFlow Probe Set (A488) ThermoFisher Scientific Cat# PF210; Assay ID: VA4-3086868-PF Deposited Data ATAC-seq data (generated here) NCBI GEO GEO: GSE146896 Human DC scRNA-seq https://singlecell.broadinstitute. org/single_cell/study/atlas-ofhuman-blood-dendritic-cellsand-monocytes Broad Single Cell Portal study ‘‘Atlas of human blood dendritic cells and monocytes’’ Mouse DC RNA-seq NCBI GEO GEO: GSE76132 Other Immune Lineage ATAC-seq NCBI GEO GEO: GSE118189 TCF4 ChIP-seq NCBI GEO GEO: GSE76147 TCF4 silencing microarray NCBI GEO GEO: GSE75650 Zbtb18 silencing microarray NCBI GEO GEO: GSE12993 Klf12 / mouse RNA-seq NCBI GEO GEO: GSE128962 Software and Algorithms GraphPad Prism 6 GraphPad Software, Inc. https://www.graphpad.com/scientific- software/prism/ MATLAB N/A https://www.mathworks.com/products/ matlab.html Cytofkit N/A https://bioconductor.riken.jp/packages/3.7/ bioc/html/cytofkit.html FlowJo Software v10.0.8 TreeStar, Inc https://www.flowjo.com/solutions/flowjo R N/A https://www.R-project.org/ ggplot2 v2.2.1 N/A https://github.com/tidyverse/ggplot2 viridis v0.3.0 N/A https://github.com/sjmgarnier/viridis limma v3.44.3 N/A https://bioconductor.org/packages/ release/bioc/html/limma.html (Continued on next page) Cell Reports 32, 108180, September 22, 2020 e4 Resource ll OPEN ACCESS
Lysis:Article Title: Chromatin Landscape Underpinning Human Dendritic Cell Heterogeneity
Article Snippet: .. N/A Chemicals, Peptides, and Recombinant Proteins Ficoll-Paque PLUS GE Healthcare Cat# 300-25 1M Tris-HCl, pH 7.4 VWR Cat# 100216-458 NaCl ThermoFisher Scientific Cat# AM9760G MgCl2 ThermoFisher Scientific Cat# AM9530G Tween-20 Millipore-Sigma Cat# 11332465001 Digitonin VWR Cat# PAG9441 Nonidet P40 Substitute Millipore-Sigma Cat# 11332473001 IGEPAL CA-630 Millipore-Sigma Cat# 18896 Tn5 transposase Produced as described in Picelli et al., 2014 N/A SYBR Green I Nucleic Acid Gel ThermoFisher Scientific Cat# S7563 Dulbecco’s Phosphate Buffered Saline Corning Cat# 21-031-CV Fetal Bovine Serum, qualified, US origin GIBCO Cat# 26140079 RPMI 1640 with L- Glutamine Corning Cat# 10040CV L-glutamine Solution Corning Cat# 25005CI Sodium Pyruvate Solution Corning Cat# 25000CI Penicillin-Streptomycin Corning Cat# 30002CI HEPES solution Corning Cat# 25060CI MEM Nonessential Amino Acid Solution Corning Cat# 25025CI Recombinant Human IL-3 R&D Systems Cat# 203IL010CF EDTA 0.5M pH 8.0 Corning Cat# 46034CI ACK Lysis Buffer Lonza Cat# 10-548E Benzonase Nuclease Millipore-Sigma Cat# E1014-25KU Cell-ID Intercalator-Ir Fluidigm Cat# 201192A Cell-ID Cisplatin Fluidigm Cat# 201064 5(6)-Carboxyfluorescein diacetate N-succinimidyl ester Millipore-Sigma Cat# 21888-25MG-F CellTrace Violet Cell Proliferation Kit ThermoFisher Scientific Cat# C34557 Bovine Serum Albumin solution 30% ± 2% in 0.85% sodium chloride, aseptically filled Millipore-Sigma Cat# A7284-50ML Dimethyl sulfoxide > 95% Millipore-Sigma Cat# D4540 Paraformaldehyde 16% aqueous solution Electron Microscopy Sciences Cat# 15710 Indium 113 metal chloride Trace Sciences International In-113 Indium 115 metal chloride Trace Sciences International In-115 CpG-A ODN 2216 Invivogen Cat# tlrl-2216-1 Imiquimod Invivogen Cat# tlrl-imqs Recombinant Human CD40 Ligand R&D Systems Cat# 6420CL025CF Critical Commercial Assays Foxp3 / Transcription Factor Fixation/ Permeabilization Concentrate and Diluent ThermoFisher Scientific Cat# 00-5521-00 Permeabilization Buffer (10X) ThermoFisher Scientific Cat# 00-8333-56 (Continued on next page) e3 Cell Reports 32, 108180, September 22, 2020 Resource ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Maxpar X8 Multimetal Labeling Kit Fluidigm Fluidigm Cat# 201300 LIVE/DEAD Fixable Dead Cell Stain Sampler Kit ThermoFisher Scientific Cat# L34960 Dynabeads Pan Mouse IgG ThermoFisher Scientific Cat# 11042 Plasmacytoid Dendritic Cell Isolation Kit II, human MACS, Miltenyi Biotec Cat# 130-097-415 Pan T cell Isolation Kit, human MACS, Miltenyi Biotec Cat# 130-096-535 Human IFN Alpha Multi-Subtype ELISA Kit (TCM) PBL Assay Science Cat# 41105-1 BD Cytometric Bead Array Human Enhanced Sensitivity Master Buffer Kit BD Biosciences Cat# 561521 BD Cytometric Bead Array Human IL-6 Enhanced Sensitivity Flex Set BD Biosciences Cat# 561512 BD Cytometric Bead Array Human TNF Enhanced Sensitivity Flex Set BD Biosciences Cat# 561516 BD CompBead Anti-Mouse Ig, k/Negative Control Compensation Particles Set BD Biosciences Cat# 552843 Alexa Fluor 647 Antibody Labeling Kit ThermoFisher Scientific Cat# A20186 NucleoSpin RNA XS kit Takara Bio Cat# 740902.10 NEBNext High Fidelity 2X PCR Master Mix New England Biolabs Cat# M0541S iScript Reverse Transcription Supermix Bio-Rad Laboratories Cat# 1708840 iTaq Universal SYBRGreen Supermix Bio-Rad Laboratories Cat# 1725120 QIAGEN MinElute PCR Purification Kit QIAGEN Cat# 28004 Nextera DNA Library Preparation Kit Illumina Cat# FC-121-1030 Zymo DNA Clean and Concentrator-5 Kit Zymo Research Corporation Cat# D4013 PrimeFlow RNA Assay Kit ThermoFisher Scientific Cat# 88-18005-204 ID2 PrimeFlow Probe Set (A488) ThermoFisher Scientific Cat# PF210; Assay ID: VA4-3086868-PF Deposited Data ATAC-seq data (generated here) NCBI GEO GEO: GSE146896 Human DC scRNA-seq https://singlecell.broadinstitute. org/single_cell/study/atlas-ofhuman-blood-dendritic-cellsand-monocytes Broad Single Cell Portal study ‘‘Atlas of human blood dendritic cells and monocytes’’ Mouse DC RNA-seq NCBI GEO GEO: GSE76132 Other Immune Lineage ATAC-seq NCBI GEO GEO: GSE118189 TCF4 ChIP-seq NCBI GEO GEO: GSE76147 TCF4 silencing microarray NCBI GEO GEO: GSE75650 Zbtb18 silencing microarray NCBI GEO GEO: GSE12993 Klf12 / mouse RNA-seq NCBI GEO GEO: GSE128962 Software and Algorithms GraphPad Prism 6 GraphPad Software, Inc. https://www.graphpad.com/scientific- software/prism/ MATLAB N/A https://www.mathworks.com/products/ matlab.html Cytofkit N/A https://bioconductor.riken.jp/packages/3.7/ bioc/html/cytofkit.html FlowJo Software v10.0.8 TreeStar, Inc https://www.flowjo.com/solutions/flowjo R N/A https://www.R-project.org/ ggplot2 v2.2.1 N/A https://github.com/tidyverse/ggplot2 viridis v0.3.0 N/A https://github.com/sjmgarnier/viridis limma v3.44.3 N/A https://bioconductor.org/packages/ release/bioc/html/limma.html (Continued on next page) Cell Reports 32, 108180, September 22, 2020 e4 Resource ll OPEN ACCESS
Electron Microscopy:Article Title: Chromatin Landscape Underpinning Human Dendritic Cell Heterogeneity
Article Snippet: .. N/A Chemicals, Peptides, and Recombinant Proteins Ficoll-Paque PLUS GE Healthcare Cat# 300-25 1M Tris-HCl, pH 7.4 VWR Cat# 100216-458 NaCl ThermoFisher Scientific Cat# AM9760G MgCl2 ThermoFisher Scientific Cat# AM9530G Tween-20 Millipore-Sigma Cat# 11332465001 Digitonin VWR Cat# PAG9441 Nonidet P40 Substitute Millipore-Sigma Cat# 11332473001 IGEPAL CA-630 Millipore-Sigma Cat# 18896 Tn5 transposase Produced as described in Picelli et al., 2014 N/A SYBR Green I Nucleic Acid Gel ThermoFisher Scientific Cat# S7563 Dulbecco’s Phosphate Buffered Saline Corning Cat# 21-031-CV Fetal Bovine Serum, qualified, US origin GIBCO Cat# 26140079 RPMI 1640 with L- Glutamine Corning Cat# 10040CV L-glutamine Solution Corning Cat# 25005CI Sodium Pyruvate Solution Corning Cat# 25000CI Penicillin-Streptomycin Corning Cat# 30002CI HEPES solution Corning Cat# 25060CI MEM Nonessential Amino Acid Solution Corning Cat# 25025CI Recombinant Human IL-3 R&D Systems Cat# 203IL010CF EDTA 0.5M pH 8.0 Corning Cat# 46034CI ACK Lysis Buffer Lonza Cat# 10-548E Benzonase Nuclease Millipore-Sigma Cat# E1014-25KU Cell-ID Intercalator-Ir Fluidigm Cat# 201192A Cell-ID Cisplatin Fluidigm Cat# 201064 5(6)-Carboxyfluorescein diacetate N-succinimidyl ester Millipore-Sigma Cat# 21888-25MG-F CellTrace Violet Cell Proliferation Kit ThermoFisher Scientific Cat# C34557 Bovine Serum Albumin solution 30% ± 2% in 0.85% sodium chloride, aseptically filled Millipore-Sigma Cat# A7284-50ML Dimethyl sulfoxide > 95% Millipore-Sigma Cat# D4540 Paraformaldehyde 16% aqueous solution Electron Microscopy Sciences Cat# 15710 Indium 113 metal chloride Trace Sciences International In-113 Indium 115 metal chloride Trace Sciences International In-115 CpG-A ODN 2216 Invivogen Cat# tlrl-2216-1 Imiquimod Invivogen Cat# tlrl-imqs Recombinant Human CD40 Ligand R&D Systems Cat# 6420CL025CF Critical Commercial Assays Foxp3 / Transcription Factor Fixation/ Permeabilization Concentrate and Diluent ThermoFisher Scientific Cat# 00-5521-00 Permeabilization Buffer (10X) ThermoFisher Scientific Cat# 00-8333-56 (Continued on next page) e3 Cell Reports 32, 108180, September 22, 2020 Resource ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Maxpar X8 Multimetal Labeling Kit Fluidigm Fluidigm Cat# 201300 LIVE/DEAD Fixable Dead Cell Stain Sampler Kit ThermoFisher Scientific Cat# L34960 Dynabeads Pan Mouse IgG ThermoFisher Scientific Cat# 11042 Plasmacytoid Dendritic Cell Isolation Kit II, human MACS, Miltenyi Biotec Cat# 130-097-415 Pan T cell Isolation Kit, human MACS, Miltenyi Biotec Cat# 130-096-535 Human IFN Alpha Multi-Subtype ELISA Kit (TCM) PBL Assay Science Cat# 41105-1 BD Cytometric Bead Array Human Enhanced Sensitivity Master Buffer Kit BD Biosciences Cat# 561521 BD Cytometric Bead Array Human IL-6 Enhanced Sensitivity Flex Set BD Biosciences Cat# 561512 BD Cytometric Bead Array Human TNF Enhanced Sensitivity Flex Set BD Biosciences Cat# 561516 BD CompBead Anti-Mouse Ig, k/Negative Control Compensation Particles Set BD Biosciences Cat# 552843 Alexa Fluor 647 Antibody Labeling Kit ThermoFisher Scientific Cat# A20186 NucleoSpin RNA XS kit Takara Bio Cat# 740902.10 NEBNext High Fidelity 2X PCR Master Mix New England Biolabs Cat# M0541S iScript Reverse Transcription Supermix Bio-Rad Laboratories Cat# 1708840 iTaq Universal SYBRGreen Supermix Bio-Rad Laboratories Cat# 1725120 QIAGEN MinElute PCR Purification Kit QIAGEN Cat# 28004 Nextera DNA Library Preparation Kit Illumina Cat# FC-121-1030 Zymo DNA Clean and Concentrator-5 Kit Zymo Research Corporation Cat# D4013 PrimeFlow RNA Assay Kit ThermoFisher Scientific Cat# 88-18005-204 ID2 PrimeFlow Probe Set (A488) ThermoFisher Scientific Cat# PF210; Assay ID: VA4-3086868-PF Deposited Data ATAC-seq data (generated here) NCBI GEO GEO: GSE146896 Human DC scRNA-seq https://singlecell.broadinstitute. org/single_cell/study/atlas-ofhuman-blood-dendritic-cellsand-monocytes Broad Single Cell Portal study ‘‘Atlas of human blood dendritic cells and monocytes’’ Mouse DC RNA-seq NCBI GEO GEO: GSE76132 Other Immune Lineage ATAC-seq NCBI GEO GEO: GSE118189 TCF4 ChIP-seq NCBI GEO GEO: GSE76147 TCF4 silencing microarray NCBI GEO GEO: GSE75650 Zbtb18 silencing microarray NCBI GEO GEO: GSE12993 Klf12 / mouse RNA-seq NCBI GEO GEO: GSE128962 Software and Algorithms GraphPad Prism 6 GraphPad Software, Inc. https://www.graphpad.com/scientific- software/prism/ MATLAB N/A https://www.mathworks.com/products/ matlab.html Cytofkit N/A https://bioconductor.riken.jp/packages/3.7/ bioc/html/cytofkit.html FlowJo Software v10.0.8 TreeStar, Inc https://www.flowjo.com/solutions/flowjo R N/A https://www.R-project.org/ ggplot2 v2.2.1 N/A https://github.com/tidyverse/ggplot2 viridis v0.3.0 N/A https://github.com/sjmgarnier/viridis limma v3.44.3 N/A https://bioconductor.org/packages/ release/bioc/html/limma.html (Continued on next page) Cell Reports 32, 108180, September 22, 2020 e4 Resource ll OPEN ACCESS
Recombinase Polymerase Amplification:Article Title: BCG vaccination induces antibacterial effector functions among Vδ1/3 T cells that are associated with protection against tuberculosis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies 116Cd anti-CD45 (clone D058-1283) BD Biosciences Cat #552566 106Cd anti-CD68 (clone KP1) BioLegend Cat #916104 172Yb anti-CD206 (clone 19.2) BD Biosciences Cat #555953 154Sm anti-CD163 (clone GHI/61) Fluidigm Cat #3154007B 151Eu anti-CD14 (clone M5E2) Fluidigm Cat #3151009B 144ND anti-CD11b (Mac-1) (clone ICRF44) Fluidigm Cat #3144001B 209Bi anti-CD16 (clone 3G8) Fluidigm Cat #3209002B 146ND anti-CD11c (clone 3.9) Fluidigm Cat #3146014B 161Dy anti-CD123 (clone 6H6) BioLegend Cat #306002 176Yb anti-HLA-DR (clone LN3) BioLegend Cat #327002 169Tm anti-NKG2A (clone Z199) Fluidigm Cat #3169013B 147Sm anti-CD20 (clone 2H7) Fluidigm Cat #3147001B 153Eu anti-IgD (Polyclonal) Southern Biotech Cat #2030-01 170Er anti-CD3 (clone SP34-2) Fluidigm Cat #3170007B APC anti-MR1-5-OP-RU Tetramer NIH Tetramer Core N/A 163Dy anti- anti-APC Fluidigm Cat #3163001B 171Yb anti-TCRγδ (clone B1) BioLegend Cat #331202 112Cd anti-TCR Vγ9 (clone B3) BioLegend Cat #331301 160Gd anti-CD161 (clone HP-3G10) BioLegend Cat #339902 111Cd anti-CD8α (clone RPA-T8) BioLegend Cat #301053 113Cd anti-CD8β (clone 2ST8.5H7) Novus Biologicals Cat #NB100-65928 114Cd anti-CD4 (clone L200) BD Biosciences Cat #550625 174Yb anti-CD45RA (clone 5H9) BD Biosciences Cat #556625 175Lu anti-CD28 (clone CD28.2) BioLegend Cat #302902 159Tb anti-CCR7 (clone G043H7) Fluidigm Cat #3159003A 156Gd anti-CXCR3 (clone G025H7) Fluidigm Cat #3156004B 145ND anti-CD69 (clone FN50) BioLegend Cat #310902 173Yb anti-Granzyme B (clone GB11) Fluidigm Cat #3173006B 165Ho anti-Granzyme K (clone GM26E7) BioLegend Cat #370502 164Dy anti-Perforin (clone Pf-80/164) Mabtech Cat #3465-3-250 143ND anti-CD107a (clone H4A3) BioLegend Cat #328601 162Dy anti-CD154 (clone 24–31) BioLegend Cat #310802 152Sm anti-TNF (clone Mab11) Fluidigm Cat #3152002B 168Er anti-IFN-g (clone B27) Fluidigm Cat #3168005B 158Gd anti-IL-2 (clone MQ1-17H12) Fluidigm Cat #3158007B 148ND anti-IL-17A (clone BL168) Fluidigm Cat #3148008B Cell-ID Intercalator Ir Fluidigm Cat #201192A Cell-ID Cisplatin Fluidigm Cat # 201064 FITC anti-TNF (clone Mab11) BD Biosciences Cat #554512 BB700 anti-CD8 (clone RPA-T8) BD Biosciences Cat #566452 PE anti-Granzyme K (clone GM26E7) BioLegend Cat #370512 PE-CF594 anti-Granzyme B (clone GB11) BD Biosciences Cat #562462 (Continued on next page) Cell Reports Medicine 7, 102536, January 20, 2026 e1 OPEN ACCESS ..
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