Key Resources Table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Fixable viability dye eFluor450 | eBioscience | Catalog number: 65-0863-14 |
| Fixable viability dye eFluor780 | eBioscience | Catalog number: 65-0865-14 |
| Monoclonal mouse anti-human CD45, clone 2D1, PE conjugated | Biolegend | Catalog number: 368510, RRID: AB_2566370 |
| Monoclonal rat anti-human CD4, clone RPA-T4, BV785 conjugated | Biolegend | Catalog number: 100552, RRID: AB_2563053 |
| Monoclonal mouse anti-human CD8, clone RPA-T8, BV650 conjugated | Biolegend | Catalog number: 301042, RRID: AB_2563505 |
| Monoclonal ratanti-human FOXP3, clonePCH101, eFluor450 conjugated | eBioscience | Catalog number: 48-4776-42, RRID: AB_1834364 |
| Monoclonal mouse anti-human CD25, clone BC96, BV711 conjugated | Biolegend | Catalog number: 302636, RRID: AB_2562910 |
| Monoclonal mouse anti-human CD56, clone HCD56, Alexa700 conjugated | Biolegend | Catalog number: 318316, RRID: AB_604104 |
| Monoclonal mouse anti-human CD19, clone HIB19, PE-Cy7 conjugated | Biolegend | Catalog number: 302216, RRID: AB_314246 |
| Monoclonal mouse anti-human CD20, clone 2H7, PerCP-Cy5.5 conjugated | eBioscience | Catalog number: 45-0209-42, RRID: AB_10717086 |
| Monoclonal mouse anti-human HLA-DR, clone L243, FITC conjugated | eBioscience | Catalog number: 11-9952-41, RRID: AB_2572542 |
| Monoclonal mouse anti-human CD123, clone 6H6, BV650 conjugated | Biolegend | Catalog number: 306020, RRID: AB_2563827 |
| Monoclonal mouse anti-human CD14, clone 63D3, Alexa700 conjugated | Biolegend | Catalog number: 367114, RRID: AB_2566716 |
| Monoclonal mouse anti-human CD11C, clone 3.9, PE-Dazzle conjugated | Biolegend | Catalog number: 301642, RRID: AB_2564083 |
| Monoclonal mouse anti-human CD15, clone W63D, BV711 conjugated | BD Bioscience | Catalog number: 563142 |
| Monoclonal mouse anti-human CD66b, clone G10F5, APC conjugated | Biolegend | Catalog number: 305118, RRID: AB_2566607 |
| Monoclonal mouse anti-human CD8, clone ACI3160A | Biocare Medical | Catalog number: ACI3160A |
| Monoclonal mouse anti-human CD20, clone L26 | Leica Biosystems | Catalog number: CD20-L26-L-CE, RRID: AB_10983209 |
| Monoclonal rabbit anti-human CD68, clone D4B9C | Cell Signaling | Catalog number: 76437S |
| Monoclonal rabbit anti-human FOXP3, clone D608R | Cell Signaling | Catalog number: 12653S |
| Monoclonal rabbit anti-human CD4, clone RM | Biocare Medical | Catalog number: API3209 AA |
| Monoclonal mouse anti-human Pan-Cytokeratin, clone AE1/AE3 | Santa Cruz | Catalog number: AE1/AE3 |
| Biological Samples | ||
| See Table S1 for a list of study subjects. | ||
| Chemicals, Peptides, and Recombinant Proteins | ||
| Foxp3 / Transcription Factor Staining Buffer Set | eBioscience | Catalog number: 00-5523-00 |
| Critical Commercial Assays | ||
| Chromium Single Cell 3' Library & Gel Bead Kit v2, 16 rxns | 10X Genomics | Catalog number: 120237 |
| Perkin Elmer 7 color manual kit | Perkin Elmer | Catalog number: NEL811001KT |
| Illumina NextSeq 500/550 High Output Kit v2 (150 cycles) | Illumina | Catalog number: TG-160–2004 |
| Deposited Data | ||
| Raw sequencing data are available through the NCBI Sequence Read Archive (BioProject ID 579178) and processed gene barcode matrices will be accessible via the Gene Expression Omnibus (GSE139324). | ||
| Software and Algorithms | ||
| CellRanger (version 2.1.0) | 10X Genomics | https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger |
| FlowJo version 10 | TreeStar | https://www.flowjo.com/ |
| R version 3.5.1 (“Feather Spray”) | The R Foundation for Statistical Computing | https://www.r-project.org/ |
| Seurat | Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija | Citation: Butler et al (Butler et al., 2018) Hosted on: https://satijalab.org/seurat/ |
| caret | Kuhn, M. Wing, J. Weston, S. Williams, A. Keefer, C. Engelhardt, A. Cooper, T. Mayer, Z. Kenkel, B. R Core Team. Benesty, M. Lescarbeau, R. Ziem, A. Scrucca, L. Tang, Y. Candan, C. Hunt, T. |
Citation: Kuhn et al (Kuhn et al, 2019) |
| Destiny | Philipp Angerer, Laleh Haghverdi, Maren Büttner, Fabian Theis, Carsten Marr, Florian Büttner | Citation: Angerer et al (Angerer et al., 2016) and Haghverdi et al (Haghverdi et al., 2016) Hosted on: https://bioconductor.org/ |
| DeteRministic Annealing Gaussian mixture mOdel clusteriNg algorithm (DRAGON) | Anthony Cillo, Vignali Lab | Hosted on: http://www.github.com/arc85/dragonsc |
| CellTalker | Anthony Cillo, Vignali Lab | Hosted on: http://www.github.com/arc85/celltalker |
| SingleSeqGset | Anthony Cillo, Vignali Lab | Hosted on: http://www.github.com/arc85/singleseqgset |
| Phenochart version 1.0.9 | Perkin Elmer | www.perkinelmer.com |
| inForm version 2.3 | Perkin Elmer | www.perkinelmer.com |
| Fiji 64-bit | ImageJ |
http://imagej.net/Fiji Citation: Schindelin et al (Schindelin et al., 2012); RRID: SCR_003070 |