KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| For a list of antibodies used for analysis by mass cytometry (CyTOF), multiplexed ion beam imaging (MIBI), and CITE-seq, please see Supplemental Table S5. | Various | Various |
| Human TruStain FcX (Fc Receptor Blocking Solution) |
Biolegend | Cat#422301 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Collagenase IV | Worthington | Cat#LS004188 |
| Deoxyribonuclease I | Sigma-Aldrich | Cat#DN25 |
| cis- Diammineplatinum(II) dichloride (Cisplatin) |
Sigma-Aldrich | Cat#P4394 |
| Paraformaldehyde aqueous solution | Electron Microscopy Sciences |
Cat#15710 |
| Zombie Aqua Fixable Viability Dye |
Thermo Fisher | Cat#L34966 |
| Candor PBS Antibody Stabilization solution |
Candor Bioscience |
Cat#13150 |
| Maxpar 10X Barcode Perm Buffer | Fluidigm | Cat#201057 |
| Cell-ID Intercalator-IR | Fluidigm | Cat#201192A |
| Maxpar Cell Acquisition Solution |
Fluidigm | Cat#201240 |
| Target Retrieval Solution | Dako Agilent | Cat#S1699 |
| PBS IHC Wash Buffer + Tween 20 |
Cell Marque | Cat#934B-06 |
| EQ Four Element Calibration Beads | Fluidigm | Cat#201078 |
| ACK Lysing Buffer | Thermo Fisher | Cat#A1049201 |
| Cell Staining Buffer | Biolegend | Cat#420201 |
| Normal Donkey Serum | Sigma-Aldrich | Cat#566460 |
| Critical Commercial Assays | ||
| Chromium Next GEM Single Cell 5’ Library |
10X Genomics | Cat#PN-1000265 |
| Kit | ||
| Chromium Single Cell V(D)J Enrichment kit |
10X Genomics | Cat#PN-1000005 |
| 5’ Feature Barcode Kit |
10X Genomics | Cat#PN-1000256 |
| MaxPar X8 Antibody Labeling Kits | Fluidigm | Various |
| Metal-Loaded MIBItags | IonPath | Various |
| Avidin/Biotin Blocking System |
Biolegend | Cat#927301 |
| Deposited Data | ||
| Single-cell genomics data | Generated by current investigators | Deposited into GEO under accession number GSE212797 |
| Mass cytometry and multiplexed ion beam imaging data | Generated by current investigators | Deposited into Mendeley Data under doi:10.17632/2zgppyr2rr.1 |
| Software and Algorithms | ||
| R Core Team (v.4.0.5) |
The R Project for Statistical
Computing |
https://www.r-project.org/ |
| RStudio | Posit | https://posit.co/ |
| Python (v.3.88) | Python Software Foundation. Python Language Reference, version 3.8. |
http://www.python.org |
| ParkerICI/Premessa | Parker Institute for Cancer
Immunotherapy |
https://github.com/ParkerICI/premessa |
| CellEngine | CellCarta | https://cellcarta.com/cellenginesoftware/ |
| CytoNorm | Van Gassen et al., 2020 | https://github.com/saeyslab/CytoNorm |
| Flowcore | Ellis et al., 2022 | https://bioconductor.org/packages/release/bioc/html/flowCore.html |
| CATALYST | Nowicka et al., 2017; Chevrier et al., 2018 | https://github.com/HelenaLC/CATALYST |
| FlowSOM | Van Gassen et al, 2015 | https://github.com/SofieVG/FlowSOM |
| diffcyt | Weber et al., 2019 | https://github.com/lmweber/diffcyt |
| Mesmer | Greenwald et al., 2021 | https://github.com/vanvalenlab/kiosk-console |
| scanpy (v.1.7.1) | Wolf et al., 2018 | https://github.com/scverse/scanpy |
| Harmony (v.0.05) | Korsunsky et al., 2019 | https://github.com/immunogenomics/harmony |
| sklearn (v.0.24.1) | Pedregosa et al., 2011 | https://github.com/scikit-learn/scikit-learn |
| corrplot | Simko, 2021 | https://github.com/taiyun/corrplot |
| scipy (v.1.6.1) | Virtanen et al., 2020 | https://github.com/scipy/scipy |
| pandas (v.1.2.3) |
McKinney,
2010; Pandas Development Team |
https://github.com/pandas-dev/pandas |
| numpy (v.3.3.4) | Harris et al., 2020 | https://github.com/numpy/numpy |
| matplotlib (v.3.3.4) | Hunter, 2007 | https://github.com/matplotlib/matplotlib |
| statsmodels (v.0.12.2) | Seabold and Perktold, 2010 | https://github.com/statsmodels/statsmodels |
| dplyr | Wickham et al., 2021 | https://github.com/tidyverse/dplyr |
| reshape2 | Wickham, 2007 | https://github.com/cran/reshape2 |
| ggplot2 | Wickham, 2009 | https://github.com/tidyverse/ggplot2 |
| RColorBrewer | Neuwirth, 2014 | https://cran.r-hub.io/web/packages/RColorBrewer/index.html |
| Other | ||
| gentleMacs C Tubes | Miltenyi Biotec | Cat#130–093-237 |
| Gold-Coated Slides | IonPath | 567001 |