KEY RESOURCES TABLE
| REAGENT or RESOURCE |
SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-Human CD14, FITC | BD Biosciences | Cat#555397; AB_395798 |
| Anti-Human CD19, FITC | BD Biosciences | Cat#555412; AB_395812 |
| Anti-Human CD3, PE | BD Biosciences | Cat#555339; AB_395745 |
| Anti-Human CD4, BUV395 | BD Biosciences | Cat#563550; AB_2738273 |
| Anti-Human CD8, APC-Vio770 | Miltenyi Biotec | Cat#130-113-155; AB_2725983 |
| Anti-Human CD45RA, BV510 | BD Biosciences | Cat#563031; AB_2722499 |
| Human BD Fc Block | BD Biosciences | Cat#564219; AB_2728082 |
| DAPI solution | BD Biosciences | Cat#564907; AB_2869624 |
| Anti-Human CD11c, FITC | BD Biosciences | Cat#561355; AB_10611872 |
| Anti-Human CD14, FITC | BD Biosciences | Cat#555397; AB_395798 |
| Anti-Human CD36, FITC | BD Biosciences | Cat#555454; AB_2291112 |
| Anti-Human CD33, FITC | BD Biosciences | Cat#555626; AB_395992 |
| Anti-Human CD16, FITC | BD Biosciences | Cat#555406; AB_395806 |
| Anti-Human CD11b, FITC | BD Biosciences | Cat#562793; AB_2737798 |
| Anti-Human CD15, FITC | BD Biosciences | Cat#555401; AB_395801 |
| Anti-Human CD34, FITC | BD Biosciences | Cat#348053; AB_2228982 |
| Anti-Human CD56, FITC | BD Biosciences | Cat#562794; AB_2737799 |
| Anti-Human CD123, FITC | BD Biosciences | Cat#558663; AB_1645485 |
| Anti-Human CD235a, FITC | BD Biosciences | Cat#559943; AB_397386 |
| IgG1 isotype | Biolegend | Cat#400187; AB_2888921 |
| IgG2a isotype | Biolegend | Cat#400293; AB_2888922 |
| IgG2b isotype | Biolegend | Cat#400381; AB_2888923 |
| Anti-Human B2M | Biolegend | Cat#316323; AB_2800837 |
| Anti-Human B7H4 | Biolegend | Cat#358116; AB_2800986 |
| Anti-Human CD10 | Biolegend | Cat#312233; AB_2800817 |
| Anti-Human CD117 | Biolegend | Cat#313243; AB_2810474 |
| Anti-Human CD11a | Biolegend | Cat# 350617; AB_2800935 |
| Anti-Human CD11b | Biolegend | Cat# 301359; AB_2800732 |
| Anti-Human CD11c | Biolegend | Cat# 371521; AB_2801018 |
| Anti-Human CD127 | Biolegend | Cat# 351356; AB_2800937 |
| Anti-Human CD134 | Biolegend | Cat# 350035; AB_2800932 |
| Anti-Human CD137 | Biolegend | Cat# 309839; AB_2800807 |
| Anti-Human CD138 | Biolegend | Cat# 356539; AB_2810567 |
| Anti-Human CD14 | Biolegend | Cat# 301859; AB_2800736 |
| Anti-Human CD15 | Biolegend | Cat# 323053; AB_2800847 |
| Anti-Human CD152 | Biolegend | Cat# 369621; AB_2801015 |
| Anti-Human CD16 | Biolegend | Cat# 302065; AB_2800738 |
| Anti-Human CD163 | Biolegend | Cat# 333637; AB_2810510 |
| Anti-Human CD18 | Biolegend | Cat# 302129; AB_2800739 |
| Anti-Human CD183 | Biolegend | Cat# 353747; AB_2800949 |
| Anti-Human CD184 | Biolegend | Cat# 306533; AB_2800791 |
| Anti-Human CD19 | Biolegend | Cat# 302265; AB_2800741 |
| Anti-Human CD194 | Biolegend | Cat# 359425; AB_2800988 |
| Anti-Human CD197 | Biolegend | Cat# 353251; AB_2800943 |
| Anti-Human CD1c | Biolegend | Cat# 331547; AB_2800871 |
| Anti-Human CD1d | Biolegend | Cat# 350319; AB_2800934 |
| Anti-Human CD20 | Biolegend | Cat# 302363; AB_2800743 |
| Anti-Human CD223 | Biolegend | Cat# 369335; AB_2814327 |
| Anti-Human CD226 | Biolegend | Cat# 338337; AB_2800899 |
| Anti-Human CD244 | Biolegend | Cat# 329529; AB_2800857 |
| Anti-Human CD25 | Biolegend | Cat# 302649; AB_2800745 |
| Anti-Human CD27 | Biolegend | Cat# 302853; AB_2800747 |
| Anti-Human CD274 | Biolegend | Cat# 329751; AB_2800860 |
| Anti-Human CD278 | Biolegend | Cat# 313553; AB_2800823 |
| Anti-Human CD279 | Biolegend | Cat# 329963; AB_2800862 |
| Anti-Human CD28 | Biolegend | Cat# 302963; AB_2800751 |
| Anti-Human CD3 | Biolegend | Cat# 300479; AB_2800723 |
| Anti-Human CD31 | Biolegend | Cat# 303139; AB_2800757 |
| Anti-Human CD314 | Biolegend | Cat# 320837; AB_2800844 |
| Anti-Human CD33 | Biolegend | Cat# 366633; AB_2801008 |
| Anti-Human CD335 | Biolegend | Cat# 331941; AB_2800874 |
| Anti-Human CD34 | Biolegend | Cat# 343537; AB_2749972 |
| Anti-Human CD38 | Biolegend | Cat# 303543; AB_2800758 |
| Anti-Human CD39 | Biolegend | Cat# 328237; AB_2800853 |
| Anti-Human CD4 | Biolegend | Cat# 300567; AB_2800725 |
| Anti-Human CD40 | Biolegend | Cat# 334348; AB_2800886 |
| Anti-Human CD44 | Biolegend | Cat# 338827; AB_2800900 |
| Anti-Human CD45 | Biolegend | Cat# 304068; AB_2800762 |
| Anti-Human CD45RA | Biolegend | Cat# 304163; AB_2800764 |
| Anti-Human CD45RO | Biolegend | Cat# 304259; AB_2800766 |
| Anti-Human CD49f | Biolegend | Cat# 313635; AB_2800825 |
| Anti-Human CD5 | Biolegend | Cat# 300637; AB_2800726 |
| Anti-Human CD56 | Biolegend | Cat# 392425; AB_2801024 |
| Anti-Human CD57 | Biolegend | Cat# 393321; AB_2801030 |
| Anti-Human CD62L | Biolegend | Cat# 304851; AB_2800770 |
| Anti-Human CD69 | Biolegend | Cat# 310951; AB_2800810 |
| Anti-Human CD70 | Biolegend | Cat# 355119; AB_2800955 |
| Anti-Human CD73 | Biolegend | Cat# 344031; AB_2800916 |
| Anti-Human CD80 | Biolegend | Cat# 305243; AB_2800783 |
| Anti-Human CD86 | Biolegend | Cat# 305447; AB_2800786 |
| Anti-Human CD8a | Biolegend | Cat# 301071; AB_2800730 |
| Anti-Human CD95 | Biolegend | Cat# 305651; AB_2800787 |
| Anti-Human HLA-DR | Biolegend | Cat# 307663; AB_2800795 |
| Anti-Human KLRG1 | Biolegend | Cat# 138433; AB_2800649 |
| Anti-Human TCRab | Biolegend | Cat# 306743; AB_2800793 |
| Anti-Human TCRgd | Biolegend | Cat# 331231; AB_2814199 |
| Anti-Human TIGIT | Biolegend | Cat# 372729; AB_2801021 |
| Anti-Human Tim3 | Biolegend | Cat# 345049; AB_2800925 |
| Biological Samples | ||
| Cryopreserved bone marrow mononuclear cells | Dana-Farber Cancer Institute | Pasquarello Tissue Bank in Hematologic Malignancies |
| Cryopreserved donor lymphocyte infusion products | Dana-Farber Cancer Institute | Pasquarello Tissue Bank in Hematologic Malignancies |
| Chemicals, Peptides, and Recombinant Proteins | ||
| DNase I | StemCell Technologies | Cat#07900 |
| Digitonin | Promega | Cat#G9441 |
| AMPure XP beads | Beckman Coulter | A63881 |
| Critical Commercial Assays | ||
| MACS Dead Cell Removal Kit | Miltenyi Biotec | Cat#130-090-101 |
| Pan T Cell Isolation Kit, human | Miltenyi Biotec | Cat#130-096-535 |
| MACS CD19 MicroBeads | Miltenyi Biotec | Cat#130-050-301 |
| 10X Chromium Single Cell 3′ Library & Gel Bead Kit (v2) | 10x Genomics | Cat#PN-120237 |
| Bioanalyzer High Sensitivity DNA Kit | Agilent | Cat#5067-4626 |
| 10x Chromium Single Cell 5’ Library & Gel Bead Kit | 10x Genomics | PN-1000006 |
| 10x Chromium Single Cell V(D)J Enrichment Kit, Human T Cell | 10x Genomics | PN-1000005 |
| 5' Feature Barcode Kit | 10x Genomics | PN-1000256 |
| 10x Chromium Next GEM Single Cell 5' Kit v2 | 10x Genomics | PN-1000263 |
| 10x Chromium Single Cell Human TCR Amplification Kit | 10x Genomics | PN-1000252 |
| Nextera DNA Library Prep Kit | Illumina | FC-121-1030 |
| NEBNext High Fidelity PCR Mix | New England Biolabs | M0541S |
| MinElute Reaction Cleanup kit | Qiagen | 28206 |
| Deposited Data | ||
| 10x scRNA-seq | dbGaP | phs001998.v3 |
| 10x scTCR-seq | dbGaP | phs001998.v3 |
| 10x CITE-seq | dbGaP | phs001998.v3 |
| ATAC-seq | dbGaP | phs001998.v3 |
| Symphony | This paper | DOI: https://zenodo.org/record/5498358 |
| Gaussian process regression models | This paper | DOI: doi.org/10.5281/zenodo.5498361 |
| Oligonucleotides | ||
| Primers for rhTCR-seq | Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute | (Li et al., 2019) |
| Software and Algorithms | ||
| Symphony | This paper | DOI: https://zenodo.org/record/5498358 |
| Gaussian process regression models | This paper | DOI: doi.org/10.5281/zenodo.5498361 |
| SEQC | (Azizi et al., 2018) | https://github.com/dpeerlab/seqc |
| Cell Ranger 5.0.1 | 10x Genomics | https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest |
| Cell Ranger V(D)J 2.1.0 | 10x Genomics | https://support.10xgenomics.com/single-cell-vdj/software/downloads/latest? |
| scanpy 1.8.0 | (Wolf et al., 2018) | https://github.com/theislab/Scanpy |
| t-SNE | (Maaten and Hinton, 2008) | https://lvdmaaten.github.io/software/ |
| Biscuit | (Azizi et al., 2018) | https://github.com/dpeerlab/BISCUIT_SingleCell_IMM_ICML_2016 |
| PhenoGraph | (Levine et al., 2015) | https://github.com/dpeerlab/phenograph |
| Pyro | (Bingham et al., 2019) | https://pyro.ai/ |
| ATAC-seq pipeline | ENCODE consortium | https://doi.org/10.5281/zenodo.156534; https://github.com/ENCODE-DCC/atac-seq-pipeline |
| MACS2 2.2.7.1 | (Zhang et al., 2008) | https://pypi.org/project/MACS2/ |