KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Human monoclonal CD16 PE-Alexa Fluor 700 | Invitrogen | Cat # MHCD1624; RRID AB_10373538 |
| Human monoclonal CD14 Spark NIR 685 | Biolegend | Cat # 367149; RRID AB_2820022 |
| Human monoclonal CD3 PerCP | Biolegend | Cat # 344813; RRID AB_10641841 |
| Human monoclonal CD56 PerCP-eFlour 710 | Invitrogen | Cat # 46–0567-42 |
| Human monoclonal CD45RA BUV496 | Invitrogen | Cat # 364–0458-42 |
| Human monoclonal CD38 BUV737 | BD Biosciences | Cat # 612825 |
| Human monoclonal HLA-DR V500 | BD Biosciences | Cat # 561224 |
| Human monoclonal CD34 PE | Biolegend | Cat # 343605; RRID AB_1732033 |
| Human monoclonal CD45 BV650 | Biolegend | Cat # 304043; RRID AB_2562498 |
| Human monoclonal CD33 PE-Vio 770 | miltenyibiotec | Cat # 130–113-350 |
| Human monoclonal CD4 BUV615 | BD Biosciences | Cat # 612988 |
| Human monoclonal CD20 BV605 | Biolegend | Cat # 302333; RRID AB_11125763 |
| Human monoclonal CD90 APC | Biolegend | Cat # 328113; RRID AB_893440 |
| Human monoclonal CD10 FITC | Biolegend | Cat # 312207; RRID AB_314918 |
| Human monoclonal CD110 BV421 | BD Biosciences | Cat # 562672 |
| Human monoclonal CD8 BV711 | BD Biosciences | Cat # 563677 |
| Chemicals, peptides, and recombinant proteins | ||
| RPMI 1640 | Fisher | Cat # 11875093 |
| fetal bovine serum | Corning | Cat # 35–015-CF |
| 200 mM L-glutamine | Fisher | Cat # 25030081 |
| HEPES | Thermo Fisher Scientific | Cat # 15630080 |
| non-essential amino acids | Thermo Fisher Scientific | Cat # 11140050 |
| essential amino acids | Thermo Fisher Scientific | Cat # 11130051 |
| PBS | Thermo Fisher Scientific | Cat # 10–010-049 |
| 100mM sodium pyruvate | Thermo Fisher Scientific | Cat # 11360070 |
| 10000U/ml penicillin-streptomycin | Thermo Fisher Scientific | Cat # 15140122 |
| 100 μm filter | Thermo Fisher Scientific | Cat # 08–771-19 |
| BSA | Miltenyi Biotec | Cat # 130–091-376 |
| LIVE/DEAD™ Fixable Blue Dead Cell Stain Kit, for UV excitation | Invitrogen | Cat # L34961 |
| F/C block solution | BD Biosciences | Cat # 564220 |
| 70 um Flowmi cell strainer | Fisher | Cat # 14–100-150 |
| Chromium Next GEM Single Cell 3' Kit v3.1, 16 rxns | 10X genomics | Cat # 1000268 |
| Chromium Next GEM Chip G Single Cell Kit, 16 rxns | 10X genomics | Cat # 1000127 |
| Dual Index Kit TT Set A 96 rxns | 10X genomics | Cat # 1000215 |
| Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit, 16 rxns | 10X genomics | Cat # 1000175 |
| Chromium Next GEM Chip H Single Cell Kit, 16 rxns | 10X genomics | Cat # 1000162 |
| Single Index Kit N, Set A, 96 rxns | 10X genomics | Cat # 1000212 |
| miRNeasy Micro kit | Qiagen | Cat # 217084 |
| Illumina TruSeq | Illumina | Cat # 20020595 |
| DynaBeads MyOne SILANE beads | Thermo Fisher Scientific | Cat # 37002D |
| SPRIselect reagent kit | Beckman Coulter | Cat # B23318 |
| KAPA Library Quantification Kit for Illumina Platforms | Roche | Cat # 7960140001 |
| Deposited Data | ||
| Raw and analyzed data | This paper | GEO: GSE248730 |
| Software and algorithms | ||
| cellranger (v6.0.2) | Zheng et al., 201737 | https://www.10xgenomics.com/support/software/cell-ranger/latest |
| Demuxlet | Kang et al., 201738 | https://github.com/statgen/demuxlet |
| Seurat (v3.2.3) | Stuart, Butler et al., 201939 | https://satijalab.org/seurat/ |
| cellranger-atac (v2.0.0) | Satpathy, Ansuman T. et al, 201940 | https://www.10xgenomics.com/support/software/cell-ranger/latest |
| ArchR (v1.0.1, ArchRGenome: hg38) | Granja et al., 202141 | https://github.com/GreenleafLab/ArchR |
| CellID | Cortal et al., 202142 | https://www.bioconductor.org/packages/release/bioc/html/CelliD.html |
| edgeR R package (version 3.34.1) | Robinson et al, 201043 | https://bioconductor.org/packages/release/bioc/html/edgeR.html |
| LIMMA | Ritchie et al., 201544 | https://bioconductor.org/packages/release/bioc/html/limma.html |
| Multivariate Adaptive Shrinkage in R (mashr version 0.2.57) | Urbut et al., 201915 | https://github.com/stephenslab/mashr |
| velocyto | La Manno et al., 201845 | https://github.com/velocyto-team/velocyto.py |
| CellRank | Lange et al., 202222 | https://github.com/theislab/cellrank |
| HINT-ATAC from the Regulatory Genomics Toolbox | Li et al., 202346 | https://github.com/CostaLab/reg-gen |
| samtools (v1.9) | Danecek et al., 202347 | https://www.htslib.org/ |
| Homer | Heinz et al., 201048 | http://homer.ucsd.edu/homer/ |
| pySCENIC | Van de Sande et al., 202030 | https://github.com/aertslab/pySCENIC |
| fgsea R package (version 1.18.0) | Korotkevich et al., 202149 | https://github.com/ctlab/fgsea |
| glmnet R package | Friedman et al., 201050 | https://glmnet.stanford.edu/ |
| Code for all analyses | This paper | DOI: 10.5281/zenodo.12680367; https://doi.org/10.5281/zenodo.12680367 |