KEY RESOURCE TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse anti-human CD45, clone HI30 | BioLegend | Cat# 304002, RRID:AB_314390 |
| Mouse anti-human HLA-DR, clone L243 | BioLegend | Cat# 307602, RRID:AB_314680 |
| Mouse anti-human CD41, clone HIP8 | BioLegend | Cat# 303702, RRID:AB_314372 |
| Mouse anti-human CD235a, clone HIR2 | BioLegend | Cat# 306602, RRID:AB_314620 |
| Mouse anti-human CD1c, clone L161 | BioLegend | Cat# 331502, RRID:AB_1088996 |
| Mouse anti-human CD19, clone HIB19 | Standard BioTools | Cat # 3142001B, RRID:AB_2651155 |
| Mouse anti-human CD123, clone 6H6 | Standard BioTools | Cat # 314014B, RRID:AB_2811081 |
| Mouse anti-human CD69, clone F50 | Standard BioTools | Cat# 3144018B, RRID:AB_2687849 |
| Mouse anti-human CD3, clone OKT3 | BioLegend | Cat# 317302, RRID:AB_571927 |
| Mouse anti-human CD11c, clone 3.9 | Standard BioTools | Cat# 3146014B |
| Mouse anti-human CD182/CXCR2, clone 5E8 | Standard BioTools | Cat# 3147010B |
| Mouse anti-human CD274/PDL1, clone 29E.2A3 | Standard BioTools | Cat# 3148017B |
| Mouse anti-human CD45RA, clone HI100 | BioLegend | Cat# 304143, RRID:AB_2562822 |
| Mouse anti-human CD206, clone 15-2 | BioLegend | Cat# 321102, RRID:AB_571923 |
| Mouse anti-human CD103, clone Ber-ACT8 | BioLegend | Cat# 3151011B, RRID:AB_2756418 |
| Mouse anti-human CD66b, clone 80H3 | Standard BioTools | Cat# 3152011B, RRID:AB_2661795 |
| Mouse anti-human CD192/CCR2, clone K036C2 | Standard BioTools | Cat# 3153023B |
| Mouse anti-human CD142, clone Ny2 | BioLegend | Cat# 365202, RRID:AB_2564564 |
| Mouse anti-human CD36, clone 5-271 | Standard BioTools | Cat# 3155012B, RRID:AB_2756286 |
| Mouse anti-human CXCR3, clone G025H7 | Standard BioTools | Cat# 3156004B, RRID:AB_2687646 |
| Mouse anti-human CD33, clone WM53 | Standard BioTools | Cat# 3158001B, RRID:AB_2661799 |
| Mouse anti-human CD357, clone 621 | Standard BioTools | Cat# 3159020B, RRID:AB_2858232 |
| Mouse anti-human CD14, clone M5E2 | Standard BioTools | Cat# 3160001B, RRID:AB_2687634 |
| Mouse Ultra-LEAF anti-human CD253 (Trail), clone RIK-2 | BioLegend | Cat# 308213, RRID:AB_2814154 |
| Mouse anti-human CD273 (PD-L2), clone MIH18 | BioLegend | Cat# 345502, RRID:AB_1953319 |
| Mouse anti-human CD33, clone WM53 | Standard BioTools | Cat# 3163023B, RRID:AB_2687857 |
| Mouse anti-human CD15/SSEA-1, clone W6D3 | Standard BioTools | Cat# 3164001B, RRID:AB_2810970 |
| Mouse anti-human CD16, clone 3G8 | Standard BioTools | Cat# 3165001B, RRID:AB_2802109 |
| Mouse anti-human CD279 (PD-1), clone EH12.2H7 | BioLegend | Cat# 329902, RRID:AB_940488 |
| Mouse anti-human CD197/CCR7, clone G043H7 | Standard BioTools | Cat# 3167009A, RRID:AB_2858236 |
| Mouse anti-human Lymphotoxin beta Receptor, clone 31G4D8 | BioLegend | Cat# 322002, RRID:AB_2139071 |
| Mouse anti-human Slan (M-DC8), clone DD-1 | Miltenyi Biotec | Cat# 130-099-128, RRID:AB_2660075 |
| Mouse anti-human CD152/CTLA4, clone 14D3 | Standard BioTools | Cat# 3170005B, RRID:AB_2858238 |
| Mouse anti-human CD9, clone SN4 C3-3A2 | Standard BioTools | Cat# 3171009B, RRID:AB_2877094 |
| Mouse anti-human Ki67, clone B56 | Standard BioTools | Cat# 3172024B, RRID:AB_2858243 |
| Mouse anti-human CD141 (Thrombomodulin), clone M80 | BioLegend | Cat# 344102, RRID:AB_2201808 |
| Mouse anti-human CD169 (Siglec-1), clone 7-239 | BioLegend | Cat# 346002, RRID:AB_2189031 |
| Mouse anti-human CD10, clone HI10a | BioLegend | Cat# 312202, RRID:AB_314913 |
| Mouse anti-human CD56, clone NCAM16.2 | Standard BioTools | Cat# 3176008B, RRID:AB_2938870 |
| Mouse anti-human CD11b/Mac-1, clone ICRF44 | Standard BioTools | Cat# 3209003B, RRID:AB_2687654 |
| Mouse anti-human CD45, clone HI30 | BioLegend | Cat# 304028, RRID:AB_893338 |
| Mouse anti-human CD3, clone UCHT1 | BioLegend | Cat# 300472, RRID:AB_2687178 |
| Mouse anti-human CD4, clone SK3 | BioLegend | Cat# 980812, RRID:AB_2820224 |
| Mouse anti-human CD8, clone SK1 | BioLegend | Cat# 980902, RRID:AB_2616623 |
| Mouse anti-human CD95, clone DX2 | BioLegend | Cat# 305624, RRID:AB_2561830 |
| Mouse anti-human CD45RA, clone HI100 | StemCell | Cat# 100-0317 |
| Mouse anti-human CD197 (CCR7), clone 150503 | BD Biosciences | Cat# 561271, RRID:AB_1056167 |
| Mouse anti-human CD62L (L-selectin), clone DREG-56 | BD Biosciences | Cat# 562720, RRID:AB_2744441 |
| Mouse anti-human CD25, clone M-A251 | BioLegend | Cat# 356138, RRID:AB_2632781 |
| Rat anti-mouse/human CD11b, clone M1/70 | BioLegend | Cat# 101243, RRID:AB_2561373 |
| Mouse anti-human CD33, clone P67.6 | BioLegend | Cat# 366612 RRID:AB_2566405 |
| Mouse anti-human CD14, clone 63D3 | BioLegend | Cat# 367140 RRID:AB_2814323 |
| Mouse anti-human CD15 (SSEA-1), clone W6D3 | BioLegend | Cat# 323008 RRID:AB_756014 |
| Mouse anti-human CD16, clone B73.1 | BioLegend | Cat# 360710 RRID:AB_2562952 |
| Mouse anti-human HLA-DR, clone L243 | BioLegend | Cat# 307636 RRID:AB_2561831 |
| Mouse anti-human CD183 (CXCR3), clone G025H7 | BioLegend | Cat# 353706 RRID:AB_10962912 |
| Mouse anti-human CD3, clone UCHT1 | BioLegend | Cat# 300468 RRID:AB_2629574 |
| Mouse anti-human Slan (M-DC8), clone DD-1 | Miltenyi Biotec | Cat# 130-117-371, RRID:AB_2733608 |
| Mouse anti-human Lineage Cocktail (CD3, CD20, CD19, CD56), clones UCHT1, HIB19, 2H7, 5.1H11 | BioLegend | Cat# 363601, RRID:AB_2916117 |
| Mouse anti-human CD66b, clone 6/40c | BioLegend | Cat# 392904, RRID:AB_2750201 |
| Mouse anti-human CD45, clone HI30 | Standard BioTools | Cat# 3089003B, RRID:AB_2938863 |
| Mouse anti-human CD3, clone UCHT1 | BioLegend | Cat# 300402, RRID:AB_314056 |
| Mouse anti-human CD27, clone O323 | BioLegend | Cat# 302839, RRID:AB_2562817 |
| Mouse anti-human CD57, clone HCD57 | BioLegend | Cat# 322325, RRID:AB_2563757 |
| Mouse anti-human CD11b/Mac-1, clone ICRF44 | Standard BioTools | Cat# 3144001B, RRID:AB_2714152 |
| Mouse anti-human CD4, clone RPA-T4 | Standard BioTools | Cat# 3145001B, RRID:AB_2661789 |
| Mouse anti-human CD8, clone RPA-T8 | Standard BioTools | Cat# 3146001B, RRID:AB_2687641 |
| Mouse anti-human CD28, clone CD28.2 | BioLegend | Cat# 302937, RRID:AB_2563737 |
| Mouse anti-human CD274/PD-L1, clone 29E.2A3 | Standard BioTools | Cat# 3175017B, RRID:AB_2687638 |
| Mouse anti-human CD45RO, clone UCHL1 | Standard BioTools | Cat# 3149001B, RRID:AB_2687851 |
| Mouse anti-human CD134/OX40, clone ACT35 | Standard BioTools | Cat# 3150023B, RRID:AB_2938869 |
| Mouse anti-human CD244/2B4, clone C1.7 | BioLegend | Cat# 329502, RRID:AB_1279194 |
| Mouse anti-human CD38, clone HIT2 | BioLegend | Cat# 303535, RRID:AB_2562819 |
| Mouse anti-human TIGIT, clone MBSA43 | Standard BioTools | Cat# 3153019B, RRID:AB_2756419 |
| Mouse anti-human PARP, clone QA17A17 | BioLegend | Cat# 669902, RRID:AB_2814517 |
| Mouse anti-human CD183/CXCR3, clone G025H7 | Standard BioTools | Cat# 3156004B, RRID:AB_2687646 |
| Mouse anti-human CD137 (4-1BB), clone 4B4-1 | Standard BioTools | Cat# 3158013B, RRID:AB_2888927 |
| Mouse anti-human CD20, clone 2H7 | BioLegend | Cat# 302302, RRID:AB_314250) |
| Mouse anti-human Tbet, clone 4B10 | Standard BioTools | Cat# 3160010B, RRID:AB_2810251 |
| Mouse anti-human CD152/CTLA-4, clone 14D3 | Standard BioTools | Cat# 3161004B, RRID:AB_2687649 |
| Mouse anti-human CD25, clone M-A251 | Biolegend | Cat# 356102, RRID:AB_2561751 |
| Mouse anti-human CD272/BTLA, clone MIH26 | Standard BioTools | Cat# 3163009B, RRID:AB_2910546 |
| Mouse anti-human CD39, clone A1 | BioLegend | Cat# 328221, RRID:AB_2563747 |
| Mouse anti-human CD223/LAG-3, clone 874501 | Standard BioTools | Cat# 3165028B, RRID:AB_2687859 |
| Mouse anti-human CD160, clone BY55 | BioLegend | Cat# 341202, RRID:AB_2074411 |
| Mouse anti-human CD197/CCR7, clone G043H7 | Standard BioTools | Cat# 3167009A, RRID:AB_2858236 |
| Mouse anti-human CD127/IL-7Ra, clone A019D5 | Standard BioTools | Cat# 3168017B, RRID:AB_2756425 |
| Mouse anti-human CD366/Tim-3, clone F38-2E2 | Standard BioTools | Cat# 3169028B, RRID:AB_2905650 |
| Mouse anti-human CD45RA, clone HI100 | Standard BioTools | Cat# 3170010B, RRID:AB_2938862 |
| Mouse anti-human Ki-67, clone Ki-67 | BioLegend | Cat# 350502, RRID:AB_1066238 |
| Mouse anti-human C122/IL-2Rbeta, clone TU27 | BioLegend | Cat# 339015, RRID:AB_2563712 |
| Mouse anti-human CD95/Fas, clone DX29 | BioLegend | Cat# 305631, RRID:AB_2563766 |
| Hamster anti-human Helios, clone 22F6 | BioLegend | Cat# 137202, RRID:AB_1090063 |
| Mouse anti-human Eomes, clone WD1928 | Thermo Fisher Scientific | Cat# 14-4877-82, RRID:AB_2572882 |
| Mouse anti-human 279/PD-1, clone EH12.2H7 | Standard BioTools | Cat# 3174020B, RRID:AB_2868402 |
| Mouse anti-human CD16, clone 3G8 | Standard BioTools | Cat# 3209002B, RRID:AB_2756431 |
| Bacterial and virus strains | ||
| Biological samples | ||
| Patient apheresis, peripheral blood and GD2-CAR product samples from phase I trial | This paper | NCT02107963 |
| Chemicals, peptides, and recombinant proteins | ||
| Critical commercial assays | ||
| Human Luminex XL Cytokine 45-Plex | RND Systems | LKTM014 |
| Human IFN-gamma DuoSet ELISA | RND Systems | DY285B |
| Deposited data | ||
| Bulk RNA-seq | This paper | dbGaP: phs003455.v1.p1 |
| Bulk ATAC-seq | This paper | dbGaP: phs003455.v1.p1 |
| Experimental models: Cell lines | ||
| Human: THP-1 cells | ATCC | TIB-202 |
| Human: 143B cells | ATCC | CRL-8303 |
| Experimental models: Organisms/strains | ||
| Oligonucleotides | ||
| Recombinant DNA | ||
| iC9-2A-14G2A.CD28.OX40Z vector | Heczey et al.11 | N/A |
| CXCR3-A Custom Vector | Twist Biosciences | NCBI Reference Sequence: NM_001504.2 |
| Software and algorithms | ||
| ChrAccR | Fabian Mueller, https://doi.org/10.5281/zenodo.6091218 | https://github.com/GreenleafLab/ChrAccR, https://zenodo.org/record/6091218 |
| DESeq2 | Love et al., 2014 http://refhub.elsevier.com/S2667-2375(22)00043-1/sref35 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| SAMtools | SAMtools | http://samtools.sourceforge.net/ |
| Macs2 | Zhang, et al., 2008 http://refhub.elsevier.com/S1097-2765(21)00753-X/sref43 | https://pypi.org/project/MACS2/ |
| ChIPseeker | Yu, et al., 2015 https://doi.org/10.1093/bioinformatics/btv145 | https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html |
| ChromVAR | Schep, et al., 2017 https://www.nature.com/articles/nmeth.4401 | https://bioconductor.org/packages/release/bioc/html/chromVAR.html |
| Seurat | Stuart et al., 2019 http://refhub.elsevier.com/S1097-2765(21)00753-X/sref38 | https://github.com/satijalab/seurat/ |
| CATALYST | Crowell, et al., 2023 https://github.com/HelenaLC/CATALYST | https://www.bioconductor.org/packages/release/bioc/html/CATALYST.html |
| SingleCellExperiment | Amezquita, et al., 2020 https://www.nature.com/articles/s41592-019-0654-x | https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html |
| flowCORE | Ellis et al., 2023 | https://bioconductor.org/packages/release/bioc/html/flowCore.html |
| caret | Kuhn et al, 2023 https://github.com/topepo/caret/ | https://cran.r-project.org/web/packages/caret/index.html |
| randomForest | Liaw, et al., 2002 https://CRAN.R-project.org/doc/Rnews/ | https://cran.r-project.org/web/packages/randomForest/index.html |
| Bead-based Normalizer | Finck et al., 2013 | https://med.virginia.edu/flow-cytometry-facility/wp-content/uploads/sites/170/2015/10/3_Finck-Rachel_CUGM_May2013.pdf |
| Single-Cell-Debarcoder | Fread et., 2017 | https://github.com/zunderlab/single-cell-debarcoder |
| cydar | Lun et al., 2017 | https://www.bioconductor.org/packages/release/bioc/html/cydar.html |
| Lme4 | Bates et al., 2015 | https://cran.r-project.org/web/packages/lme4/index.html |
| Destiny | Angerer et al., 2016 | https://bioconductor.org/packages/release/bioc/html/destiny.html |
| RIMA | Liu et al., 2022 | https://liulab-dfci.github.io/RIMA/ |
| STAR | Dobin at al., 2013 | https://hbctraining.github.io/Intro-to-rnaseq-hpc-O2/lessons/03_alignment.html |
| RSeQC | Wang et al., 2012 | https://rseqc.sourceforge.net/ |
| Salmon | Patro et al., 2017 | https://combine-lab.github.io/salmon/ |
| ClusterProfile | Wu et al., 2021 | https://github.com/YuLab-SMU/clusterProfiler |
| CIBERSORT | Chen et al., 2018 | https://cibersortx.stanford.edu/ |
| Immunedeconv | Sturm et al., 2020 | https://github.com/omnideconv/immunedeconv |
| Other | ||