REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Fixable viability dye efluor 506	ThermoFisher	Cat# 65-0866-14
Mouse Anti-CCL2 PE-Cy7	Biolegend	Cat# 502613; RRID: AB_2734490
Mouse Anti-CCR7 PE-Fire810	Biolegend	Cat# 353269; RRID: AB_2894572
Mouse Anti-CD123 APC-Fire810	Biolegend	Cat# 306053; RRID: AB_2904334
Mouse Anti-CD127 Spark NIR 685	Biolegend	Cat# 351361; RRID: AB_2860913
Mouse Anti-CD163 BUV563	BD Biosciences	Cat# 752879; RRID: AB_2917834
Mouse Anti-CD19 BV480	BD Biosciences	Cat# 566164; RRID: AB_2739561
Mouse Anti-CD1c APC-R700	BD Biosciences	Cat# 566615; RRID: AB_2869795
Mouse Anti-CD3 APC-Cy7	Biolegend	Cat# 344817; RRID: AB_10644011
Mouse Anti-CD3 BUV615	BD Biosciences	Cat# 612993; RRID: AB_2870264
Mouse Anti-CD31 BV711	Biolegend	Cat# 303135; RRID: AB_2716212
Mouse Anti-CD3 PE	BioLegend	Cat# 317308; RRID: AB_571913
Mouse Anti-CD4 BUV496	BD Biosciences	Cat# 612937; RRID: AB_2916881
Mouse Anti-CD4 cYG584	Cytek	Cat# SKU R7-20042
Mouse Anti-CD4 FITC	Biolegend	Cat# 357406; RRID: AB_2562357
Mouse Anti-CD45 BUV395	BD Biosciences	Cat# 563791; RRID: AB_2744400
Mouse Anti-CD56 PE-Cy5	Biolegend	Cat# 318308; RRID: AB_604105
Mouse Anti-CD56 APC	Biolegend	Cat# 318310; RRID: AB_604098
Recombinant Anti-CD68 APC-Vio770	Miltenyi	Cat# 130-114-654; RRID: AB_2726730
Mouse Anti-CD74 BV786	BD Biosciences	Cat# 743736; RRID: AB_2741709
Mouse Anti-CD8 PerCP	Biolegend	Cat# 980916; RRID: AB_2890877
Mouse Anti-CD8 PE	Biolegend	Cat# 344706; RRID: AB_1953244
Mouse Anti-CD96 BV421	Biolegend	Cat# 338417; RRID: AB_2629536
Mouse Anti-CTLA-4 APC	Biolegend	Cat# 349907; RRID: AB_10680785
Mouse Anti-GD2 FITC	Biolegend	Cat# 563439; RRID: AB_2738206
Mouse Anti-GD2 BV750	BD Biosciences	Cat# 746863; RRID: AB_2871665
Mouse Anti-GZMB RY586	BD Biosciences	Cat# 568134
Mouse Anti-ICOS PE-Cy5.5	ThermoFisher	Cat# 35-9948-41; RRID: AB_2815129
Rat Anti-IL10 BB700	BD Biosciences	Cat# 566568; RRID: AB_2869786
Mouse Anti-IL1B BV421	BD Biosciences	Cat# 567792
Mouse Anti-Ki-67 BV650	BD Biosciences	Cat# 563757; RRID: AB_2688008
Mouse Anti-LAG3 APC-R700	BD Biosciences	Cat# 565775; RRID: AB_2744329
Mouse Anti-cMAF eF450	ThermoFisher	Cat# 48-9855-42; RRID: AB_2762608
Recomb Anti-NECTIN2 PE-Vio615	Miltenyi	Cat# 130-122-784; RRID: AB_2819430
Mouse Anti-PD-1 BV605	BD Biosciences	Cat# 563245; RRID: AB_2738091
Mouse Anti-PD-L1 PE-Fire810	Biolegend	Cat# 329755; RRID: AB_2894668
Mouse Anti-Perforin PE-Cy7	Biolegend	Cat# 308125; RRID: AB_2572049
Mouse Anti-PVR AF647	Biolegend	Cat# 748275; RRID: AB_2872703
Mouse Anti-S100A9 APC	Biolegend	Cat# 565833; RRID: AB_2739373
Mouse Anti-TCRgd APC-Vio770	Miltenyi	Cat# 130-114-027; RRID: AB_2751186
Mouse Anti-TCRgd BV421	Biolegend	Cat# 331217; RRID: AB_2562317
Mouse Anti-TIGIT PE	Biolegend	Cat# 372704; RRID: AB_2632729
Mouse Anti-TIGIT BB700	BD Biosciences	Cat# 747846; RRID: AB_2872309
Mouse Anti-TIM-3 AF647	BD Biosciences	Cat# 565559; RRID: AB_2744367
Mouse Anti-CD25 APC-Fire810	Biolegend	Cat# 356149; RRID: AB_2876679
Rat Anti-FOXP3 eF450	ThermoFisher	Cat# 48-4776-42; RRID: AB_1834364
Fixable viability dye UV blue	Thermofisher	Cat# L23105
Anti-CD19 BUV563	BD Biosciences	Cat# 749028; RRID: AB_2873425
Anti-CD4 BUV737	BD Biosciences	Cat# 612761; RRID: AB_2870092
Anti-MHCII Vioblue	Miltenyi	Cat# 130-112-394; RRID: AB_2652908
Anti-CD11b BV605	Biolegend	Cat# 101257; RRID: AB_2565431
Anti-F4/80 BV711	Biolegend	Cat# 123147; RRID: AB_2564588
Anti-Ly6C BV785	Biolegend	Cat# 128041
Anti-CD45 FITC	Biolegend	Cat# 103107; RRID: AB_312972
Anti-CD8a NovaFluor™ Blue 660-120S	ThermoFisher	Cat# M003T02B08; RRID: AB_2896728
Anti-CD38 PE	Miltenyi	Cat# 130-102-607; RID:AB_2657877
Anti-LY6G PE-dazzle594	Biolegend	Cat# 127647; RRID: AB_2566318
Anti-CD3 PE-Fire700	Biolegend	Cat# 100271; RRID: AB_2876394
Anti-muB7H3 PE-Cy7	Biolegend	Cat# 135613; RRID: AB_2800636
Anti-GD2 APC	Biolegend	Cat# 357305; RRID: AB_2563083
Anti-CD206 Alexa Fluor 700	Biolegend	Cat# 141734; RRID: AB_2629637
Anti-CD49b APC-Vio770	Miltenyi	Cat# 130-105-249; RRID: AB_2660464
Anti-CD3 (IHC)	Leica	Cat# PA0553
Anti-SOX10 (IHC)	Cell Marque	Cat# 383R-18
Anti-TIGIT	Abcam	Cat# 233404; RRID: AB_2827380
Anti-PD-1	Cell Signaling Technology	Cat# 64651
Anti-PD-L1	Cell Signaling Technology	Cat# 64988s
Mouse Anti-TGFβ	eBioscience	Cat# 16-9243-85; RRID: AB_2573124
Anti-TIGIT (Tiragolumab)	Roche	Cat# N/A
Anti-PD-1 (Atezolizumab)	Roche	Cat# N/A
Anti-GD2 (Dinutuximab)	BioXcell	Cat# BE0318; RRID: AB_2819045
Biological samples
Pediatric patient tumor tissue	This paper, Princess Máxima Center for Pediatric Oncology	N/A
Healthy donor blood samples	This paper, University Medical Center Utrecht	N/A
Healthy donor buffy coats	Sanquin	N/A
PRAME-TCR transduced T cells	Dr. Stefan Nierkens; Cornel et al.98	N/A
Chemicals, peptides, and recombinant proteins
Recombinant Human TGFβ	Preprotech	Cat# 100-21-10UG
Haematoxylin	BOOM BV	Cat# 840.154.912.500
Eosine Y alcoholic	VWR International	Cat# 10047103
Collagenase I	ThermoFisher	Cat# 17100017
Collagenase II	ThermoFisher	Cat# 17100015
Collagenase IV	ThermoFisher	Cat# 17100019
Dulbecco’s modified Eagle’s medium (DMEM) with low glucose and Glutamax™	ThermoFisher	Cat# 21885-108
Ham’s F-12 Nutrient Mix	ThermoFisher	Cat# 31765027
B-27 supplement minus vitamin A (50×)	ThermoFisher	Cat# 12587010
N-2 supplement (100×)	ThermoFisher	Cat# 17502048
Recombinant human EGF	Peprotech	Cat# AF-100-15
Recombinant human FGF-2	Peprotech	Cat# 100-18B
Recombinant human IGF-1	R&D	Cat# 100-11
Recombinant human PDGF-AA	Peprotech	Cat# 100-13A
Recombinant human PDGF-BB	Peprotech	Cat# 100-14B
NeuroCult dissociation kit	Stemcell™ Technologies	Cat# 05707
DAPI	Miltenyi Biotec	Cat# 130-111-570
DRAQ5	Sigma Aldrich	Cat# GE17-1440-03
Ficoll-Paque	Sigma Aldrich	Cat# GE17-1440-03
Accutase	Sigma Aldrich	Cat# A6964-100ML
RPMI 1640	Gibco	Cat# 21875091
L-Glutamine	ThermoFisher	Cat# 25030
D-luciferin	Perkin Elmer	Cat# 122799
Temozolomide	Sigma-Aldrich	Cat# #T2577
Irinotecan	Sigma-Aldrich	Cat# #I1406
Vincristine sulfate	Sigma-Aldrich	Cat# V8879
Doxorubicin hydrochloride	Sigma-Aldrich	Cat# D1515
Cyclophosphamide monohydrate	Sigma-Aldrich	Cat# C0768
IL-2	Miltenyi	Cat# 130-097-744
IL-15	Miltenyi	Cat# 130-095-762
Critical commercial assays
Foxp3/Transcription Factor Staining Buffer Set	eBioscience	Cat# 00-5523-00
Deposited data
Single-cell RNA sequencing data of 24 tumors and 5 healthy controls	This paper	GSE218003; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?&acc=GSE218003
Single-cell RNA sequencing data of 24 tumors	This paper	EGAD00001009766; https://ega-archive.org/datasets/EGAD00001009766
Experimental models: Cell lines
Neuro-2a cell line	Hamprecht	RRID: CVCL_0470
N1E-115 cell line	Hamprecht	RRID: CVCL_0451
N18 cell line	Hamprecht	RRID: CVCL_4724
Patient-derived tumoroids AMC691B transduced with eGFP-luciferase	Amsterdam University Medical Center and Princess Máxima Center Utrecht; Bate-Eya et al.; Kholosy et al.81,82	N/A
Patient-derived tumoroid AMC691T transduced with eGFP-luciferase	Amsterdam University Medical Center and Princess Máxima Center Utrecht; Bate-Eya et al.; Kholosy et al.81,82	N/A
Experimental models: Organisms/strains
Mouse: A/Jax-000646	The Jackson Laboratory	RRID: IMSR_JAX:000646
Mouse: Th-ALKF1174L/MYCN 129/SvJ	ICR57	N/A
Software and algorithms
Sharq pipeline	Candelli et al.84	N/A
STAR version 2.6.1	http://code.google.com/p/rna-star/; Dobin et al.100	RRID: SCR_004463
GENCODE version 26	https://www.gencodegenes.org; Harrow et al.101	RRID: SCR_014966
DecontX	Yang et al.85	N/A
R version 4.0.2	http://www.r-project.org/; Dessau et al.102	RRID: SCR_001905
Seurat version 3.2.2	http://seurat.r-forge.r-project.org/	RRID: SCR_007322
SingleR version 1.2.4	Aran et al.87	N/A
ggplot2 version 3.3.2	https://cran.r-project.org/web/packages/ggplot2/index.html	RRID: SCR_014601
Reactome	https://reactome.org; D’Eustachio et al.103	RRID: SCR_003485
GSEA broad institute	http://www.broadinstitute.org/gsea/; Subramanian et al.95	RRID: SCR_003199
GEO2R	Edgar et al.96	N/A
CellChat	https://github.com/sqjin/CellChat; Williams et al.54	RRID: SCR_021946
CellPhoneDB	http://www.cellphonedb.org/; Efremova et al.104	RRID: SCR_017054
Flowjo version 10.8.1	LLC	RRID: SCR_008520
Graphpad Prism	GraphPad Software	RRID: SCR_002798
Code	This paper	https://bitbucket.org/princessmaximacenter/neuroblastoma_nectin2_tigit/src/master/