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. Author manuscript; available in PMC: 2023 Oct 5.
Published in final edited form as: Cell Rep. 2023 Aug 2;42(8):112879. doi: 10.1016/j.celrep.2023.112879

KEY RESOURCES TABLE.

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Rabbit anti-human CD3 DAKO A0452
Mouse anti-human CD20 DAKO M0755
Goat anti-human CD4 R&D Systems AF-379-NA; RRID:AB_354469
Rabbit anti-human CD8 Thermo RB-9009-P0
Alexa 488 anti-Rabbit Life Technologies A21206
Alexa 594 Anti-Mouse Life Technologies A11032
Alexa 488 anti-Goat Life Technologies A11055
Alexa 594 anti-Rabbit Life Technologies A21207
DAPI Hydrochloride Sigma 32670
anti-Ki-67:Alexa Fluor 647 direct conjugate Abcam ab196907
Biological samples
Tumor RNA Children’s Oncology Group N/A
Tumor genomic DNA Children’s Oncology Group N/A
Tumor FFPE sections Children’s Oncology Group N/A
Chemicals, peptides, and recombinant proteins
Antigen unmasking solution Vector Laboratories H-3300
Deposited data
Neuroblastoma tumor transcriptomes TARGET-NBL Dataset, NCBI https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000467.v17.p7
TCRbeta reference dataset, healthy and CMV adults (786 individuals) Emerson, R et al.49 https://www.adaptivebiotech.com/immuneACCESS DOI https://doi.org/10.21417/B7001Z
Neuroblastoma tumor transcriptomes, this paper https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE189367 GSE189367
Neuroblastoma TCRbeta repertoires, this paper (Adaptive) https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE189742 GSE189742
Neuroblastoma IgH repertoires, this paper (Adaptive) https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE189741 GSE189741
Software and algorithms
R v4.1 Hornik and R Core Team (2022), “The R FAQ”. https://CRAN.R-project.org/doc/FAQ/R-FAQ.html https://www.R-project.org/
python scikit-learn (version 0.18.2) https://scikit-learn.org/0.18/install.html
HLAProfiler Buchkovich, M et al.42 https://expressionanalysis.github.io/HLAProfiler/
XGboost Chen T and Guestrin C.36 https://github.com/dmlc/xgboost
SHAP Lundberg S and Lee S-I82 https://github.com/slundberg/shap
Alakazam software Gupta NT, et al.83 https://github.com/cran/alakazam/blob/master/DESCRIPTION
Change-O Gupta NT, et al.83 http://clip.med.yale.edu/changeo/
IgBlast Ye, J et al.84 https://ncbi.github.io/igblast/
Shazam Gupta NT, et al.83 https://shazam.readthedocs.io/en/stable/
Immune Subtype Classifier Thorsson, V et al.,33 Gibbs DL85 https://github.com/Gibbsdavidl/ImmuneSubtypeClassifie
RAbHIT package Peres A, et al.86 https://cran.r-project.org/web/packages/rabhit/
coseq Rau, A. and Maugis-Rabusseau, C.26 https://www.bioconductor.org/packages/devel/bioc/vignettes/coseq/inst/doc/coseq.html
GENIE3 Huynh-Thu VA et al.87 https://www.bioconductor.org/packages/release/bioc/html/GENIE3.html
cytoscape Shannon, P et al.88 https://cytoscape.org/
limma4 Ritchie, ME et al.89 http://bioconductor.org/packages/release/bioc/html/limma.html
DESeq2 Anders, S and Huber, W90 https://bioconductor.org/packages/release/bioc/html/DESeq2.html
edgeR Robinson, MD et al.91 https://bioconductor.org/packages/release/bioc/html/edgeR.html
EBseq Leng, N et al.92 https://bioconductor.org/packages/release/bioc/html/EBSeq.html