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. 2023 Jun 21;4(7):101092. doi: 10.1016/j.xcrm.2023.101092
REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies

CD20 Agilent M075501-2
CD4 Spring Biosciences M3352; RRID: AB_11217932
CD8 Spring Biosciences M5392
Ki67 Agilent M724029-2; RRID: AB_2687528
CD163 Merck 163M-1; RRID: AB_1159110
DAPI Thermo P36935
Human IgA (capture) Biolegend 411502; RRID: AB_2650697
HRP-conjugated human IgA (detection) Thermo PA1-74395; RRID: AB_10985660
Human IgA standard Thermo 31148
Human IgG (capture) R&D MAB11012
HRP-conjugated human IgG (detection) Biolegend 410902; RRID: AB_2686937
Human IgG standard R&D 1-001-A
Alexa Fluor 488-conjugated human IgG Invitrogen A-11013; RRID: AB_2534080
RBM39 Bethyl laboratories A300-291A-T
Calnexin Enzo adi-spa-860-day
HRP-conjugated rabbit Dako P044801-2

Biological samples

Human HGSOC FFPE sections Imperial College Healthcare Tissue Bank https://www.imperial.ac.uk/imperial-college-healthcare-tissue-bank/
Human HGSOC fresh frozen DNA samples Imperial College Healthcare Tissue Bank https://www.imperial.ac.uk/imperial-college-healthcare-tissue-bank/
Human HGSOC CT scans at diagnosis Imperial College Healthcare Tissue Bank https://www.imperial.ac.uk/imperial-college-healthcare-tissue-bank/
Human NSCLC CT scans at diagnosis Imperial College Healthcare Tissue Bank https://www.imperial.ac.uk/imperial-college-healthcare-tissue-bank/

Chemicals, peptides, and recombinant proteins

RPMI-1640 Sigma R5886-500ML
L-glutamine Thermo 25030081
FCS First Link 02-05-850
PBS Internal prepared NA
Trypsin/EDTA Sigma T4049
Myo-inositol Sigma I-7508
2-mercaptoethanol Gibco 21985-023
Folic acid Sigma F-8758
Human recombinant IL-2 Peprotech 200-02
Horse serum ATCC 30-2040
Histo-Clear National diagnostics HS-200
Goat serum Vector Laboratories S-1000-20
Avidin-biotin complex solution Vector Laboratories PK-6100
DAB Vector Laboratories SK-4105
DPX VWR 317616-100ML
Coating buffer Biolegend 421701
TMB substrates Biolegend 421101
HRP substrate Millipore WBLUF0500
MTT Sigma 475989

Critical commercial assays

GZMB ELISA assay R&D DY2906-05
Caspase 3/7 assay Merck Millipore MCH100108
BCA assay Thermo 23225

Deposited data

Whole exome sequencing for HGSOC This study Mendeley Data: https://doi.org/10.17632/h98925j75g.21
Bulk RNA-sequencing data for HGSOC TCGA https://xena.ucsc.edu/
Bulk RNA-sequencing data for NSCLC TCGA https://xena.ucsc.edu/
CNA data for HGSOC TCGA https://xena.ucsc.edu/
CNA data for NSCLC TCGA https://xena.ucsc.edu/
Single cell RNA-sequencing data Qian et al.,39 Olbrecht et al.46 https://lambrechtslab.sites.vib.be/en
Single cell RNA-sequencing data Olalekan et al.41 GEO: GSE14708244
Single cell RNA-sequencing data Davies et al.74 GEO: GSE165897

Experimental models: Cell lines

PEO1 ECACC 10032308
OVCAR4 MERCK SCC258
OSEC Zhang et al.75 Gift
OVCAR3 ATCC HTB-161
NK-92 ATCC CRL-2407

Software and algorithms

MCP counter Becht et al.38 https://github.com/ebecht/MCPcounter
Seurat 4.3.0 Pinato et al.76 https://satijalab.org/seurat/
SingleR Birtley et al.77 https://github.com/dviraran/SingleR
ggplot2 Aran et al.78 https://github.com/tidyverse/ggplot2
Glmnet Li et al.79 https://cran.r-project.org/web/packages/glmnet/index.html
survival Li et al.80 https://cran.r-project.org/web/packages/survival/index.html
Limma Talevich et al.81 http://bioconductor.org/packages/release/bioc/html/limma.html
BWA Carter et al.82 https://github.com/lh3/bwa
samtools Mermel et al.83 https://samtools.sourceforge.net/
PicardTools Broad institute https://broadinstitute.github.io/picard/
CNVkit Arshad et al.84 https://cnvkit.readthedocs.io/en/stable/
ABSOLUTE Hao et al.85 https://github.com/genepattern/genepattern-server/releases/tag/v3.9_22.11_b389
GISTIC2.0 Wickham et al.86 https://cloud.genepattern.org
TexLab v2.0 Lu et al.30 Available upon request
R 4.1.0 The R Project for Statistical
Computing
https://www.r-project.org
GraphPad PRISM 6 GraphPad software https://www.graphpad.com/
BioRender BioRender website https://www.biorender.com/