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/ |