|
| Antibodies |
|
| Multiplex immunohistochemistry antibody panel |
|
See Table S3
|
| Rat monoclonal anti-mouse/human PNAd, clone MECA-79 |
BioLegend |
Cat#120802; RRID: AB_493555 |
| Mouse monoclonal anti-Human LAG-3, clone 17B4 |
Novus Biologicals |
Cat#NBP1-97657SS; RRID: AB_11162489 |
| Rabbit monoclonal anti-Human TIM-3, clone DRDR5 |
Cell Signaling Technology |
Cat#45208S; RRID: AB_2716862 |
| Monoclonal Biotin anti-rat IgM, clone MRM-47 |
BioLegend |
Cat#408903; RRID: AB_10571208 |
| Mouse monoclonal anti-Human CD4 PE-CF594, clone RPA-T4 |
BioLegend |
Cat#562281; RRID: AB_11154597 |
| Mouse monoclonal anti-Human CD8 APC, clone SK1 |
BioLegend |
Cat#344722; RRID: AB_2075388 |
| Mouse monoclonal anti-Human CD19 PE, clone HIB19 |
BioLegend |
Cat#555413; RRID: AB_395813 |
| Mouse monoclonal anti-Human CD11b BV421, clone LM2 |
BioLegend |
Cat#393114; RRID: AB_2750258 |
|
| Biological samples |
|
| Tumor biopsy before treatment |
This paper |
N/A |
| Tumor samples after surgery |
This paper |
N/A |
| Peripheral blood mononuclear cells |
This paper |
N/A |
|
| Chemicals, peptides, and recombinant proteins |
|
| Hematoxylin |
Dako |
Cat#S3301 |
| Citra Plus Solutions |
BioGenex |
Cat# HK086-9K |
| EDTA buffer |
Sigma-Aldrich |
Cat# E1161 |
| Hydrogen peroxide solution |
Sigma-Aldrich |
Cat#H1009-500ML |
| HistoFine Simple Stain MAX PO (Mouse) |
Nichirei Bioscience |
Cat#414132F |
| HistoFine Simple Stain MAX PO (Rabbit) |
Nichirei Bioscience |
Cat#414142F |
| HistoFine Simple Stain MAX PO (Rat) |
Nichirei Bioscience |
Cat#414311F |
| VectaMount AQ Mounting Medium |
Vector Laboratories |
Cat#H-5501-60 |
| Ficoll-Paque Plus |
Sigma-Aldrich |
Cat#GE17-1440-02 |
|
| Critical commercial assays |
|
| AEC Substrate Kit |
Vector Laboratories |
Cat#SK-4200 |
| ImmPRESS HRP Goat Anti-Rabbit IgG Polymer Detection Kit |
Vector Laboratories |
Cat#MP-7451 |
| ImmPRESS HRP Goat Anti-Mouse IgG Polymer Detection Kit |
Vector Laboratories |
Cat#MP-7452 |
| ImmPRESS DAB peroxidase substrate Kit |
Vector Laboratories |
Cat#SK-4105 |
| AllPrep DNA/RNA Micro Kit |
Qiagen |
Cat#80284 |
| Qubit RNA HS Assay Kit |
Invitrogen |
Cat#Q32852
|
| SMART-Seq v4 Ultra Low Input RNA Kit |
Takara |
Cat#634894 |
| Zombie Green™ Fixable Viability Kit |
BioLegend |
Cat#423111 |
|
| Deposited data |
|
| Transcriptomic Data (raw) |
This paper |
GEO database: GSE197613
|
| Whole exome sequencing data |
This paper |
dbGAP: phs003002.v1.p1 |
| Code for genomics analysis |
This paper |
github.com/FertigLab/J1568_Bulk
|
| scRNA-seq database |
Kinny-Koster et al., 2022
|
https://doi.org/10.1101/2022.07.14.500096
|
|
| Software and algorithms |
|
| Aperio ImageScope v.12.3.2.8013 |
Leica Biosystems |
https://www.leicabiosystems.com/us/digital-pathology/manage/aperio-imagescope/
|
| CellProfiler pipeline v.2.1.1 |
Tsujikawa et al., 2017
|
https://github.com/multiplexIHC/cppipe
|
| ImageJ v1.48 |
Schneider et al., 2012
|
https://imagej.nih.gov/ij/
|
| FCS Express 7 Image Cytometry v7.10.0007 |
De Novo Software |
https://denovosoftware.com/full-access/download-landing/
|
| Halo Image Analysis Platform v3.4.2986 |
Indica Labs |
https://indicalab.com/halo/
|
| Kallisto v0.45.0 |
Bray et al., 2016
|
http://pachterlab.github.io/kallisto/
|
| Tximport v1.22.0 |
Soneson et al., 2015
|
http://bioconductor.org/packages/tximport
|
| DESeq2 v1.36.0 |
Love et al., 2014
|
http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html
|
| apeglm v1.18.0 |
Zhu et al., 2019
|
https://bioconductor.org/packages/release/bioc/html/apeglm.html
|
| MSigDb v7.5.1 |
Zhu et al., 2019
|
http://www.gsea-msigdb.org/gsea/msigdb
|
| LIMMA v3.52.2 |
Ritchie et al., 2015
|
http://www.bioconductor.org/packages/release/bioc/html/limma.html
|
| CIBERSORTx |
Korotkevich et al., 2021
|
https://cibersortx.stanford.edu/
|
| MGIEasy Universal DNA Library Prep Set |
MGI Tech Co., Ltd. |
https://en.mgi-tech.com/products/reagents_info/id/8
|
| MGIEasy Exome Capture V4 Probe Set |
MGI Tech Co., Ltd. |
https://en.mgi-tech.com/products/reagents_info/9/
|
| SOAPnuke v2.0.7 |
BGI Genomics |
https://github.com/BGI-flexlab/SOAPnuke
|
| VCF2MAF v1.6.16 |
Kandoth and Qwangmsk, 2018
|
https://zenodo.org/record/1185418#.YugPFHZBxD8
|
| Maftools package v2.8.05 |
Mayakonda et al., 2018
|
https://github.com/PoisonAlien/Maftools
|
| NetMHCpan v4.1b |
Jurtz et al., 2017
|
https://services.healthtech.dtu.dk/service.php?NetMHCpan-4.1
|
| MiXCR v4.0 |
Bolotin et al., 2015
|
https://github.com/milaboratory/mixcr/releases
|
| IMMUNARCH v0.6.7 |
ImmunoMindTeam, 2019
|
https://immunarch.com/index.html
|
| Normalized Shannon’s Entropy algorithm |
Hopkins et al., 2018
|
https://doi.org/10.1172/jci.insight.122092
|
| monocle3 v1.0.0 |
Cao et al., 2019; Qiu et al., 2017; Trapnell et al., 2014
|
http://cole-trapnell-lab.github.io/monoclerelease/monocle3/#installing-monocle-3
|
| Seurat v4.1.1 |
Butler et al., 2018; Hao et al., 2021; Stuart et al., 2019; Zeng et al., 2018
|
https://cran.r-project.org/web/packages/Seurat/index.html
|
| fgsea v1.22.0 |
Korotkevich et al., 2021
|
https://bioconductor.org/packages/release/bioc/html/fgsea.html
|
| Domino v0.1.1 |
Cherry et al., 2021
|
https://github.com/Shamir-Lab/DOMINO/releases
|
| pySCENIC v0.11.0 |
Aibar et al., 2017; Van de Sande et al., 2020
|
https://github.com/aertslab/pySCENIC
|
| CellPhoneDB v2.0.0 |
Efremova et al., 2020; Garcia-Alonso et al., 2021
|
https://github.com/Teichlab/cellphonedb
|
| GraphPad Prism v9.3.1 |
GraphPad Software |
https://www.graphpad.com/scientificsoftware/prism/
|
|
| Other |
|
| Clinical trial protocol |
This paper |
Data S1
|
