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. Author manuscript; available in PMC: 2024 Oct 9.
Published in final edited form as: Cancer Cell. 2023 Oct 9;41(10):1788–1802.e10. doi: 10.1016/j.ccell.2023.09.003

Key resources table.

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Alexa Fluor® 700 anti-mCD8α (clone53–6.7) Biolegend Cat# 100730
Ultra-LEAF™ Purified anti-mouse CD3 Antibody Biolegend Cat# 100239
Ultra-LEAF™ Purified anti-mouse CD28 Antibody Biolegend Cat# 102115
Chemicals, peptides, and recombinant proteins
MitoTracker™ green FM ThermoFisher Cat# M7514
MitoTracker™ red CMXRos ThermoFisher Cat# M7512
PEI MAX Polysciences Cat# 24765–1
Fixable viability Dye eFluor 506 eBioscience Cat# 65–0866-18
Critical commercial assays
CD8+ T cell isolation kit Stem Cell Technologies Cat# 19853
Chromium Next GEM Single Cell ATAC Kit v2 10x Genomics PN-1000406
Chromium Single Cell V(D)J Reagent Kit v1.1 10x Genomics PN-1000167
Chromium Next GEM Chip H Single Cell Kit 10x Genomics PN-1000162
Agilent High Sensitivity DNA Kit Agilent Technologies Cat# 5067–4626
Mitochondria Isolation Kit for Cultured Cells Thermo Fisher Scientific Cat# 89874
Deposited data
Raw and processed data This paper GEO: GSE235675
Processed data This paper Zenodo:https://doi.org/10.5281/zenodo.8065206
Human reference genome UCSC, GRCh38; Murine reference genome UCSC, mm10 University of California Santa Cruz https://genome.ucsc.edu/cgi-bin/hgGateway
Full list of public single cell datasets used in this study N/A Table S1
scRNA-seq data for BCC samples Yost et al.37 GEO: GSE123814
scRNA-seq data for ESCC samples Zhang et al.38 GEO: GSE160269
scRNA-seq data for NSCLC samples Zeng et al.41 EBI: E-MTAB-6149
scRNA-seq data for CRC samples Zeng et al.41 EBI: E-MTAB-8410
scRNA-seq data for MCC samples Zeng et al.41 GEO: GSE117988
scRNA-seq data for MCC samples Zeng et al.41 GEO: GSE118056
scRNA-seq data for LUAD samples Zeng et al.41 GEO: GSE123904
scRNA-seq data for STAD samples Zeng et al.41 GEO: GSE134520
scRNA-seq data for NSCLC samples Zeng et al.41 GEO: GSE143423
scRNA-seq data for TNBC samples Zeng et al.41 GEO: GSE148673
scRNA-seq data for MIUBC samples Zeng et al.41 GEO: GSE145137
scRNA-seq data for PDAC samples Zeng et al.41 GSA: PRJCA001063
bulk RNA sequencing data for cancer samples TCGA https://portal.gdc.cancer.gov/
Experimental models: Cell lines
KrasG12D/p53ko (KP) lung cancer cells Dr. Esra Akbay N/A
KP-mito-DsRed This paper N/A
MC38 colon cancer cells ATCC N/A
Experimental models: Organisms/strains
C57BL/6J Jackson Laboratory Cat# 000664
Recombinant DNA
pDsRed2-Mito Takara Cat# 632421
Software and algorithms
MERCI-mtSNP and MERCI R package code This paper https://github.com/shyhihihi/MERCI
CytExpert Beckman Coulter, Inc https://www.beckman.com/coulter-flow-cytometers/cytoflex/cytexpert
FlowJo Tree Star Inc. https://www.flowjo.com/solutions/flowjo
GraphPad Prism software 7.0 GraphPad Software, Inc. https://graphpad.com/scientific-software/prism/
Python version 3.8 Python Software Foundation https://www.python.org/downloads/
R version 4.0.2 The R Foundation https://www.r-project.org/
Cell Ranger 3.1.0 10x Genomics https://10xgenomics.com/
Cell Ranger ATAC 2.0.0 10x Genomics https://10xgenomics.com/
Seurat 3.1.2 Seurat developers https://satijalab.org/seurat/articles/get_started.html
pysam pysam developers https://github.com/pysam-developers/pysam
e1071(version 1.7.4) N/A https://cran.r-project.org/web/packages/e1071/index.html
fgesa(version 1.16.0) N/A https://bioconductor.org/packages/release/bioc/html/fgsea.html
msigdbr (version 7.2.1) N/A https://cran.r-project.org/web/packages/msigdbr/index.html
simplifyEnrichment (version 1.0.0) N/A https://bioconductor.org/packages/release/bioc/html/simplifyEnrichment.html
Cytoscape (version 3.9.1) Cytoscape developers https://cytoscape.org/
GSVA Hänzelmann et al.43 https://bioconductor.org/packages/release/bioc/html/GSVA.html
BioRender biorender.com https://www.biorender.com/