Key resources table

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited data
Raw and analyzed data	This paper	https://singlecell.broadinstitute.org/single_cell/study/SCP1348/ https://cellxgene.cziscience.com/collections/02b01703-bf1b-48de-b99a-23bef8cccc81
Single-cell RNA sequencing data for RCC	dbGaP	dbGaP:phs002252.v1.p1 at https://www.ncbi.nlm.nih.gov/gap/
Single-cell RNA sequencing data for mouse spleen	NCBI Gene Expression Omnibus	GEO:GSE132901
Single-cell RNA sequencing data for melanoma	European Genome-Phenome Archive	EGAS0000100511
Software and algorithms
Slide-seq-tools for processing spatial arrays
Robust decomposition of cell type mixtures	Cable et al., 2021	doi: 10.1038/s41587-021-00830-w.
MiXCR: software for comprehensive adaptive immunity profiling	Bolotin et al., 2015	doi: 10.1038/nmeth.3364
Minimap2: pairwise alignment for nucleotide sequences	Li et al., 2018	doi: 10.1093/bioinformatics/bty191
Seurat v3	Stuart et al., 2019	doi: 10.1016/j.cell.2019.05.031
sctransform	Hafemeister et al. 2019	doi: 10.1186/s13059-019-1874-1
UMAP	McInnes et al. 2018	doi: 10.48550/arXiv.1802.03426
Cell2location	Kleshchevnikov et al., 2022	doi: 10.1038/s41587-021-01139-4
C-SIDE	Cable et al., 2020	doi: 10.1101/2021.12.26.474183.
Other
Code and analyses	This paper	https://github.com/soph-liu/Slide-TCR-seq