Key resources table

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
rat anti-CD3	Abcam	Cat #ab11089
rabbit anti-CD8	Cell Signaling	Cat #85336
mouse anti-CXCR3	Abcam	Cat #ab64714
rabbit anti-Aβ	Cell Signaling	Cat #42284
goat anti-Ibal	Abcam	Cat #ab5076
CD8α-Pacific blue	BioLegend	Cat #344718
CD3-BV650	BD Biosciences	Cat #563916
CD45RA-PE	BioLegend	Cat #304108
CCR7-488	BioLegend	Cat #353206
CD27-PE-Cy7	BioLegend	Cat #302838
CXCR3-647	BioLegend	Cat #353712
Fixable Live/dead dye	Thermo	Cat #L34992
Bacterial and virus strains
Biological samples
Adult PBMCs	Stanford University Alzheimer’s Disease Research Center (ADRC)	n/a
Table 1 Demographic information	This paper	n/a
Chemicals, peptides, and recombinant proteins
Critical commercial assays
10x Genomics Chromium Next GEM Single Cell 5’ v2 with immune profiling kit	10x Genomics	User Guide CG000331, Rev D
10x Genomics Chromium Next GEM Single Cell ATAC v1.1 kit	10x Genomics	User Guide CG000209, Rev F
10x Genomics Nuclei Isolation for Single Cell ATAC Sequencing	10x Genomics	Demonstrated protocol CG000169, Rev D
Deposited data
Raw and processed single cell RNA+TCR sequencing data	This study	GEO: GSE226602
Raw and processed single cell ATAC sequencing data	This study	GEO: GSE226267
Experimental models: Cell lines
Experimental models: Organisms/strains
Oligonucleotides
Recombinant DNA
Software and algorithms
Code for analysis	This study	https://github.com/gatelabnw/ad_apoe_pub and DOI: 10.5281/zenodo.10472192
Cellranger v6.0.0	10x Genomics	https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
SoupX v1.6.2	Young and Behjati24	https://github.com/constantAmateur/SoupX
DoubletFinder v2.0.3	McGinnis et al.59	https://github.com/chris-mcginnis-ucsf/DoubletFinder
Cell Ranger ATAC v2.0.0	10x Genomics	https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac
ArchR v1.0.2	Granja et al.22	https://github.com/GreenleafLab/ArchR
ArchR2Signac v1.0.2	Shi et al.25	https://github.com/swaruplabUCI/ArchRtoSignac
Seurat v4.1.0	Hao et al.23	https://satijalab.org/seurat/
edgeR from Delegate v1.0.0	Christoph Hafemeister, Developmental Cancer Genomics group at St. Anna Children’s Cancer Research Institute (CCRI)	https://github.com/cancerbits/DElegate
DESeq2 from Delegate v1.0.0	Christoph Hafemeister, Developmental Cancer Genomics group at St. Anna Children’s Cancer Research Institute (CCRI)	https://github.com/cancerbits/DElegate
Signac v1.8.0	Stuart et al.26	https://github.com/stuart-lab/signac
maxATAC v1.0.0	Cazares et al.33	https://github.com/MiraldiLab/maxATAC
Cicero v1.3.8	Pliner et al.35	https://github.com/cole-trapnell-lab/cicero-release
Other
ShinyCell app for interactive data analysis	This paper	https://gatelabnu.shinyapps.io/ad_apoe_rna/