KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited data
GWAS Catalog	Buniello et al.44	https://www.ebi.ac.uk/gwas/
SNPnexus	Oscanoa et al.28	https://www.snp-nexus.org/v4/
GTEx	Lonsdale et al.24; GTEx Consortium25	https://gtexportal.org/home/datasets
Ensembl Regulatory Build	Zerbino et al.27	https://grch37.ensembl.org/index.html
ENCODE	Kundaje et al.29	https://www.encodeproject.org/
NIAGADS	NA	https://www.niagads.org
The Alzheimer’s disease Knowledge portal	NA	https://adknowledgeportal.synapse.org/
Human protein-protein interactome	Zhou et al.89	https://alzgps.lerner.ccf.org
Gene Ontology	Mi et al.30	http://geneontology.org
AlzGene	Bertram et al.38	http://www.alzgene.org
DistiLD	Palleja et al.39	http://distild.jensenlab.org
TIGA	Yang et al.40	https://unmtid-shinyapps.net/shiny/tiga/
DISEASES	Pletscher-Frankild et al.41	https://diseases.jensenlab.org/Search
Human microarray: 31 late-stage AD and 32 controls	Miller et al.90; Zhou et al.89	GEO: GSE29378; https://alzgps.lerner.ccf.org
Human microarray: 42 late-stage AD and 173 controls	Berchtold et al.91; Zhou et al.89	GEO: GSE48350; https://alzgps.lerner.ccf.org
Human microarray: 328 late-stage AD and 214 controls	Wang et al.92; Zhou et al.89	GEO: GSE84422; https://alzgps.lerner.ccf.org
Human bulk-RNA seq: 4 late-stage AD and 4 controls	Zhou et al.89; Magistri et al.93	https://alzgps.lerner.ccf.org
Human bulk-RNA seq: 6 late-stage AD and 6 controls	Zhou et al.89; Annese et al.94	https://alzgps.lerner.ccf.org
Human bulk-RNA seq: 20 late-stage AD and 10 controls	Zhou et al.89; van Rooij, et al.95	https://alzgps.lerner.ccf.org
Mouse single-cell RNA seq: 6-month-old 16 5xFAD and16 WT mouses	Keren-Shaul et al.96	GEO: GSE98696; http://taca.lerner.ccf.org/
Mouse single-nucleus RNA seq: 7-month-old 3 TREM2-KO WT, 3 TREM2-KO 5xFAD, 3 5xFAD, and 3 WT mouses	Zhou et al.97	GEO: GSE140511; http://taca.lerner.ccf.org/
Human single-nucleus RNA seq: 3 Braak stage 0, 4 Braak stage and 3 Braak stage brain samples	Leng et al.98	GEO: GSE147528; http://taca.lerner.ccf.org/
Human single-nucleus RNA seq: 6 AD and 6 controls	Grubman et al.99	GEO: GSE138852; http://taca.lerner.ccf.org/
Human single-nucleus RNA seq: 12 AD and 9 controls	Lau et al.100	GEO: GSE157827; http://taca.lerner.ccf.org/
Mouse proteomic data (7- and 10-month-old ADLP mouse models [JNPL3 mouse model cross with 5xFAD mouse model])	Zhou et al.89; Kim et al.101	https://alzgps.lerner.ccf.org
Mouse proteomic data (7- and 10-month-old 5xFAD mouse model)	Zhou et al.89; Kim et al.101	https://alzgps.lerner.ccf.org
Mouse proteomic data (12-month-old 5xFAD mouse model)	Zhou et al.89; Savas et al.102	https://alzgps.lerner.ccf.org
Mouse proteomic data (12-month-old hAPP mouse model)	Zhou et al.89; Savas et al.102	https://alzgps.lerner.ccf.org
Software and algorithms
NETTAG	This paper	https://github.com/ChengF-Lab/NETTAG
diffusr R package	Valdeolivas et al.23	https://github.com/dirmeier/diffusr
Seurat R package	Butler et al.103	https://github.com/satijalab/seurat
MAST R package	Finak et al.104	https://github.com/RGLab/MAST
scikit-learn Python package: spectral clustering, k-means, SVD	Pedregosa et al.105	https://scikit-learn.org/stable/index.html
Enrichment analysis	Chen et al.106; Kuleshov et al.107	https://maayanlab.doud/Enrichr/