Datasets

Accelerating Medicines Partnership – Alzheimer's Disease (AMP-AD)

Major public resource for AD genomics and transcriptomics. Includes ROSMAP, Mount Sinai, Mayo Clinic RNA-seq cohorts. Requires registration for access.

Last reviewed: June 1, 2026

Lundbeck, VIB-KU Leuven, Netherlands Brain Bank, and collaborators

Maps early inflammatory and late antigen-presenting plaque-induced gene programs across six spatial pathology domains. Raw human sequencing data are controlled-access through EGA (Visium EGAD50000002431; snRNA-seq EGAD50000002432), so this is not an unrestricted download.

Last reviewed: October 5, 2026

University Medical Center Freiburg and international collaborators

A disease- and species-spanning reference that organizes CNS myeloid cells into 27 superclusters and 192 clusters with spatial context. Human raw reads require EGA authorization; processed Seurat objects and reproducible figure code are public on Zenodo, and mouse reads are public in GEO.

Last reviewed: October 5, 2026

Icahn School of Medicine at Mount Sinai, NIH, and AMP-AD collaborators

Large human myeloid reference resolving six subclasses and 13 subtypes. A GPNMB-high microglial subtype expands with AD pathology and is linked to MITF and TREM2-dependent biology. Access uses the AD Knowledge Portal and may require an account and data-use agreement.

Last reviewed: October 5, 2026

Vall d'Hebron Research Institute and collaborators

Cross-disease integration resolving eight microglial populations and one border-associated macrophage population. HuMicA is an integrated secondary atlas; batch, tissue-state, brain-region, and source-study effects remain important when reusing its state annotations.

Last reviewed: October 5, 2026

Kampmann Lab (UCSF)

MICA represents a massive functional genomic screen mapping the transcriptomic and phenotypic consequences of knocking out thousands of genes in iPSC-derived human microglia.

Last reviewed: June 3, 2026

Chongqing Medical University and collaborators

Harmonizes major AD mouse models and resolves a trajectory from homeostatic through activated-response and pre-DAM states to DAM. MoMicA is a secondary integration; its source studies remain distributed across Figshare and nine GEO accessions rather than a single new downloadable atlas object.

Last reviewed: October 5, 2026

Amit Lab (Weizmann Institute)

The foundational 2017 dataset establishing the concept of Disease-Associated Microglia (DAM). Contains the scRNA-seq mapping of homeostatic microglia transitioning into the TREM2-dependent effector state during Alzheimer's pathogenesis.

Last reviewed: June 3, 2026

Karolinska Institutet and international collaborators

Cross-condition resource designed to compare vascular and microglial responses. Microglial programs were disease-specific, with convergence between late-stage TBI and AD. Data are split across GEO accessions GSE318960, GSE300113, and GSE327284.

Last reviewed: October 5, 2026

Recursion Pharmaceuticals, Roche, Genentech

A machine learning-powered, high-content imaging-based map of microglial biology using whole-genome perturbation in human iPSC-derived microglia. Targeting neurological disease target discovery. Data availability not yet public at time of review.

Last reviewed: June 1, 2026

Rush Alzheimer's Disease Center (RADC)

ROSMAP is a longitudinal clinical-pathologic cohort study. It is heavily utilized in microglial computational biology because of the massive statistical power linking longitudinal cognitive scores to post-mortem multi-omics.

Last reviewed: June 2, 2026

Allen Institute, UW Medicine, Kaiser Permanente Washington

The SEA-AD atlas precisely maps the single-cell trajectory of Alzheimer's disease across all six Braak stages. Features a robust microglial sub-clustering showing the continuum of microglial states transitioning from homeostatic to disease-associated phenotypes along the cascade.

Last reviewed: June 2, 2026