Table 4 Information about publicly available human transcriptomic datasets for the analysis in this study including human AD gene signatures derived from brain bulk tissue transcriptomics datasets as well as scRNA-seq. of microglia from human AD brain with details including cohort labels (used in the portal and figures), data information, brain regions, cell types and references

Allen (Mayo)

Brain transcriptomes from patients with AD, progressive supranuclear palsy (a primary tauopathy), and control subjects in the Mayo clinic cohort.

Cerebellum region, temporal cortex

Mixed cell population

[181]

Avramopoulos

Microarray: identify genes involved in normal aging and genes involved in AD. RNA extracted from the temporal lobe of 22 late onset AD and 23 control brain donors.

Temporal lobe

Mixed cell population

[182]

Blalock

Microarray: nine control and 22 AD subjects of varying severity.

Hippocampus

Mixed cell population

[183]

Colangelo

Microarray: Hippocampal regions was pooled from six controls and six AD subjects.

Hippocampus CA1 region

Mixed cell population

[184]

Liang

Microarray (Affymetrix Human Genome U133 Plus 2.0 microarrays): Normal cortical neurons collected with laser capture microdissection. Overall regional analyses consisted of 11 to 13 control subjects and 10 to 23 AD subjects that varies from different brain regions.

6 brain regions: (1) entorhinal cortex, (2) hippocampus, (3) medial temporal gyrus, (4) posterior cingulate, (5) superior frontal gyrus, and (6) primary visual cortex.

Mixed cell population

[185]

Miller

Microarray (Illumina HumanHT-12 V3.0 expression beadchip): 32 control, 31 AD.

Hippocampus CA1 and CA3 regions

Mixed cell population

[186]

Mostafavi (ROSMAP)

RNA-Seq from the ROSMAP cohort (total n = 478). Parameters such as signature correlated with B amyloid, cognitive decline, clinical diagnostic of AD and AD pathology were considered.

Dorsal lateral frontal cortex (DLPFC)

Mixed cell population

[187]

Satoh

RNA-Seq Data Mining

Frontal cortex

Mixed cell population

[188]

Webster

Analyzed samples with a confirmed pathologic diagnosis of late-onset Alzheimer disease (LOAD; final n = 188 controls, 176 cases. AD signature).

Temporal cortex

Mixed cell population

[190]

Zhang (HBTRC)

Postmortem brain tissues from LOAD patients and nondemented subjects in the Harvard brain tissue resource center (HBTRC). Analysis of parametrs such as atrophy and Braak staging.

Cerebellum, prefrontal cortex

Mixed cell population

[189]

Wang (MSBB)

RNA-seq of four cortical areas from 364 donors in the Mount Sinai Brain Bank (MSBB) cohort with varying degrees of severity regarding 4 cognitive/pathological phenotypes. Study investigated parameters such as CERAD Definite AD vs NL or AD vs NL; Plaque Mean Normal, Mild and Severe. CDR Demented vs MCI vs nondemented. Braak score AD vs NL.

Brodmann area 10 frontal pole (BM10-FP), Brodmann area 22 superior temporal gyrus (BM22-STG), Brodmann area 36 parahippocampal gyrus (BM36-PHG), and Brodmann area 44 inferior frontal gyrus (BM44-IFG)

Mixed cell population

[191]

Olah (ROSMAP)

Single cell RNA-seq of human microglia obtained at autopsy from 9 AD and 4 MCI cases.

Dorsolateral prefrontal cortex (DLPFC)

Microglia

[192]

Lee

Single cell RNA-seq of myeloid cells from postmortem brain specimens of two cohorts (n = 137 and 1,470) with varying degrees of AD neuropathology.

Prefrontal cortex

Myeloid

medRxiv.2023.10.25.23297558

Sun (ROSMAP)

Single-nucleus microglial transcriptomes and epigenomes of 194,000 nuclei across 443 human subjects and diverse Alzheimer’s disease (AD) pathological phenotypes.

Prefrontal cortex, hippocampus, mid-temporal cortex, angular gyrus, entorhinal cortex, and thalamus

Microglia

[193]