Human brains were accessed from the Mount Sinai/JJ Peters VA Medical Center Brain Bank (MSBB–Mount Sinai NIH Neurobiobank) cohort, which holds over 2,040 well-characterized brains. This cohort was assembled after applying stringent inclusion/exclusion criteria and represents the full spectrum of cognitive and neuropathological disease severity in the absence of discernable non-AD neuropathology. For each sample, neuropathological assessment was performed according to the Consortium to Establish a Registry for Alzheimer’s Disease (CERAD) protocol and included assessment by hematoxylin and eosin, modified Bielschowski, modified thioflavin S, and anti-β amyloid (4G8), anti-tau (AD2) and anti-ubiquitin. A Braak AD-staging score for progression of neurofibrillary neuropathology was assigned to each case. Quantitative data regarding the mean of the density of neuritic plaques in the middle frontal gyrus, orbital frontal cortex, superior temporal gyrus, inferior parietal cortex and calcarine cortex were also collected. Clinical dementia rating scale (CDR) was conducted for assessment of dementia and cognitive status. (Wang, M., Beckmann, N., Roussos, P. et al. The Mount Sinai cohort of large-scale genomic, transcriptomic and proteomic data in Alzheimer’s disease. Sci Data 5, 180185 (2018).