DOI: 10.5281/zenodo.15526235
title: Single-Cell RNA Data Portal for Alzheimer's Disease

description: Single-Cell RNA Data Portal for Alzheimer's Disease

The single cell Alzheimer's Disease Data Portal is an aggregated data portal created as part of the Enfield EU Funded program for the single-cell Generative Pretrained Transformer (scGPT-AD) model research. The data portal contains human data from the ssREAD data portal, along with single-cell AD data from latest studies (dharsini et al, pan et al, rexach et al). The data from the individual studies where accessed through the cellXgene data portal, a vast portal for single cell data. The data have been uploaded in two seperate .zip files (part1, part2).

The single cell data follow the Annotated Data format. The core data for each sample is the gene-expression matrix, which refers to the level of expression of each gene in a single cell. Additionally, the dataset contains the `.obs` attributed which includes core cell metadata for each of the sample (cell type, brain region, braak stage, donor age, disease condition, donor gender, etc.), along with the gene names accessed via `.var` attribute.

The source data have been processed to create a unified data portal ready to be used as training dataset for a Transformer model. The main processing steps were:



convert ssREAD data from `.qsave` format to `.h5ad` format that aligns with the AnnData framework

discard some unprocessable data samples

standardize metadata column names





handle mouse genes





Remove mouse genes (based on regex pattern or given mouse identifiers)

Remove cells that express any of the mouse genes









remove genes that are not expressed in any of the cells



process categorical data to create a unified namespace (e.g.: merge `microglia` and `microgrial` cell type names into one)

standardize all gene names to be upper-cased

discard dimensionality reduction and clustering attributes, to make a lightweight version of the data portal, since they are not meant to be used in Transformer model training


Aggregated Data Statistics










Total Cells 









1.7M 











AD Cells 









954k 











Control Cells 









776k 











Unique Genes 





60k









Donors 









166 







Characteristics of Dataset grouped by Data Source










Data Source 









Unique Genes 









Total Cells 









AD Cells 









Control Cells 









Donors 









Cell Type Label 









Brain Region 









Tissue Type 









Braak Stage 









Donors Id 









Donor Gender 









Donor Age 











rexach et al 









30k 









217k 









118k 









99k 









20 









✅ 









✘ 


 








✅ 









✘ 









✅ 









✅ 









✅ 











pan et al 









33k 









43k 









11k 









32k 









7 









✅ 









✅ 









✅ 









✅ 









✅ 









✅ 









✅ 











dharsini et al 









39k 









425k 









311k 









114k 









46 









✅ 









✅ 









✅ 









✅ 









✅ 









✅ 









✅ 











ssREAD 









34k 









1M 









514k 









531k 









93 









✅ 









✅ 









✘ 









✅ 









✅ 









✅ 









✅