Single-Cell RNA Data Portal for Alzheimer's Disease

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 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

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

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 

2.3M 

AD Cells 

1.2M 

Control Cells 

1.1M 

Unique Genes 

107k 

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 

61k 

43k 

11k 

32k 

7 

✅ 

✅ 

✅ 

✅ 

✅ 

✅ 

✅ 

dharsini et al 

61k 

425k 

311k 

114k 

46 

✅ 

✅ 

✅ 

✅ 

✅ 

✅ 

✅ 

ssREAD 

62k 

2.42M 

1.14M 

1.28M 

135 

✅ 

✅ 

✘ 

✅ 

✅ 

✅ 

✅