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 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 ✅ ✅ ✘ ✅ ✅ ✅ ✅