GSE217665: Single cell transcriptomic analysis of cortical cell type composition underlying diabetes-associated cognitive decline

scRNA-seq Viewer
Info Studies were incorporated in a barcode, matrix, feature format. This format can be found on the 10x Genomics website for processing of single cell studies to obtain the gene expression matrices. For each study, the metadata incorporated in GEO were manually curated into profiles and the samples were separated based on applicable groups and conditions. The expression data from the cells for the samples within the same profile and condition were aggregated into an expression matrix with the cell barcodes having the sample name appended to it to ensure unique cell names.

Description (from GEO)

Submission Date: Nov 09, 2022

Summary: Type 2 diabetes (T2D) is associated with increased risk of cognitive decline although the precise underlying pathogenesis remains obscure. Based on the single-cell RNA sequencing approach applied to the cerebral cortex of a T2D mouse model (db/db), we identified novel regulatory mechanisms underlying diabetes-associated cognitive deficits. Our data adds detail to the highly complex neurovascular pathology associated with T2D and highlights key cell-specific deficits in mitochondrial bioenergetics linked to neuroinflammation, which underlie T2D-linked cognitive impairment.

GEO Accession ID: GSE217665

PMID: No Pubmed ID

Select Condition to compute Visualization and Analysis
Info Preprocessing and downstream analysis were computed using the scanpy Python library and the steps of processing followed the Seurat vignette. Cells and genes with no expression or very low expression were removed from the dataset based on a predefined threshold. The data was then normalized across the expression within the cells and log normalized. The top 2000 highly variable genes were extracted to be used for downstream analysis. For each of these aggregated data matrices, the clusters were computed using the leiden algorithm. Scanpy was then used to compute the PCA, t-SNE, and UMAPs. The points in the plots are labelled by their corresponding cell type labels. The cell type labels were computed using the wilcoxon method as the differential gene expression method. The top 250 genes were then used for enrichment analysis against the CellMarker library in order to determine the most appropriate cell type label with the lowest p-value.
PCA, tSNE, and UMAP Visualizations Labeled by Cell Types:
Gene Expression Data Explorer
Enter gene symbol:

Select conditions below to toggle them from the plot:

Cell Types Cell Samples
Differential Gene Expression Analysis
Info Differential gene expression can be computed for a single cell type labeled group of cells vs the rest. These include wilcoxon, DESeq2, or characteristic direction.
Select Cluster for differential gene expression analysis:
Select differential expression analysis method: