GSE183276: Human Kidney Proximal Tubule Cell States in AKI vs Healthy Controls

Intermediate outputs from a pseudo-bulk transcriptomic analysis of the human kidney single-cell RNA-seq dataset GSE183276, focusing on comparisons between Acute Kidney Injury (AKI) and Healthy Control (HC) samples. The data provides processed metadata, quality control metrics, and batch-corrected dimensionality reduction coordinates for five proximal tubular epithelial cell subtypes (PT-S1/2, PT-S3, cycPT, dPT, aPT) and all major kidney cell types. These files support the finding that AKI is associated with coordinated downregulation of gluconeogenic genes and upregulation of fibrosis-related genes in human proximal tubule cells.

Use Cases

• Conducting differential expression analysis (pseudo-bulk DESeq2) for specific proximal tubule cell subtypes.
• Visualizing batch-corrected cell landscapes (UMAP/t-SNE) of kidney samples from AKI, HC, and CKD groups.
• Validating cell type composition and quality control filtering steps (nFeature_RNA, percent.mt) for tubular epithelial subsets.
• Reproducing the computational pipeline for comparing gene expression changes between disease states in kidney cell atlas data.

Strengths

• Provides traceable intermediate outputs from a complete bioinformatics pipeline, including R scripts.
• Includes batch-effect corrected coordinates (Harmony) for multiple sample groupings (AKI/HC, all cells).
• Focuses on five annotated proximal tubule cell subtypes, enabling detailed subtype-specific analysis.

Limitations

• Does not contain the raw or processed gene expression matrix; only metadata and coordinates are provided.
• Row counts and specific column names are not detailed in the provided metadata.
• The dataset consists of intermediate processing files, requiring familiarity with the Seurat/Harmony workflow for full utilization.

Provenance

Source

Processed from the public single-cell RNA-seq dataset GSE183276.

Collection Method

Single-cell RNA-seq data processed with Seurat, filtered (nFeature_RNA 500-5000, percent.mt <25), batch-corrected with Harmony, and analyzed with pseudo-bulk DESeq2.

Time Range

null

Freshness

Last updated 2026-03-22.

Geography

null