Project description:Kidney stone disease causes significant morbidity and increases health care utilization. In this dataset, we applied a single-nucleus assay to renal papila samples in order to charachterize the cellular and molecular niches in patients with calcium oxalate (CaOx) stone disease and healthy subjects. In addition to identifying cell types important in papillary physiology, we characterize collecting duct cell subtypes and an undifferentiated epithelial cell type that was more prevalent in stone patients. Despite the focal nature of mineral deposition in nephrolithiasis, we uncover a global injury signature characterized by immune activation, oxidative stress and extracellular matrix remodeling. We also identify the association of MMP7 and MMP9 expression with stone disease and mineral deposition, respectively. MMP7 and MMP9 are significantly increased in the urine of patients with CaOx stone disease, and their levels correlate with disease activity. Our results define the spatial molecular landscape and specific pathways contributing to stone-mediated injury in the human papilla and identify associated urinary biomarkers.

2023-05-04 | GSE231569 | GEO

Freshwater samples (Beaches samples)

Project description:Freshwater samples (Beaches samples) Raw sequence reads

| PRJNA478197 | ENA

Polarization profiling of renal macrophages in stone model mice

Project description:We recently reported elimination of renal crystals and migration of macrophages (Mφ) around crystals in hyperoxaluric mice, suggesting Mφs might eliminate crystals. Mφs are of 2 phenotypes: inflammatory (M1) and anti-inflammatory (M2). Because M2Mφs are considered to be involved in tissue repair and regeneration, we focused attention on their suppressive role in renal crystal formation. Hence, we investigated the gene array profiling of renal macrophages in stone model mice and CSF-1-deficient stone model mice.

2013-10-22 | GSE51466 | GEO

Microbiota samples

Project description:Microbiota samples Raw sequence reads

| PRJNA495486 | ENA

sludge samples

Project description:sludge samples Raw sequence reads

| PRJNA1125634 | ENA

Fecal samples

Project description:Fecal samples Raw sequence reads

| PRJNA420628 | ENA