Distal-scRNAseq - Web Archive

The Epithelial Systems Biology Laboratory (DIR,NHLBI,NIH), headed by Mark Knepper, has developed a number of databases archiving previously published omic data in kidney and have made them available to the community. The .zip file contains web architecture for access to "Transcriptomes of Mouse Distal Nephron Cells: Targeted Single-Cell RNA-Seq". Full documentation is included on the various pages. The various links allow users to access databases with capability to search, browse or download data sets. Please see: https://esbl.nhlbi.nih.gov/Databases/Distal-scRNA-seq/ for current implementation as of July 12, 2026. Summary: This database provides abundance values for all transcripts expressed in mouse distal nephron cell clusters as ascertained from distillation of targeted single-cell RNA-Seq data. AverageExpression (Seurat) was used to caculate the average gene expression in each cluster. The data are on log10(AverageExpression) scale. A UMAP display showing the clusters is included. Brief Method: We found embigin (Emb) is a negative surface marker for mouse renal proximal tubule cells. Here we used it to enrich non-proximal cell types by FACS sorting. We profiled ~9000 embigin positive cells at a median depth of ~3000 genes. Single-cell RNA-seq analysis of Emb+CD45--LTL-PNA-Hoechst+7-AAD- cells indicated an enrichment of DCT cells (Slc12a3+ cells). Microdissected mouse renal tubule segments transcriptome data can be accessed at Mouse Renal Epithelial Cell Atlas. Reference: Chen L, Chou CL, Knepper MA. Targeted Single-Cell RNA-seq Identifies Minority Cell Types of Kidney Distal Nephron. J Am Soc Nephrol. 2021, PMID: 33769948.