Single cell profiling reveals sex, lineage and regional diversity in adult mouse kidney

To obtain new insight into the mammalian kidney, anatomy-guided, single cell RNA sequencing was performed on the adult male and female mouse kidney. Key observations were followed up through a variety of secondary studies including genetic lineage tracing. The data document novel cell diversity, unexpected origins to key cell types, and significant sex differences centered on proximal tubules segments of the nephron and principal cells of the collecting system. A searchable database integrating these data will facilitate an understanding of gene to cell relationships in the normal and diseased mammalian kidney. Overall design: With regard to generating the scRNASeq dataset, single cell dissociation was optimized for micro-dissected kidney zones [cortex, outer medulla and inner medulla ] of two adult male and female C57BL6/J mice. Single cell suspensions were processed through the 10X Genomics Chromium platform with Illumina Hi-Seq sequencing of barcoded single-cell libraries. Gene/barcode matrices were merged and further processed using the Seurat R package to perform unsupervised clustering. Profiles were annotated by matching enriched gene sets with kidney cell-type specific markers. Key observations were followed up through a variety of secondary studies including genetic lineage tracing.