Bulk-tissue RNA-Seq is seeing increasing use in the study of physiological and pathophysiological processes in the kidney. However, the presence of multiple cell types in kidney complicates the interpretation of the data. Here we address the question, What cell types are represented in whole-kidney RNA-Seq data? to identify circumstances in which bulk-kidney RNA-Seq can successfully be interpreted. We carried out RNA-Seq in mouse whole kidneys and microdissected proximal S2 segments. To aid in the interpretation of the data, we compiled a database of cell-type selective protein markers for 43 cell types believed to be present in kidney tissue. The whole-kidney RNA-Seq analysis identified transcripts corresponding to 17742 genes, distributed over 5 orders of magnitude of expression level. Markers for all 43 curated cell types were detectable. Analysis of the cellular makeup of a mouse kidney, calculated from published literature, suggests that proximal tubule cells likely account for more than half of the mRNA in a kidney. Comparison of RNA-Seq data from microdissected proximal tubules with whole-kidney data supports this view. RNA-Seq data for cell-type selective markers in bulk-kidney samples provide a valid means to identify changes in minority-cell abundances in kidney tissue. Although proximal tubules make up a substantial fraction of whole-kidney samples, changes in proximal tubule gene expression could be obscured by the presence of mRNA from other cell types.
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