Renal-tubule epithelial cell nomenclature for single-cell rna-sequencing studies

Lihe Chen, Jevin Z. Clark, Jonathan W. Nelson, Brigitte Kaissling, David H. Ellison, Mark A. Knepper

Research output: Contribution to journalReview articlepeer-review

58 Scopus citations


In this review, we have provided a set of terms for each renal tubule epithelial cell type, recommended for use in cluster naming in single-cell RNA-seq studies. A consistent nomenclature is critical to ensure accurate mapping of the pertinent transcriptomes to other types of information in the literature accruedovermany decades. We have pointed out examples of ambiguous cell-type names (i.e., loop of Henle cells and distal tubule cells) that impede such mapping tasks. The controlled vocabulary introduced here is likely to be useful for naming tasks that extend beyond single cell RNAseq studies as measurements in single cells expand to other modalities, e.g., chromatin accessibility measurements using ATAC-seq.60 In this report, we not only described preferred names for each cell type, but also included information on widely accepted mRNA/protein markers that are considered pre-requisites for identification of individual cell types and on the percentage of each epithelial cell type in mouse kidney.

Original languageEnglish (US)
Pages (from-to)1358-1364
Number of pages7
JournalJournal of the American Society of Nephrology
Issue number8
StatePublished - Aug 2019

ASJC Scopus subject areas

  • Nephrology


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