RNA sequencing (RNA‐Seq) is a sensitive means of global identification and quantification of mRNAs. In kidney, we have carried out RNA‐Seq analysis to identify transcriptomes of single microdissected renal tubules and single cells. The resulting datasets provide a community resource for gene expression in kidney structures in the form of a publicly accessible website at https://hpcwebapps.cit.nih.gov/ESBL/Database/Targets/TranscriptomicData.html. We now have added new whole‐kidney RNA‐Seq data for mice (male, age 8 weeks). This dataset reports 13,334 transcripts with mean TPM (“normalized transcripts per million”) greater than 1 for whole kidney (n=3). A large fraction of these are housekeeping genes or genes expressed in multiple cell types. Whole‐kidney RNA‐Seq analysis is of limited use in studying responses in these genes since the responses may be variable among cell types. However, signals were readily quantified for major cell‐type specific transcripts including podocytes (podocin, Nphs2), proximal convoluted tubule (sodium coupled glucose transporter 2, Slc5a2), proximal straight tubule (sodium coupled glucose transporter 1, Slc5a1), thin descending limb of Henle (follistatin, Fst), thin ascending limb (chloride channel ClC‐Ka, Clcnka), thick ascending limb (NKCC2, Slc12a1), distal convoluted tubule (NCC, Slc12a3), principal cell of collecting duct (ENaC gamma subunit, Scnn1g), type A intercalated cell (AE1, Slc4a1), type B intercalated cell (pendrin, Slc26a4), and inner medullary collecting duct cell (urea channel UT‐A1, Slc14a2 long isoform). Beyond this, transcripts were quantifiable for marker genes corresponding to rare cell types in the kidney including granular cells of the afferent arteriole (renin, Ren1), macrophages (macrophage colony‐stimulating factor 1 receptor, Csf1r), dendritic cells (dendritic cell‐specific ICAM‐3‐grabbing non‐integrin, Cd209a), and umbrella cells of the transitional epithelium (uroplakin 1a, Upk1a). In conclusion, numerous cell‐type specific mRNAs are represented in whole‐kidney RNA‐Seq analysis. These markers provide a means of measuring physiological regulatory responses (e.g. renin expression in granular cells) or measuring changes in cell numbers, which can occur with proliferative responses or infiltration of the kidney as part of inflammatory responses (e.g. macrophages and dendritic cells).This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.