This database provides mean TPM values for the most abundant transcripts expressed in mouse whole kidney samples and microdissected mouse renal tubules. See column headers for numbers of replicates.

Brief Method: Proximal tubules (S2), cortical collecting ducts, and thick ascending limbs were manually dissected in ice-cold Burg dissection solution (120 mM NaCl, 2.5 mM Na₂HPO₄, 1.2 mM MgSO₄, 5 mM KCl, 2 mM CaCl₂, 5.5 mM glucose, 5 mM HEPES, 5 mM Na acetate, pH 7.4) under a Wild M8 dissection stereomicroscope equipped with on-stage cooling. After washes in ice-cold PBS (2 times), the microdissected tubules were transferred to Trizol reagent for RNA extraction. 1 to 4 tubules were collected for each sample. cDNAs were synthesized by SMARTer V4 kit (Clontech) and cDNA libraries were constructed for paired-end sequencing and sequenced on Illumina HiSeq3000 platform. Reads were mapped to mouse Ensembl Genome by STAR and transcript abundances were calculated in the units of transcripts per million (TPM) using RSEM (https://github.com/deweylab/RSEM).

Terminology: WK, whole kidney; S2, middle segment of proximal tubule; CCD, cortical collecting duct; cTAL, cortical thick ascending limb of the loop of Henle; TPM, transcripts per million

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References:
1. Clark JZ, Chen L, Chou CL, Jung HJ, Lee JW, Knepper MA. Representation and relative abundance of cell-type selective markers in whole-kidney RNA-Seq data. Kidney Int. 2019; 95:787-796 PMID: 30826016.
2. Chen L, Lee JW, Chou CL, Nair AV, Battistone MA, Păunescu TG, Merkulova M, Breton S, Verlander JW, Wall SM, Brown D, Burg MB, Knepper MA. Transcriptomes of major renal collecting duct cell types in mouse identified by single-cell RNA-seq. Proc Natl Acad Sci U S A. 2017;114:E9989-E9998. PMID: 29089413.

This website was created by Lihe Chen, Jevin Z. Clark and Mark Knepper. Contact us with questions or comments: knep@helix.nih.gov.

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Sort database by: Choose from Menu Whole Kidney TPM Mean S2 Proximal Tubule TPM Mean cTAL TPM Mean CCD TPM Mean S2-WK cTAL-WK CCD-WK