This database provides mean TPM values and gene ranks for all transcripts expressed in mouse coritical collecting ducts (11 replicates, 7 mice) and cortical thick ascending limbs (8 replicates, 7 mice) ascertained from RNA-Seq data.

Brief Method: Kidneys were removed from 5 week male mice and immediately placed in ice-cold PBS. Cortical collecting ducts and thick ascending limbs were manually dissected in ice-cold Burg dissection solution (135 mM NaCl, 1 mM Na₂HPO₄, 1.2 mM Na₂SO₄, 1.2 mM MgSO₄, 5 mM KCl, 2 mM CaCl₂, 5.5 mM glucose, 5 mM HEPES, 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: CCD, cortical collecting duct; cTAL, cortical thick ascending limb of the loop of Henle; TPM, transcripts per million; SE, standard error

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Reference: Chen L, Lee JW, Chou CL, Nair AV, Battistone MA, Paunescu 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 Gene Symbol CCD Rank CCD Selective Transcripts cTAL Rank cTAL Selective Transcripts Median TPM