This database provides mean TPM values and gene ranks for all transcripts expressed in mouse renal type A intercalated cells (A-IC), type B intercalated cells (B-IC) and principal cells (PC) ascertained from distillation of single-cell RNA-Seq data.

Brief Method: We used cell surface markers to enrich intercalated cells and principal cells from mouse kidney by FACS and carried out single-cell RNA-Seq of those cells using a microfluidic chip (Fluidigm C1 system). Single-cell 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). Unsupervised clustering analysis revealed five different cell types, namely type A intercalated cells, type B intercalated cells, principal cells, proximal tubule cells and non-epithelial cells. The data presented below shows the mean TPM values of A-ICs (n=87), B-ICs(n=23) and PCs (n=74).

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Reference: 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, 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 A-IC Rank A-IC Selective Transcripts B-IC Rank B-IC Selective Transcripts IC Selective Transcripts PC Rank PC Selective Transcripts Transcription Factors Only Transporters and Channels Only Protein Kinases Only 7-Membrane Spanning Receptors Only Metabolic Enzymes Only E3 Ubiquitin Ligases Only Median TPM Dropout Rate