Representation and relative abundance of cell-type selective markers in whole-kidney RNA-Seq data

Purpose: We used RNA-seq to determine the mRNA species and cell types presented in the whole kidney tissue. Methods: We extracted RNA from the whole kidney tissue and microdissected proximal tubules. 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). Results and conclusion: Based on a variety of data types we curated a list of 43 cell types that are thought to exist in the kidney. Our data indicated that, If mRNA levels parallel protein levels, the contribution of proximal tubules to total mRNA in the renal tubule is also likely to be in the vicinity of 66%. cDNAs from whole kidney tissue and microdissected proximal tubules were generated and sequenced using Illumina HiSeq 3000.