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.研究目的：我们通过RNA测序（RNA-seq）确定全肾组织中存在的mRNA种类与细胞类型。 研究方法：我们从全肾组织及显微切割的近端肾小管中提取RNA，构建cDNA文库以开展双端测序，并在Illumina HiSeq3000平台上完成测序。将测序读段（reads）比对至小鼠Ensembl基因组（采用STAR工具），并通过RSEM（https://github.com/deweylab/RSEM）以每百万转录本（transcripts per million, TPM）为单位计算转录本丰度。 结果与结论：基于多类数据，我们整理得到了一套共计43种被认为存在于肾脏中的细胞类型列表。我们的研究数据表明，若mRNA水平与蛋白质水平呈正相关，则近端肾小管在肾小管总mRNA中的占比同样大概率接近66%。本研究完成了全肾组织及显微切割近端肾小管的cDNA制备与测序，所用平台为Illumina HiSeq 3000。