Defining Housekeeping Genes Suitable for RNA-seq Analysis of the Human Allograft Kidney Biopsy Tissue

This study has used nine different normalization methods to derive housekeeping genes from a RNA-seq data set of 47611 transcripts derived from 30 biopsies. The biopsies were collected in a variety of clinical settings, with 5 replicates each of the following clinicla settings: normal function, acute tubular injury, acute rejection, interstitial nephritis, interstitial fibrosis/tubular atrophy and polyomavirus nephropathy. Transcripts with coefficient of variation below the 2nd percentile were designated as housekeeping genes, and validated by showing their virtual absence in diseased allograft derived transcriptomic data sets available in the Gene Expression Omnibus.

本研究采用9种不同的归一化方法，从源自30份活检样本的47611个转录本的RNA测序（RNA-seq）数据集中筛选管家基因（housekeeping genes）。该批活检样本采集自多种临床场景，以下6种临床状态各设置5次生物学重复：肾功能正常、急性肾小管损伤、急性排斥反应、间质性肾炎、间质性纤维化/肾小管萎缩以及多瘤病毒肾病。将变异系数低于第2百分位数的转录本划定为管家基因，并通过验证其在基因表达综合数据库（Gene Expression Omnibus，GEO）中公开的病变同种异体移植转录组数据集内近乎无表达，完成了该基因集的有效性验证。