Supporting data for "A curated human cellular microRNAome based on 196 primary cell types"

An incomplete picture of the expression distribution of microRNAs (miRNAs) across human cell types has long hindered our understanding of this important regulatory class of RNA. With the continued increase in available public small RNA sequencing datasets, there is an opportunity to more fully understand the general distribution of miRNAs at the cell level. <br>From the NCBI Sequence Read Archive, we obtained 6,054 human primary cell datasets and processed 4,184 of them through the miRge3.0 small RNA-seq alignment software. This dataset was curated down, through shared miRNA expression patterns, to 2,077 samples from 196 unique cell types derived from 175 separate studies. Of 2,731 putative miRNAs listed in miRBase (v22.1), 2,452 (89.8%) were detected. Among reasonably expressed miRNAs, 108 were designated as cell specific/near specific, 59 as infrequent, 52 as frequent, 54 as near ubiquitous and 50 as ubiquitous. The complexity of cellular microRNA expression estimates recapitulates tissue expression patterns and informs on the miRNA composition of plasma. <br>This study represents the most complete reference, to date, of miRNA expression patterns by primary cell type. The data is available through the human cellular microRNAome track at the UCSC Genome Browser and an R/Bioconductor package.

长期以来，我们对人类细胞类型中微小核糖核酸（microRNAs, miRNAs）表达分布的认知存在缺口，这始终阻碍着我们对这一重要调控类RNA的理解。随着公开可用的小RNA测序数据集持续增长，我们得以更全面地解析细胞层面的微小核糖核酸整体分布格局。
本研究从NCBI序列读取档案库（NCBI Sequence Read Archive）中获取了6054份人类原代细胞数据集，并通过miRge3.0小RNA测序比对软件完成了其中4184份的处理。经共享微小核糖核酸表达模式筛选，本数据集最终被精简至来自175项独立研究的196种独特细胞类型的2077份样本。在miRBase（v22.1）收录的2731种推定微小核糖核酸中，我们共检测到2452种（占比89.8%）。在表达水平合理的微小核糖核酸中，108种被归类为细胞特异性/近特异性表达，59种为低频率表达，52种为高频表达，54种为近乎普遍表达，50种为普遍表达。细胞微小核糖核酸表达谱的复杂性可复现组织表达模式，并可为血浆中的微小核糖核酸组成提供参考依据。
本研究构建了截至目前最为完整的原代细胞类型微小核糖核酸表达谱参考数据集。相关数据可通过UCSC基因组浏览器（UCSC Genome Browser）的人类细胞微小核糖核酸组（human cellular microRNAome）轨道获取，同时也可通过R/Bioconductor软件包获得。