Assembly and validation of conserved long non-coding RNAs in the ruminant transcriptome

mRNA-like long non-coding RNAs (lncRNA) are a significant component of mammalian transcriptomes, although most are expressed only at low levels, with high tissue-specificity and/or at specific developmental stages. This dataset demonstrates that few lncRNA are fully captured by biological replicates of the same RNA-seq library. In a transcriptional atlas of the domestic sheep (https://doi.org/10.1371/journal.pgen.1006997), 31 diverse tissues/cell types were sampled in each of 6 individual adults (3 females, 3 males, all unrelated virgin animals approximately 2 years of age). By taking a subset of 31 common tissues per individual, each of the 6 adults (f1, f2, f3, m1, m2, and m3) was represented by ~0.75 billion reads. In a typical lncRNA assembly pipeline, read alignments from all individuals are merged, to maximise the number of candidate gene models (using, for instance, StringTie --merge). With n = 6 adults (and ~0.75 billion reads per adult), there are (2^n)-1 = 63 possible combinations of data for which GTFs can be made with StringTie --merge. This dataset comprises those GTFs.

类mRNA长链非编码RNA（mRNA-like long non-coding RNAs，lncRNA）是哺乳动物转录组的重要组成部分，尽管多数仅以低水平表达，且具有高度组织特异性，或仅在特定发育阶段表达。本数据集表明，仅通过同一RNA测序（RNA-seq）文库的生物学重复实验，仅有极少部分lncRNA能够被完全捕获。在针对家绵羊的转录组图谱研究（https://doi.org/10.1371/journal.pgen.1006997）中，研究人员对6只成年个体（3只雌性、3只雄性，均为约2岁的未交配无关个体）的31种不同组织/细胞类型进行了采样。每只个体均选取31种共有组织，最终6只成年个体（编号依次为f1、f2、f3、m1、m2、m3）的测序数据量均约为7.5亿条读段（reads）。在典型的lncRNA组装流程中，研究人员通常会合并所有个体的测序比对结果，以最大化候选基因模型的数量（例如使用StringTie --merge工具）。当n=6只成年个体（单个体测序数据量约为7.5亿条读段）时，可通过StringTie --merge生成基因转移格式（Gene Transfer Format，GTF）文件的数据集组合共有(2ⁿ)-1=63种。本数据集即包含上述全部63种GTF文件。