Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
Nucleic Acids Res. 2012 Jun;40(11):e86. doi: 10.1093/nar/gks228. Epub 2012 Mar 9.
Non-coding RNAs (ncRNA) account for a large portion of the transcribed genomic output. This diverse family of untranslated RNA molecules play a crucial role in cellular function. The use of 'deep sequencing' technology (also known as 'next generation sequencing') to infer transcript expression levels in general, and ncRNA specifically, is becoming increasingly common in molecular and clinical laboratories. We developed a software termed 'RandA' (which stands for ncRNA Read-and-Analyze) that performs comprehensive ncRNA profiling and differential expression analysis on deep sequencing generated data through a graphical user interface running on a local personal computer. Using RandA, we reveal the complexity of the ncRNA repertoire in a given cell population. We further demonstrate the relevance of such an extensive ncRNA analysis by elucidating a multitude of characterizing features in pathogen infected mammalian cells. RandA is available for download at http://ibis.tau.ac.il/RandA.
非编码 RNA（ncRNA）占据了转录基因组输出的很大一部分。这个多样化的未翻译 RNA 分子家族在细胞功能中起着至关重要的作用。使用“深度测序”技术（也称为“下一代测序”）来推断一般转录物表达水平，特别是 ncRNA，在分子和临床实验室中越来越普遍。我们开发了一种称为“RandA”的软件（代表 ncRNA 读取和分析），它通过在本地个人计算机上运行的图形用户界面，对深度测序生成的数据进行全面的 ncRNA 分析和差异表达分析。使用 RandA，我们揭示了给定细胞群体中 ncRNA 谱的复杂性。我们通过阐明感染哺乳动物细胞的病原体的大量特征来进一步证明这种广泛的 ncRNA 分析的相关性。RandA 可在 http://ibis.tau.ac.il/RandA 下载。
