Novel insight into the non-coding repertoire through deep sequencing analysis

Ofer Isakov, Roy Ronen, Judit Kovarsky, Aviram Gabay, Ido Gan, Shira Modai, Noam Shomron

Research output: Contribution to journalArticlepeer-review

Abstract

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.

Original languageEnglish
JournalNucleic Acids Research
Volume40
Issue number11
DOIs
StatePublished - Jun 2012

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