title: Novel insight into the non-coding repertoire through deep sequencing analysis.
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.
authors.affiliation: Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
authors.forename: Ofer
authors.initials: O
authors.lastname: Isakov
authors.forename: Roy
authors.initials: R
authors.lastname: Ronen
authors.forename: Judit
authors.initials: J
authors.lastname: Kovarsky
authors.forename: Aviram
authors.initials: A
authors.lastname: Gabay
authors.forename: Ido
authors.initials: I
authors.lastname: Gan
authors.forename: Shira
authors.initials: S
authors.lastname: Modai
authors.forename: Noam
authors.initials: N
authors.lastname: Shomron
mesh_terms: D045744:Cell Line, Tumor; D020869:Gene Expression Profiling; D006678:HIV / Q000502:physiology; D004854:Herpesvirus 4, Human / Q000235:genetics / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009174:Mycoplasma / Q000235:genetics / Q000378:metabolism; D058727:RNA, Small Untranslated / Q000737:chemistry / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D058727:RNA, Small Untranslated