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

Isakov O, Ronen R, Kovarsky J, Gabay A, Gan I, Modai S, Shomron N - Nucleic Acids Res. (2012)

Bottom Line: This diverse family of untranslated RNA molecules play a crucial role in cellular function.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.

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.

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Distribution of organisms when running the deep sequencing output against all human transcripts combined with all bacterial transcripts. Abundance of Mycoplasma derived sequences within the most differentially expressed transcripts (P < 0.01) with a base mean of over 100 demonstrates its' presence in the infected sample. Mycoplasma infection was previously validated (29).
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gks228-F1: Distribution of organisms when running the deep sequencing output against all human transcripts combined with all bacterial transcripts. Abundance of Mycoplasma derived sequences within the most differentially expressed transcripts (P < 0.01) with a base mean of over 100 demonstrates its' presence in the infected sample. Mycoplasma infection was previously validated (29).

Mentions: Using RandA, we demonstrated that expression of Mycoplasma derived transcripts was indeed significantly different between samples. These transcripts were highly expressed in the infected sample in opposition to the uninfected sample in which they were not detected. The analysis resulted in 2748 different RNA transcripts detected in at least one of the samples. Out of these, 273 transcripts exhibited significantly different expression (P < 0.01), of which 148 had a base mean count of over 100. Of these 148 transcripts, 121 were human transcripts, 24 Mycoplasma and only 3 from other bacterial sequences (Figure 1).Figure 1.


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

Isakov O, Ronen R, Kovarsky J, Gabay A, Gan I, Modai S, Shomron N - Nucleic Acids Res. (2012)

Distribution of organisms when running the deep sequencing output against all human transcripts combined with all bacterial transcripts. Abundance of Mycoplasma derived sequences within the most differentially expressed transcripts (P < 0.01) with a base mean of over 100 demonstrates its' presence in the infected sample. Mycoplasma infection was previously validated (29).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3367215&req=5

gks228-F1: Distribution of organisms when running the deep sequencing output against all human transcripts combined with all bacterial transcripts. Abundance of Mycoplasma derived sequences within the most differentially expressed transcripts (P < 0.01) with a base mean of over 100 demonstrates its' presence in the infected sample. Mycoplasma infection was previously validated (29).
Mentions: Using RandA, we demonstrated that expression of Mycoplasma derived transcripts was indeed significantly different between samples. These transcripts were highly expressed in the infected sample in opposition to the uninfected sample in which they were not detected. The analysis resulted in 2748 different RNA transcripts detected in at least one of the samples. Out of these, 273 transcripts exhibited significantly different expression (P < 0.01), of which 148 had a base mean count of over 100. Of these 148 transcripts, 121 were human transcripts, 24 Mycoplasma and only 3 from other bacterial sequences (Figure 1).Figure 1.

Bottom Line: This diverse family of untranslated RNA molecules play a crucial role in cellular function.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.

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.

Show MeSH
Related in: MedlinePlus