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Novel insight into the non-coding repertoire through deep sequencing analysis
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 level...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3367215/ https://www.ncbi.nlm.nih.gov/pubmed/22406831 http://dx.doi.org/10.1093/nar/gks228 |
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author | Isakov, Ofer Ronen, Roy Kovarsky, Judit Gabay, Aviram Gan, Ido Modai, Shira Shomron, Noam |
author_facet | Isakov, Ofer Ronen, Roy Kovarsky, Judit Gabay, Aviram Gan, Ido Modai, Shira Shomron, Noam |
author_sort | Isakov, Ofer |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-3367215 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-33672152012-06-05 Novel insight into the non-coding repertoire through deep sequencing analysis Isakov, Ofer Ronen, Roy Kovarsky, Judit Gabay, Aviram Gan, Ido Modai, Shira Shomron, Noam Nucleic Acids Res Methods Online 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. Oxford University Press 2012-06 2012-02-09 /pmc/articles/PMC3367215/ /pubmed/22406831 http://dx.doi.org/10.1093/nar/gks228 Text en © The Author(s) 2012. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Methods Online Isakov, Ofer Ronen, Roy Kovarsky, Judit Gabay, Aviram Gan, Ido Modai, Shira Shomron, Noam Novel insight into the non-coding repertoire through deep sequencing analysis |
title | Novel insight into the non-coding repertoire through deep sequencing analysis |
title_full | Novel insight into the non-coding repertoire through deep sequencing analysis |
title_fullStr | Novel insight into the non-coding repertoire through deep sequencing analysis |
title_full_unstemmed | Novel insight into the non-coding repertoire through deep sequencing analysis |
title_short | Novel insight into the non-coding repertoire through deep sequencing analysis |
title_sort | novel insight into the non-coding repertoire through deep sequencing analysis |
topic | Methods Online |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3367215/ https://www.ncbi.nlm.nih.gov/pubmed/22406831 http://dx.doi.org/10.1093/nar/gks228 |
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