Abstract
MicroRNAs are critical regulators of gene expression programs. It has been demonstrated that during the maturation of miRNAs some changes can happen leading to the production of isoforms called isomiRs. During our study, a PERL pipeline was developed to find all the miRs (miRNAs) and isomiRs in two sets of Next Generation Sequencing (NGS) of small RNA libraries derived from naïve and activated CD4+ T cells. Then, a differential expression analysis was performed using Bioconductor package DESeq. Our pipeline allowed us to find all the different types of isomiRs in both of conditions. Also, we found that the isoforms coming from changes on 3’ are more frequent that in 5’ ends. Tailing isoforms are described as the less frequent isomiRs. The use of DESeq on the read count dataset of these miRs and isomiRs identified a total of 5 miRs and 22 isomiRs which were differentially expressed. So, in addition to creating a new tool for isomiR analysis, we have been able to obtain evidence that upon activation miRs and isomiRs in T-cells are differentially expressed.
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Do Souto, L., González-Briones, A., Amaral, A.J., Gama-Carvalho, M., De Paz, J.F. (2016). Large-Scale Transcriptomic Approaches for Characterization of Post-Transcriptional Control of Gene Expression. In: Saberi Mohamad, M., Rocha, M., Fdez-Riverola, F., Domínguez Mayo, F., De Paz, J. (eds) 10th International Conference on Practical Applications of Computational Biology & Bioinformatics. PACBB 2016. Advances in Intelligent Systems and Computing, vol 477. Springer, Cham. https://doi.org/10.1007/978-3-319-40126-3_12
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DOI: https://doi.org/10.1007/978-3-319-40126-3_12
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