Despite the fact that next-generation sequencing approaches, in particular RNA sequencing, provide deep genome-wide expression data that allow both careful annotations/mapping of long noncoding RNA (lncRNA) molecules and de-novo sequencing, lncRNA expression studies by microarray is a still cost-effective procedure that could allow to have a landscape of the most characterized lncRNA species. However, microarray design does not always correctly address the overlap between coding and noncoding samples to discriminate between the original transcript source. In order to overcome this issue, in this chapter we present a bioinformatics pipeline that enables accurate annotation of GeneChip® microarrays, to date the most commonly adopted among the commercial solutions. Overall, this approach holds two main advantages, a gain in specificity of transcript detection and the adaptability to the whole panel of GeneChip® arrays.

Bioinformatics Pipeline to Analyze lncRNA Arrays / K. Todoerti, D. Ronchetti, M. Manzoni, E. Taiana, A. Neri, L. Agnelli (METHODS IN MOLECULAR BIOLOGY). - In: Long Non-Coding RNAs in Cancer / [a cura di] A. Navarro. - [s.l] : Springer, 2021. - ISBN 9781071615805. - pp. 45-53 [10.1007/978-1-0716-1581-2_3]

Bioinformatics Pipeline to Analyze lncRNA Arrays

K. Todoerti;D. Ronchetti;M. Manzoni;E. Taiana;A. Neri;L. Agnelli
2021

Abstract

Despite the fact that next-generation sequencing approaches, in particular RNA sequencing, provide deep genome-wide expression data that allow both careful annotations/mapping of long noncoding RNA (lncRNA) molecules and de-novo sequencing, lncRNA expression studies by microarray is a still cost-effective procedure that could allow to have a landscape of the most characterized lncRNA species. However, microarray design does not always correctly address the overlap between coding and noncoding samples to discriminate between the original transcript source. In order to overcome this issue, in this chapter we present a bioinformatics pipeline that enables accurate annotation of GeneChip® microarrays, to date the most commonly adopted among the commercial solutions. Overall, this approach holds two main advantages, a gain in specificity of transcript detection and the adaptability to the whole panel of GeneChip® arrays.
Microarrays; lncRNA
Settore ING-INF/05 - Sistemi di Elaborazione delle Informazioni
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/2434/853836
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