Deep sequencing analysis of nucleolar small RNAs: Bioinformatics

Baoyan Bai, Marikki Laiho

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Small RNAs (size 20–30 nt) of various types have been actively investigated in recent years, and their subcellular compartmentalization and relative concentrations are likely to be of importance to their cellular and physiological functions. Comprehensive data on this subset of the transcriptome can only be obtained by application of high-throughput sequencing, which yields data that are inherently complex and multidimensional, as sequence composition, length, and abundance will all inform to the small RNA function. Subsequent data analysis, hypothesis testing, and presentation/visualization of the results are correspondingly challenging. We have constructed small RNA libraries derived from different cellular compartments, including the nucleolus, and asked whether small RNAs exist in the nucleolus and whether they are distinct from cytoplasmic and nuclear small RNAs, the miRNAs. Here, we present a workflow for analysis of small RNA sequencing data generated by the Ion Torrent PGM sequencer from samples derived from different cellular compartments.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages243-248
Number of pages6
Volume1455
DOIs
StatePublished - 2016

Publication series

NameMethods in Molecular Biology
Volume1455
ISSN (Print)10643745

Keywords

  • Ion torrent PGM
  • miRNA
  • Nucleolus
  • Small RNA sequencing
  • snoRNA

ASJC Scopus subject areas

  • Medicine(all)
  • Molecular Biology
  • Genetics

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  • Cite this

    Bai, B., & Laiho, M. (2016). Deep sequencing analysis of nucleolar small RNAs: Bioinformatics. In Methods in Molecular Biology (Vol. 1455, pp. 243-248). (Methods in Molecular Biology; Vol. 1455). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-3792-9_19