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The Nucleolus pp 243-248 | Cite as

Deep Sequencing Analysis of Nucleolar Small RNAs: Bioinformatics

  • Baoyan Bai
  • Marikki LaihoEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1455)

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.

Key words

Nucleolus Small RNA sequencing Ion torrent PGM snoRNA miRNA 

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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  1. 1.Department of Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, and Centre for Cancer BiomedicineUniversity of OsloOsloNorway
  2. 2.Department of Radiation Oncology and Molecular Radiation SciencesJohns Hopkins University School of MedicineBaltimoreUSA
  3. 3.Sidney Kimmel Comprehensive Cancer CenterJohns Hopkins University School of MedicineBaltimoreUSA

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