title: Deep Sequencing Analysis of Nucleolar Small RNAs: Bioinformatics.
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.
authors: Department of Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, and Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway.
authors: Baoyan
authors: B
authors: Bai
authors: Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, 1550 Orleans Street, CRB2, Room 444, Baltimore, MD, 21287, USA. mlaiho1@jhmi.edu.|Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA. mlaiho1@jhmi.edu.
authors: Marikki
authors: M
authors: Laiho
mesh_terms: D019295:Computational Biology / Q000379:methods; D004275:DNA, Ribosomal / Q000235:genetics; D030561:Databases, Nucleic Acid; D020869:Gene Expression Profiling; D015894:Genome, Human; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D035683:MicroRNAs / Q000235:genetics; D020537:RNA, Small Nucleolar / Q000235:genetics*; D012984:Software; D059467:Transcriptome; D064878:Web Browser
chemical_list: D004275:DNA, Ribosomal; D035683:MicroRNAs; D020537:RNA, Small Nucleolar
keywords: Ion torrent PGM; Nucleolus; Small RNA sequencing; miRNA; snoRNA