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Transcriptional Profiling of Dictyostelium with RNA Sequencing

  • Edward Roshan Miranda
  • Gregor Rot
  • Marko Toplak
  • Balaji Santhanam
  • Tomaz Curk
  • Gad ShaulskyEmail author
  • Blaz ZupanEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 983)

Abstract

Transcriptional profiling methods have been utilized in the analysis of various biological processes in Dictyostelium. Recent advances in high-throughput sequencing have increased the resolution and the dynamic range of transcriptional profiling. Here we describe the utility of RNA sequencing with the Illumina technology for production of transcriptional profiles. We also describe methods for data mapping and storage as well as common and specialized tools for data analysis, both online and offline.

Key words

Dictyostelium RNA sequencing Multiplexing Web-based applications Visual programming Data mining Differential expression Orange dictyExpress PIPA 

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Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  • Edward Roshan Miranda
    • 1
    • 2
  • Gregor Rot
    • 3
  • Marko Toplak
    • 3
  • Balaji Santhanam
    • 1
    • 4
  • Tomaz Curk
    • 3
  • Gad Shaulsky
    • 1
    • 2
    • 4
    Email author
  • Blaz Zupan
    • 1
    • 3
    Email author
  1. 1.Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUSA
  2. 2.Graduate Program in Developmental BiologyBaylor College of MedicineHoustonUSA
  3. 3.Faculty of Computer and Information ScienceUniversity of LjubljanaLjubljanaSlovenia
  4. 4.Graduate Program in Structural Computational Biology and Molecular BiophysicsBaylor College of MedicineHoustonUSA

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