Introduction

We present a genome-wide messenger RNA (mRNA) sequencing technique that converts small amounts of RNA from many samples into molecular phenotypes. It encompasses all steps from sample preparation to sequence analysis and is applicable to baseline profiling or perturbation measurements.Multiplex sequencing of transcript 3' ends identifies differential transcript abundance independent of gene annotation. We show that increasing biological replicate number while maintaining the total amount of sequencing identifies more differentially abundant transcripts.This method can be implemented on polyadenylated RNA from any organism with an annotated reference genome and in any laboratory with access to Illumina sequencing.

Publications

  1. High-throughput and quantitative genome-wide messenger RNA sequencing for molecular phenotyping.
    Cite this
    Collins JE, Wali N, Sealy IM, Morris JA, White RJ, Leonard SR, Jackson DK, Jones MC, Smerdon NC, Zamora J, Dooley CM, Carruthers SN, Barrett JC, Stemple DL, Busch-Nentwich EM, 2015-08-01 - BMC genomics

Credits

  1. John E Collins
    Developer

    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, United Kingdom of Great Britain and Northern Ireland

  2. Neha Wali
    Developer

    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, United Kingdom of Great Britain and Northern Ireland

  3. Ian M Sealy
    Developer

    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, United Kingdom of Great Britain and Northern Ireland

  4. James A Morris
    Developer

    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, United Kingdom of Great Britain and Northern Ireland

  5. Richard J White
    Developer

    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, United Kingdom of Great Britain and Northern Ireland

  6. Steven R Leonard
    Developer

    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, United Kingdom of Great Britain and Northern Ireland

  7. David K Jackson
    Developer

    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, United Kingdom of Great Britain and Northern Ireland

  8. Matthew C Jones
    Developer

    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, United Kingdom of Great Britain and Northern Ireland

  9. Nathalie C Smerdon
    Developer

    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, United Kingdom of Great Britain and Northern Ireland

  10. Jorge Zamora
    Developer

    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, United Kingdom of Great Britain and Northern Ireland

  11. Christopher M Dooley
    Developer

    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, United Kingdom of Great Britain and Northern Ireland

  12. Samantha N Carruthers
    Developer

    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, United Kingdom of Great Britain and Northern Ireland

  13. Jeffrey C Barrett
    Developer

    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, United Kingdom of Great Britain and Northern Ireland

  14. Derek L Stemple
    Developer

    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, United Kingdom of Great Britain and Northern Ireland

  15. Elisabeth M Busch-Nentwich
    Investigator

    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, United Kingdom of Great Britain and Northern Ireland

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Summary
AccessionBT000233
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByElisabeth M Busch-Nentwich