Reproducible mRNA and small RNA sequencing across different laboratories

from F1000 Posters



Peter AC ‘t Hoen*, Marc R Friedländer, Jonas Almlöf, Michael Sammeth, Irina Pulyakhina, S Yahya Anvar, Jeroen FJ Laros, Olof Karlberg, Johan T den Dunnen, Gert-Jan B van Ommen, Ivo G Gut, Roderic Guigó, Xavier Estivill, Ann-Christine Syvänen, Emmanouil T Dermitzakis, Tuuli Lappalainen

*Corresponding author: Peter AC ‘t Hoen
Human Genetics, Leiden University Medical Center, Leiden, Netherlands

F1000Posters 2013, 4: 1093 (poster) [English]

Poster [693.06 KB]

Presented at
Joint 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 12th European Conference on Computational Biology (ECCB) 2013, 19 – 23 Jul 2013, F49

Background / Purpose:
RNA-sequencing is an increasingly popular technology for genome-wide analysis of transcript structure and abundance. However, the sources of technical and inter-laboratory variation have not been assessed in a systematic manner.
Main conclusion:
(i) RNA-sequencing is a robust technology: technical variation is small compared to already limited biological variation.
(ii) Distributed RNA-sequencing is feasible, given proper standardization and randomization procedures.
(iii) Differences in GC-content and insert size are amongst the most important sources of variation in RNA-seq experiments.
(iv) Transcript quantifications show more variation between laboratories than exon quantifications.
(v) miRNA content differs greatly between samples but does not affect relative quantifications.
No relevant competing interests disclosed.
European Research Council (ERC), supported by the European Community’s Seventh Framework Programme (FP7/2007-2013) GEUVADIS (grant no. 261123)

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