PT  - JOURNAL ARTICLE
AU  - Lukas Paul
AU  - Petra Kubala
AU  - Gudrun Horner
AU  - Michael Ante
AU  - Igor Holländer
AU  - Seitz Alexander
AU  - Torsten Reda
TI  - SIRVs: Spike-In RNA Variants as External Isoform Controls in RNA-Sequencing
AID  - 10.1101/080747
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 080747
4099  - http://biorxiv.org/content/early/2016/10/13/080747.short
4100  - http://biorxiv.org/content/early/2016/10/13/080747.full
AB  - Spike-In RNA variants (SIRVs) enable for the first time the validation of RNA sequencing workflows using external isoform transcript controls. 69 transcripts, derived from seven human model genes, cover the eukaryotic transcriptome complexity of start- and end-site variations, alternative splicing, overlapping genes, and antisense transcription in a condensed format. Reference RNA samples were spiked with SIRV mixes, sequenced, and exemplarily four data evaluation pipelines were challenged to account for biases introduced by the RNA-Seq workflow. The deviations of the respective isoform quantifications from the known inputs allow to determine the comparability of sequencing experiments and to extrapolate to which degree alterations in an RNA-Seq workflow affect gene expression measurements. The SIRVs as external isoform controls are an important gauge for inter-experimental comparability and a modular spike-in contribution to clear the way for diagnostic RNA-Seq applications.