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Impact of RNA degradation on measurements of gene expression

View ORCID ProfileIrene Gallego Romero, Athma A. Pai, Jenny Tung, Yoav Gilad
doi: https://doi.org/10.1101/002261
Irene Gallego Romero
1Department of Human Genetics, University of Chicago. 920 E 58th St, CLSC 317. Chicago, IL, 60637, USA
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  • ORCID record for Irene Gallego Romero
Athma A. Pai
1Department of Human Genetics, University of Chicago. 920 E 58th St, CLSC 317. Chicago, IL, 60637, USA
2Present address: Department of Biology, Massachusetts Institute of Technology. 31 Ames Street, 68-271A. Cambridge, MA 02139-4307, USA
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Jenny Tung
1Department of Human Genetics, University of Chicago. 920 E 58th St, CLSC 317. Chicago, IL, 60637, USA
3Present address: Department of Evolutionary Anthropology and Duke Population Research Institute, Duke University. 125 Science Drive, Durham, NC 27708, USA
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Yoav Gilad
1Department of Human Genetics, University of Chicago. 920 E 58th St, CLSC 317. Chicago, IL, 60637, USA
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Abstract

The use of low quality RNA samples in whole-genome gene expression profiling remains controversial. It is unclear if transcript degradation in low quality RNA samples occurs uniformly, in which case the effects of degradation can be normalized, or whether different transcripts are degraded at different rates, potentially biasing measurements of expression levels. This concern has rendered the use of low quality RNA samples in whole-genome expression profiling problematic. Yet, low quality samples are at times the sole means of addressing specific questions – e.g., samples collected in the course of fieldwork. We sought to quantify the impact of variation in RNA quality on estimates of gene expression levels based on RNA-seq data. To do so, we collected expression data from tissue samples that were allowed to decay for varying amounts of time prior to RNA extraction. The RNA samples we collected spanned the entire range of RNA Integrity Number (RIN) values (a quality metric commonly used to assess RNA quality). We observed widespread effects of RNA quality on measurements of gene expression levels, as well as a slight but significant loss of library complexity in more degraded samples. While standard normalizations failed to account for the effects of degradation, we found that a simple linear model that controls for the effects of RIN can correct for the majority of these effects. We conclude that in instances where RIN and the effect of interest are not associated, this approach can help recover biologically meaningful signals in data from degraded RNA samples.

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Posted January 30, 2014.
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Impact of RNA degradation on measurements of gene expression
Irene Gallego Romero, Athma A. Pai, Jenny Tung, Yoav Gilad
bioRxiv 002261; doi: https://doi.org/10.1101/002261
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Impact of RNA degradation on measurements of gene expression
Irene Gallego Romero, Athma A. Pai, Jenny Tung, Yoav Gilad
bioRxiv 002261; doi: https://doi.org/10.1101/002261

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