Effect of RNA integrity on uniquely mapped reads in RNA-Seq.
| Autor: | Chen EA; Department of Genetic, Molecular, and Cellular Biology, Keck School of Medicine, Zilkha Neurogenetic Institute, University of Southern California, 1501 San Pablo Street, ZNI 401, MC 2821, Los Angeles, CA 90089-2821, USA. emilyach@med.usc.edu., Souaiaia T, Herstein JS, Evgrafov OV, Spitsyna VN, Rebolini DF, Knowles JA |
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| Jazyk: | angličtina |
| Zdroj: | BMC research notes [BMC Res Notes] 2014 Oct 23; Vol. 7, pp. 753. Date of Electronic Publication: 2014 Oct 23. |
| DOI: | 10.1186/1756-0500-7-753 |
| Abstrakt: | Background: We examined the performance of three RNA-Sequencing library preparation protocols as a function of RNA integrity, comparing gene expressions between heat-degraded samples to their high-quality counterparts. This work is invaluable given the difficulty of obtaining high-quality RNA from tissues, particularly those from individuals with disease phenotypes. Results: With the integrity of total RNA being a critical parameter for RNA-Sequencing analysis, degraded RNA can heavily influence the results of gene expression profiles. We discovered that gene expression read results are influenced by RNA quality when a common library construction protocol is used. These results are based on one technical experiment from a pool of 4 neural progenitor cell lines. Conclusions: The use of alternative protocols can allow samples with a wider range of RNA qualities to be used, facilitating the investigation of disease tissues. |
| Databáze: | MEDLINE |
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