Format

Send to

Choose Destination
BMC Res Notes. 2014 Oct 23;7:753. doi: 10.1186/1756-0500-7-753.

Effect of RNA integrity on uniquely mapped reads in RNA-Seq.

Author information

1
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.

Abstract

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.

PMID:
25339126
PMCID:
PMC4213542
DOI:
10.1186/1756-0500-7-753
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for BioMed Central Icon for PubMed Central
Loading ...
Support Center