title: Effect of RNA integrity on uniquely mapped reads in RNA-Seq.
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.
authors.affiliation: 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.
authors.forename: Emily A
authors.initials: EA
authors.lastname: Chen
authors.forename: Tade
authors.initials: T
authors.lastname: Souaiaia
authors.forename: Jennifer S
authors.initials: JS
authors.lastname: Herstein
authors.forename: Oleg V
authors.initials: OV
authors.lastname: Evgrafov
authors.forename: Valeria N
authors.initials: VN
authors.lastname: Spitsyna
authors.forename: Danea F
authors.initials: DF
authors.lastname: Rebolini
authors.forename: James A
authors.initials: JA
authors.lastname: Knowles
mesh_terms: D002460:Cell Line; D020869:Gene Expression Profiling / Q000379:methods*; D015723:Gene Library; D006358:Hot Temperature; D006801:Humans; D058953:Neural Stem Cells / Q000378:metabolism; D012313:RNA / Q000235:genetics* / Q000378:metabolism; D020871:RNA Stability; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D012313:RNA