title: Comparison of Analysis Tools for miRNA High Throughput Sequencing Using Nerve Crush as a Model.
abstract: Recent advances in sample preparation and analysis for next generation sequencing have made it possible to profile and discover new miRNAs in a high throughput manner. In the case of neurological disease and injury, these types of experiments have been more limited. Possibly because tissues such as the brain and spinal cord are inaccessible for direct sampling in living patients, and indirect sampling of blood and cerebrospinal fluid are affected by low amounts of RNA. We used a mouse model to examine changes in miRNA expression in response to acute nerve crush. We assayed miRNA from both muscle tissue and blood plasma. We examined how the depth of coverage (the number of mapped reads) changed the number of detectable miRNAs in each sample type. We also found that samples with very low starting amounts of RNA (mouse plasma) made high depth of mature miRNA coverage more difficult to obtain. Each tissue must be assessed independently for the depth of coverage required to adequately power detection of differential expression, weighed against the cost of sequencing that sample to the adequate depth. We explored the changes in total mapped reads and differential expression results generated by three different software packages: miRDeep2, miRNAKey, and miRExpress and two different analysis packages, DESeq and EdgeR. We also examine the accuracy of using miRDeep2 to predict novel miRNAs and subsequently detect them in the samples using qRT-PCR.
authors: Collaborative Bioinformatics Center, Translational Genomics Research Institute Phoenix, AZ, USA.
authors: Raghu Prasad Rao
authors: RP
authors: Metpally
authors: Sara
authors: S
authors: Nasser
authors: Ivana
authors: I
authors: Malenica
authors: Amanda
authors: A
authors: Courtright
authors: Elizabeth
authors: E
authors: Carlson
authors: Layla
authors: L
authors: Ghaffari
authors: Stephen
authors: S
authors: Villa
authors: Waibhav
authors: W
authors: Tembe
authors: Kendall
authors: K
authors: Van Keuren-Jensen
keywords: analysis; miRNA; muscle; nerve injury; next generation sequencing; plasma; small RNA