Comparison of Analysis Tools for miRNA High Throughput Sequencing Using Nerve Crush as a Model

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...

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Main Authors:	Metpally, Raghu Prasad Rao, Nasser, Sara, Malenica, Ivana, Courtright, Amanda, Carlson, Elizabeth, Ghaffari, Layla, Villa, Stephen, Tembe, Waibhav, Van Keuren-Jensen, Kendall
Format:	Online
Language:	English
Published:	Frontiers Media S.A. 2013
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3585423/

id	pubmed-3585423
recordtype	oai_dc
spelling	pubmed-35854232013-03-04 Comparison of Analysis Tools for miRNA High Throughput Sequencing Using Nerve Crush as a Model Metpally, Raghu Prasad Rao Nasser, Sara Malenica, Ivana Courtright, Amanda Carlson, Elizabeth Ghaffari, Layla Villa, Stephen Tembe, Waibhav Van Keuren-Jensen, Kendall Genetics 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. Frontiers Media S.A. 2013-03-01 /pmc/articles/PMC3585423/ /pubmed/23459507 http://dx.doi.org/10.3389/fgene.2013.00020 Text en Copyright © 2013 Metpally, Nasser, Malenica, Courtright, Carlson, Ghaffari, Villa, Tembe and Van Keuren-Jensen. http://creativecommons.org/licenses/by/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and subject to any copyright notices concerning any third-party graphics etc.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Metpally, Raghu Prasad Rao Nasser, Sara Malenica, Ivana Courtright, Amanda Carlson, Elizabeth Ghaffari, Layla Villa, Stephen Tembe, Waibhav Van Keuren-Jensen, Kendall
spellingShingle	Metpally, Raghu Prasad Rao Nasser, Sara Malenica, Ivana Courtright, Amanda Carlson, Elizabeth Ghaffari, Layla Villa, Stephen Tembe, Waibhav Van Keuren-Jensen, Kendall Comparison of Analysis Tools for miRNA High Throughput Sequencing Using Nerve Crush as a Model
author_facet	Metpally, Raghu Prasad Rao Nasser, Sara Malenica, Ivana Courtright, Amanda Carlson, Elizabeth Ghaffari, Layla Villa, Stephen Tembe, Waibhav Van Keuren-Jensen, Kendall
author_sort	Metpally, Raghu Prasad Rao
title	Comparison of Analysis Tools for miRNA High Throughput Sequencing Using Nerve Crush as a Model
title_short	Comparison of Analysis Tools for miRNA High Throughput Sequencing Using Nerve Crush as a Model
title_full	Comparison of Analysis Tools for miRNA High Throughput Sequencing Using Nerve Crush as a Model
title_fullStr	Comparison of Analysis Tools for miRNA High Throughput Sequencing Using Nerve Crush as a Model
title_full_unstemmed	Comparison of Analysis Tools for miRNA High Throughput Sequencing Using Nerve Crush as a Model
title_sort	comparison of analysis tools for mirna high throughput sequencing using nerve crush as a model
description	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.
publisher	Frontiers Media S.A.
publishDate	2013
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3585423/
_version_	1611958616846237696

Comparison of Analysis Tools for miRNA High Throughput Sequencing Using Nerve Crush as a Model

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